Functional Specifications

Chromeleon 7.3.1
Revision 1.0 • Nov 2021
 Chromeleon 7

Copyright
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Functional Specifications, 7.3.1, Rev. 1.0

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Table of Contents
1 About this Document 1
1.1 Scope 1
1.2 Other Documentation 1

2 Overview of System 2

3 Chromeleon Console 3
3.1 Menu Bar 4
3.1.1 Station Qualification 5
3.1.2 Instrument Qualification 5
3.1.3 Custom Variables Editor 5
3.1.4 Custom For mulas Editor 6
3.1.5 Administration Console 7
3.1.6 Pr eferences 7
3.1.7 Virtual Column Separation Simulator 7
3.1.8 Import 8
3.2 Instruments Category 9
3.2.1 Instruments Category Bar 9
3.2.2 Instrument Queue 17
3.2.3 Instrument Audit Trail 19
3.2.4 Instrument Overview Grid 20
3.3 Data Category 21
3.3.1 Sequence Status Bar 22
3.3.2 Sequence Toolbar 22
3.3.3 Sequence Table Context Menu 23
3.3.4 Sequence Context Menu 24
3.4 eWor kflows Category 26
3.4.1 Editing an eWor kflow 26
3.5 Command Line Parameters 32

4 Objects in the Data Category 34

4.1 Data Vaults 34
4.1.1 Data Vault Properties 34
4.1.2 General 34
4.1.3 Access Control 34
4.1.4 Dow ntime 35
4.1.5 Database Statistics 35
4.1.6 Raw Data Statistics 35
4.2 Folders 35
4.2.1 General 35
4.2.2 Access Control 35
4.2.3 Raw Data Statistics 35
4.3 Sequences 35
4.3.1 Injection List 36
4.3.2 Sequence Properties 38
4.3.3 Injection Rac k View 40
4.8 Deleted Items 51
4.9 Instrument Method 51
4.9.1 DA D-3000(RS) 51
4.9.2 Mass Spectrometers 53
4.9.3 Startup / Shutdow n 53

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5 Chromatography Studio 55
5.1 Studio Button 55
5.2 View Settings 56
5.3 Pr ocessing Method 57
5.3.1 Detection 58
5.3.2 Component Table 63
5.3.3 Calibration 74
5.3.4 Peak Group Table 75
5.3.5 Chromatogram Subtraction 76
5.3.6 UV Spectral Library Screening 76
5.3.7 SST/IRC 77
5.3.8 Advanced Settings 83
5.3.9 Composite Scor ing 83
5.3.10 MS Detection 84
5.3.11 MS Settings 86
5.3.12 MS Library Screening 87
5.3.13 Peptide Table 87
5.3.14 QD Calibration 88
5.3.15 MS Component Table Import 88
5.3.16 MS Component Table Export 89
5.3.17 Cobra Wizard 92
5.3.18 SmartPeaks 92
5.3.19 Component Table Wizard 93
5.3.20 Layouts 94
5.4 Data Processing Category 94
5.4.1 Chromatogram Pane 95
5.4.2 Calibration Plot Pane 110
5.4.3 Peak Properties Pane 113
5.4.4 Interactive Charts Pane 116
5.4.5 Contour/3D Plot 122
5.4.6 UV-Vis Spectra Pane 127
5.4.7 Fluorescence Spectra Pane 135
5.4.8 I-t Plot Pane 140
5.4.9 Interactive Results Pane 144
5.4.10 Injection Rac k Pane 145
5.4.11 Fraction Tray Pane 146
5.4.12 Mass Spectrum Pane 147
5.4.13 MS Components Pane 159
5.4.14 Tentatively Identified Peaks Pane 168
5.4.15 MS AutoFilters Pane 168
5.4.16 SmartLink 172
5.4.17 On- Demand View Updating 174
5.5 Non-Targeted MS Processing Category (SIEV E) 174
5.5.1 Ribbon Bar 174
5.5.2 Pr ocessing Pane 175
5.5.3 Frame Plot Pane 176
5.5.4 Frame Report Pane 178
5.5.5 Chromatogram Plot Pane 178
5.5.6 Mass Spectra Pane 178
5.5.7 Pr ocessing Parameters Pane 179
5.6 Non-Targeted MS Processing Category (BioPhar ma Finder) 180
5.6.1 Ribbon Bar 180
5.7 Intact Protein Deconvolution Category 190

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5.7.1 Ribbon Bar 190

5.7.2 Pr ocessing Method Pane 191
5.7.3 Pr ocessing Parameters Pane 194
5.7.4 Component Results Pane 195
5.7.5 Chromatogram Pane 196
5.7.6 Deconvoluted Spectrum Pane 200
5.7.7 Source Spectrum Pane 204
5.8 Report Template 207
5.8.1 Chromatogram Plot 208
5.8.2 Calibration Plot 215
5.8.3 UV-Vis Spectra Plot 217
5.8.4 Contour Plot 222
5.8.5 Mass Spectrum Plot 223
5.8.6 MS Components Plot 229
5.8.7 IPD Chromatogram Plot 234
5.8.8 IPD Mass Deconvoluted Spectra Plot 238
5.8.9 IPD Mass Source Spectra Plot 241
5.8.10 SIEV E Frame Plot 243
5.8.11 Injection Rac k View 245
5.8.12 Fraction Tray Plot 245
5.8.13 Fluorescence Spectra Plot 246
5.8.14 I-t Plot 251
5.8.15 Chromeleon Report Tables 255
5.8.16 Composite Scor ing Parameters Table 282
5.8.17 IPD Processing Parameters Table 283
5.8.18 IPD Component Results Table 284
5.8.19 SIEV E Processing Parameters Table 286
5.8.20 BioPhar ma Finder Processing Parameters Table 287
5.8.21 BioPhar ma Finder Component Results Table 290
5.8.22 Result/Scatter Charts 292
5.8.23 General Charts 297
5.8.24 Illustrations 297
5.8.25 Chromeleon Report Variables 298
5.8.26 Spreadsheet For mulas 299
5.8.27 Page Setup 302
5.8.28 Autorepeat Areas 303
5.8.29 Pr otection 307
5.8.30 Check for Errors 307
5.8.31 Custom For mulas 307
5.9 Electronic Reports 309
5.9.1 Creation Settings 309
5.10 Spectral Library 310
5.11 MS Spectral Library 311
5.12 Data Audit Trail 312
5.13 Injection Audit Trail 314

6 Versioning 316

7 Chromeleon Variables 317

7.1 Global Functions 317
7.2 General 317
7.3 Sequence 317
7.4 Injection 322
7.5 Audit Trail 325

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7.5.1 HPG-3200RS Pump Audit Trail Variables 325

7.5.2 DA D-3000(RS) 325
7.6 Pr econditions 326
7.7 Data Audit Trail 326
7.8 Audit Trail Event 326
7.9 Chromatogram 327
7.9.1 Standard Variables 327
7.10 MS Signal Extraction Parameters 331
7.11 Peak Results 331
7.12 Peak Calibration 336
7.13 Peak Purity and Identification 339
7.14 Composite Scor ing ( Peak Pur ity and Identification) 340
7.15 FL Spectrum 341
7.16 Hit Mass Spectrum 341
7.17 Mass Spectrum 342
7.18 UV Spectrum 344
7.19 Hit Spectrum 344
7.20 Peak Tentative Identification 346
7.21 Pr ocessing Method 346
7.22 Composite Scor ing ( Processing Method) 350
7.23 MS Library Screening 351
7.24 MS Settings 351
7.25 System Suitability Test Case Details 352
7.26 Spectral Library Screening Parameters 353
7.27 UV Spectra Settings 353
7.28 Detection Parameters 353
7.29 Component 354
7.30 Peak Group 354
7.31 Instrument Method 354
7.32 Mass Spectrometry 356
7.33 MS Dev ice 356
7.34 MS Detection Parameters 356
7.35 Peptide 357
7.36 Isotope 357
7.37 Non-Targeted MS Processing ( SIEV E) 358
7.39 Intact Protein Deconvolution 360
7.40 Frame 363
7.41 Report Template 363
7.42 eWor kflow 365

8 Electronic Signatures 366

8.1 Submit Signature 366
8.2 Rev iew Signature 366
8.3 Approve Signature 367
8.4 Remove Signature 367
8.5 Verify Report 367
8.6 Report Signed results 367

9 Chromeleon Services Manager 368

9.1 Instrument Controller Service 368
9.1.1 Instrument Controller Service – Manage Services 368
9.2 Other Chromeleon services 369

10 Instrument Configuration Manager 370

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10.1 Pr operties 370

10.1.1 Access Control 370
10.1.2 Queue Settings 370

11 Administration Console 372

11.1 License Manager 372
11.1.1 Client Licenses 372
11.1.2 Instrument Controller Licenses 373
11.1.3 License Overview 373
11.1.4 Manage Licences 374
11.2 Scheduler 378
11.2.1 Scheduler ( Chromeleon Domain) 378
11.3 User Database 380
11.3.1 Toolbar 380
11.3.2 User Database Policies 380
11.3.3 Chromeleon Users 383
11.3.4 User Properties 383
11.3.5 Access Groups 385
11.3.6 Roles 385
11.3.7 Audit Trail 390
11.4 Global Polic ies 390
11.4.1 Toolbar 390
11.4.2 User Mode 390
11.4.3 Host Name Resolution 390
11.4.4 Multi- User Logon 391
11.4.5 Injection Locking 391
11.4.6 Remote Data Vaults 391
11.4.7 Instrument Audit Trails 391
11.4.8 Detection Algorithm Version 391
11.4.9 User Templates Location 391
11.4.10 Water mark 392
11.4.11 UI Customizations 392
11.4.12 Pr ivileged Actions 392
11.4.13 Email Configuration 392
11.4.14 Station Audit 393
11.4.15 License 393
11.4.16 Raw Data 393
11.4.17 Updater 393
11.4.18 Audit Trail Events 393
11.4.19 Auto Reporting Settings 394
11.5 Define Polic ies in Organizational Units 394
11.5.1 Separate Policy Settings for Organizational Units 394
11.5.2 Use <Global> Settings 395
11.6 eWor kflow Tags 395
11.6.1 Toolbar 395
11.6.2 Create New Tag 395
11.7 Domain Resources 395
11.7.1 All Resources 395
11.7.2 Computers 397
11.7.3 Data Vaults 398
11.7.4 Instruments 399
11.7.5 Chromeleon Consoles 399
11.7.6 System Printers 399

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11.8 Local Machine 399

11.8.1 Manage Data Vaults 400
11.9 Configure Discovery 402
11.9.1 Discovery Configuration 402

12 Administrative Audit Trails 403

13 Time Zone Information 405

14 Changes Introduced in Version 406

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1 About this Document

This document details the functions available in ChromeleonTM 7.3.1. Every effort has been made to provide details of all
functionality.
The blue text in the document describes functionality introduced in the current Chromeleon version, the black text describes
functionality previously available.

1.1 Scope
The functional specifications cover all functions available in version 7.3.1 of the Chromeleon softw are. The document w ill be
updated for future main versions of Chromeleon, including service releases.

1.2 Other Documentation

There are a number of other documents available that w ill help you to learn more about Chromeleon. The documents are
available in electronic form on the installation disk in the Documents folder.

Functional Specifications, 7.3.1, Rev. 1.0 Page 1

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2 Overview of System
Thermo Scientific™ Dionex™ Chromeleon™ 7 Chromatography Data System (“Chromeleon“) is a PC softw are package for
chromatography instrument control, data acquisition, data management and reporting. It is designed for Window s Operating
Systems and has the follow ing main features:
• True Client/server architecture for data acquisition and instrument control; support of all common netw ork protocols;
• True 32-bit algorithms guarantee high processing speed and maximum system stability;
• Access to data via a netw ork allow s sharing of data betw een different laboratories and/or different company sites;

• Easy-to-use user interface w ith a Microsoft Outlook style Console and spreadsheet-based Report Designer;
• Context sensitive help functions and comprehensive Quick Start Guide;
• Provides instrument control HPLC, GC, IC and MS instruments;
• Uniform user interface and operation, independent from operating system and connected chromatographs;
• GLP/GMP and 21 CFR part 11 compliant audit trails/history; documentation of all events and user actions;

• Proven algorithms for virtually parameter-free, automatic integration of difficult chromatograms;

• Unique SmartPeaks tool for fast and easy integration of unresolved peaks;
• Workflow management via eWorkflow s tool;
• Dynamic data processing for fast and efficient optimization of the integration, calibration and reports;
• Integrated relational database for efficient management and fast access to data; flexible database concept w ith
support for MS-SQL-Express and/or MS-SQL-Server databases and Oracle databases;

• Pow erful chromatography data-mining tools for fast evaluation of chromatographic results; more than 130 variables
are available for queries on the relational database; report templates can be directly linked to a query;

• Excel-like spreadsheet Report Designer; custom calculations, formulas and charts;

• User management for the administration and tuning of user privileges, access rights, and so on.

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3 Chromeleon Console
The Chromeleon console is the user interface for accessing all major aspects of a Chromeleon installation. It is designed to
look like Microsoft Outlook. The figure below show s an example of the brow ser w indow and also show s all the main
Chromeleon file types.

Figure 1: Overview of the Chromeleon console

1. Category Bars – These provide direct access to

• Instruments (see section 3.2)

• Data (see section 3.2.3)

• eWorkflow s (see section 3.4)

2. Navigation Area – This displays all objects associated w ith a specific category bar. Details are provided in the
relevant section for the category bars.
3. Work Area – This displays details about the selected object in the navigation area. More details are provided in the
relevant section for the category bars.
4. The Filter Toolbar offers different views of the list in the Navigation Pane:

• Local: Items available on the local Chromeleon station.

• Global: Items available on the Chromeleon Domain.

• Favorites: Items that have been designated as favorites.

• Custom: Filter based on text input.

5. Menu Bar – provides major commands relevant to the console (see section 3.1).
6. The Sequence Toolbar is available w hen a Sequence is selected in the Navigation Pane.
7. The Sequence Status Bar indicates the sequence status.
8. Status Bar show s general information such as the currently logged on user and role.

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Chromeleon 7

3.1 Menu Bar

The follow ing options are available from the menu tool bar:

Function Sub Function Description

Navigation Buttons Go Back One step back in the navigation history
Go Forward One step forward in the navigation history

Create Button Folder Creates a new folder

Sequence Creates a new sequence

Sequence from Worklist Creates a new sequence from a LIMS Workli st i n X ML o r

CSV format
Instrument Method Creates a new instrument method

Processing Method Creates a new processing method

Report Template Creates a new report template

Query Opens a new query window for:

• Injections
• Data Audit Trails
• Instrument Audit Trails
• Administration Audit Trails
Spectral Library Creates a new spectral library

View Settings Creates a new view setting

eWorkflow Creates a new eWorkflow

Electronic Report Creates a new electronic report

File Send To Creates an external file (.cmbx) containing all selected

objects. This file can be used to transfer data from one
Chromeleon 7 installation to another.
Two formats; Chromeleon data files (*.cmbx) which
corresponds to the v2.0 format. The v1.0 format is
represented by Chromeleon 7.0 – 7.2 SR2 data files (*.
cmbx)
Import Allows the importing of Chromeleon data and Non-
Chromeleon data (see 3.1.8).
Save As Allows the selected object to be save d u n de r a d iff ere nt
name
Lock Client Manually locks the Chromeleon client

Exit Exits Chromeleon

Edit Undo Undoes previous command

Redo Repeats previous command

Cut Prepares selected object for a move operation

Copy Copies the selected object to the clipboard

Paste Pastes the selected object (moves an object that has
previously been selected as Cut)
Rename Allows renaming of an object

Delete Deletes the selected object

View Instruments Switch to the Instrument category

Data Switch to the Data category

eWorkflows Switch to the eWorkflows category

Refresh Refresh the on-screen display

Tools Station Qualification See 3.1.1

Instrument Qualification See 3.1.2

Custom Variables Editor See 3.1.3

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Function Sub Function Description

Custom Formulas Editor See 3.1.4

Administration Console See 3.1.5

Preferences See 3.1.6

Virtual Column Separation See 3.1.7

Simulator
Help Index Opens Chromeleon Client Help file

About Chromeleon Allows viewing of information about the Chromeleon

installation including the license key serial number

3.1.1 Station Qualification

Station Qualification allow s users to run either the Chromeleon IQ or Chromeleon OQ or Chromeleon PQ.
The automated Installation Qualification (IQ) procedure checks if all relevant files required by Chromeleon have been
installed correctly.
The automated Operational Qualification procedure checks that Chromeleon correctly calculates data. A data set is
imported in to Chromeleon, integrated and then processed. The data set report contains the expected values and the values
calculated by Chromeleon. These values must match in order for Chromeleon to report the OQ has passed.
The automated Performance Qualification (PQ) analyzes the performance of your Chromeleon installation. It w ill provide a
report on the performance measurements and an assessment of observed values in comparison to standard Chromeleon
installations or previously executed performance qualification runs.
The follow ing Components for Performance Qualification are available:

Parameter Description

Discovery This test provides and removes temporary data a nd m ea su res t h e a ccord ing
timings.
User Management This test performs actions on the user database, e.g. crea te /d ele te u se r. T he
Manage User Database privilege is required.
Licensing The time necessary for license retrieval on your workstation is analyzed.

Instrument Control Four different sequences are tested:

• empty sequences w ith 10 injections
• sequences w ith raw data in 10 injections
• sequences w ith raw data in 100 injections
• sequences w ith 3D data in 10 injections
This test performs actions on the instrument, e.g. launch a n e Workf l ow, a dd a
sequence to queue.
Data Vault You can verify whether the newly created data vault is suitable and identify
problems in existing data vaults. Empty sequences, sequences with raw data a n d
sequences with 3D data are tested. The same sequences are t e st e d a s f o r t h e
Instrument Control component. The actions performed for the respective
component during Performance Qualification represent typical user actions. E a ch
action is labelled with a weight which indicates the importance of its act io n. E ach
action is repeated several times to obtain an average f or t h e d u rat ion of e ach
action. This test performs typical actions on a data vault, such as create a
directory, import or copy a sequence etc..

3.1.2 Instrument Qualification

The automated Instrument Qualification procedure allow s for automatically running the installation qualification (IQ), the
operational qualification (OQ), and the performance qualification (PQ).

3.1.3 Custom Variables Editor

This allow s for the creation or import of custom variables for the sequence, injection list, and the component table in the
processing method. The follow ing options are available:

Variable Sub Function Description

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Chromeleon 7

Variable Sub Function Description

Name N/A Name of custom variable.
Context N/A The object the variable will be applied to. This can be
Sequence, Injection, or Component.
Value Type Text Any combination of text and numeric characters can be
entered. The following properties can also be set:
• Empty values are Allow ed
• Maximum length
• Default value

Numeric Numerical values can be stored. The following properties c a n

be applied:
• Default
• Empty values are Allow ed
• Maximum
• Minimum

• Precision
• Units

Date and Time Only date and time values can be ente red o r a llow e mp ty
values.
List Provides a selection list for the user to choose from. The
following properties can be set:
• Default
• Empty values are Allow ed

• List items

Description N/A Description of the custom variable.

Add Create a new custom variable Creates a new custom variable with unique properties.

Import a custom variab le f ro m a Imports a custom variable from the selected data vault.
data vault
Import a custom sequence Imports a custom sequence variable from the selected
variable from a sequence sequence.
Import a custom injection variable Imports a custom injection variable from the selected
from a sequence sequence.

Import a custom component Imports a custom component variable from the selected
variable from a processing method processing method.
Delete N/A Delete custom variables from list.

3.1.4 Custom Formulas Editor

This allow s for the creation of custom formula templates for the data vault. The user then imports an instance into any
sequence. The follow ing options are available:

Variable Sub Function Description

Name N/A Name of custom formula.

Description N/A Free text description of custom formula

Formula N/A Any combination of Chromeleon variables from section 7 c an

be entered
Header N/A Defines the report column header.
Unit N/A Defines the unit.

Format N/A Defines the number or date format for displaying results.

Add New Custom Formula Create a new custom formula Create a new custom formula with unique properties.

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Variable Sub Function Description

Import a custom formula templat e Import a custom formula template f ro m t he se l ecte d d at a

from a data vault vault.

Import a custom formula from a Import a custom formula from the selected sequence.
sequence

3.1.5 Administration Console

The Chromeleon Administration Console is a central access point for administrative tasks (see section 11).

3.1.6 Preferences
This allow s for setting general Chromeleon preferences to specify what occurs when you drag items betw een folders.

Variable Sub Function Description

When dragging items between Ask Chromeleon will ask each time what to do with the se le cte d
folders: item.
Copy Chromeleon will automatically copy from the source to the
destination folder.
Move Chromeleon will automatically move from the so u rce t o t h e
destination folder.

3.1.7 Virtual Column Separation Simulator

The Virtual Column Separation Simulator is a tool that uses know n ion chromatographic retention data to predict new
retention data and chromatograms on the most popular Dionex anion-exchange and cation-exchange columns. The know n
retention data w ere acquired at Dionex using an appropriate experimental design and then embedded into Virtual Column.
Figure 2 below show s the Virtual Column Separation Simulator interface.

A B

Figure 2: Virtual Column Separation Simulator

The follow ing options can be set for the Separation Simulator (Figure 2A):

Function Description
Reset All Resets all data entries to blank.

Analyte Category Drop-down list of available analyte categories:

Anions
Cations
Carbohydrates

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Chromeleon 7

Function Description
Response By Drop-down list of following categories:
• Peak Area
• Concentration (mg/L)
• Concentration (mM)

Inj. Volume Edit Box to change the Injection Volume. Only available after selecting the
Concentration option for Response By.
Analytes Allows the user to select the analytes of interest.

Results Displays the separation results of the analytes of interest.

Column Types Allows the user to select the column type:
• Standard Bore (4 mm & 5 mm ID)

• Microbore (2 mm & 3 mm ID)

• Capillary (<1 mm ID)

Methodologies Allows the user to select the methodology of interest:

Carbonate – Isocratic
Hydroxide – Gradient
Hydroxide – Isocratic
MSA – Isocratic
MSA – Gradient
Column Selection Allows the user to select a specific column.
Temperature Allows the user for some columns to select a temperature and view the effect o n t he
separation.
Gradient Start Allows the user to select an eluent concentration at the beginning of the gradient fro m
a drop-down box, after selecting a column for a gradient simulation.
Flow rate Allows the user to define a flow rate.

Void Volume Allows the user to define a void volume.

For the Resolution Response Surface and Virtual Chromatogram (Figure 2B) the follow ing

Variable Sub Function Description

Optimize for Critical Pairs Optimizes separation for the critical peak pair.
All Analytes Optimizes separation for all analytes.

Selected Analyte Optimizes separation for selected analyte.

Eluent Preparation N/A Provides detailed instructions for eluent preparation

corresponding to the currently selected conditions. This option
is available only when an isocratic simulation is selected.
Fast Separation Resolution N/A Allows user to set minimum resolution required for fast
separations.

3.1.8 Import

3.1.8.1 Chromeleon Data

• Imports single Chromeleon data files of type:
• Chromeleon 7 data file (*. cmbx)

• Chromeleon 6 data files (*.cmb)

• Chromeleon eWorkflow files (*. ew fx)
• Chromeleon ePanel files (*. panx)

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3.1.8.2 Bulk Import

Imports multiples of Chromeleon data files and also non-Chromeleon data from an external location to Chromeleon. Here
you can add files and folders for import, sort them, and adjust their import settings. You can also drag and drop files for
import into the left pane of the External Data Import dialog box.
Supported files types:

• Chromeleon 7 data file (*. cmbx)

• Chromeleon 6 data files (*.cmb)
• AnDI file (*.cdf)
• GAML file (*. gaml)

• Xcalibur Raw Data (*.raw )

• Xcalibur Sequence File (*.sld)
• Atlas Workbook (*.ana)
• ChemStation Data files (.D)

3.1.8.3 ChemStation Method files (.M )

• ChemStation Signal files (.CH) (16 and 32 bit)
• ChemStation UV Spectral Data files (.UV) (16 and 32 bit)

• ChemStation Data Analysis Register files (.REG) (16 bit)

• ChemStation Sequence Template files (.S) (16 bit)
• ChemStation Batch files (.B) (16 bit)
• ChemStation Comma-Separated Values format files (.CSV) (16 bit)
• ChemStation Spectral Libraries (.UVL) (16 bit)

• Empow er 2D data
• Empow er 3D data
• Empow er Instrument Methods
• Empow er Processing Methods
The follow ing options can be set for the Bulk Data Import:

Function Description

Add Files and folders are added to the left pane and are listed in a tree view.

Remove To remove a file or folder from the list.

Sort grouped files Sort grouped files (e.g., several Xcalibur Raw Data files: *.raw), with the options:
• Move Up to move the selected files up the order in the list.

• Move Dow n to move the selected files dow n the order in the list.
• Sort by Acquisition Date/Time to sort the files by acquisition time and
date

3.2 Instruments Category

3.2.1 Instruments Category Bar
Selecting the instruments category bar changes the contents in the navigation area to a list of all instruments registered on
the discovery server, and the Overview option. The w ork area displays the ePanel Sets for the selected instrument (see
Figure 3 below ).

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Chromeleon 7

Figure 3: Console view when the instruments category bar is selected

A. List of instruments in the navigation area that can be sorted by Locals, All, Favorites or by filtered by free text entry, and
Overview option w hich displays the Instrument Overview grid (see section 3.2.4).
B. ePanel tabs providing direct access to the control options for individual modules (e.g. pump, sampler, etc.).
C. The Audit tab is alw ays available and show s the instrument audit trail (see section 3.2.3).
D. The Startup tab is available for instruments supporting Smart Startup and show s the instrument’s status during startup.
E. The Queue tab is alw ays available and show s the list of sequences queued for analysis. Also, automatic instrument
startup, shutdow n and standby can be activated here.
The follow ing functions are alw ays offered for all instruments in the toolbar:

Function Sub Function Description

Launch eWorkflow N/A Select eWorkflows associated with currently selected

instruments and runs eWorkflow wizard.
Smart Startup Using Queue Settings Starts up an instrument with the instrument method of the first
idle injection (that has an instrument method) in the first
sequence that is not finished.
Using Instrument Method Starts up an instrument with settings specified in a se le cte d
instrument method.
Smart Shutdown Smart Shutdown Shuts down an instrument.
Smart Standby Sets the instrument to standby mode so that a n i nst ru men t
can be re-activated quickly. A minimum flow is retained.
Take Control N/A Allows a user to take control of an instrument.

Monitor Baseline Monitor Baseline Starts a baseline monitor for each channel you select to
monitor.

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 Chromeleon 7

Function Sub Function Description

Stop Stops baseline monitoring and saves the m onit or b a se line

data in the Manual sequence
Stop and Save Stops baseline monitoring and appends the data to the
sequence specified in the Monitor Baseline Save Preferences
dialog box.
Stop and Save As Stops baseline monitoring and opens a dialog box for yo u t o
specify either a new sequence or an exist i ng se q uen ce i n
which to save the data.
Preferences Define a preference for which monitor save action is preferred;
Stop, Stop and Save or Stop and Save As.
Command N/A Opens a dialog that offers access to all instrument commands
(e.g. pump flow).
Fluidic Configuration N/A Opens a wizard to describe the fluidic co nf igu rat ion o f t h e
system. The wizard allows the user to select a capillary kit f o r
a specific workflow from those capillary kits compa tib le wi t h
the current hardware configuration. Alternatively, the user can
import a custom fluidic description from file.
Detach ePanel N/A Creates a new window for the ePanel that is accessible f ro m
the PC taskbar.
Consumables Inventory Opens a floating panel that provides deta iled g u ida nce o n
installation of the selected consumable. Wi l l list t o p -level
<Device> device(s) that are compatible with this feature, and any
associated consumable installation guides.
Troubleshooting N/A Will either open a floating panel that offers direct access t o a
specified section of the instrument user m anu al, a n HT ML
landing page that offers access to diagnostic tests for the
Vanquish Core instrument and an overview of test results, o r
an HTML landing page with content, links, and required
controls to guide user through various troubleshooting actions.

Additionally, the follow ing options are available for the ePanel Set:

Option Description
Autogenerated Activates automatically generated ePanel set.
Last Used Activates ePanel set contain the last manual changes.

Custom Activates a custom created ePanel set.

Manage ePanel Sets… Opens ePanel Set manager (see 3.2.1.2).

Options available w hen right clicking an ePanel Tab:

Option Description
Save ePanel Set As… Save customized ePanel Set.

Add ePanels… Add ePanel using the ePanel Manager.

Remove ePanel Remove currently selected ePanel.

Edit ePanel… Edit ePanel using ePanel editor (section 3.2.1.3).

Detach ePanel… Creates a new window for the ePanel that is accessible from the PC taskbar.
Manage ePanels… Opens ePanel manager (section 3.2.1.1).

Move Left Moves current ePanel left (also available by dragging the ePanel)

Move Right Moves current ePanel right (also available by dragging the ePanel)

Options available w hen right clicking an instrument in the navigation pane:

Option Description
Group by Controller Group instruments by instrument controller.

Add to Favorites Add instrument to favorites list.

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Chromeleon 7

Option Description
Remove from Favorites Remove instrument from favorites list.

3.2.1.1 ePanel Manager

The ePanel Manager manages all default and customer ePanels. The follow ing options are available:

Option Description
Name ePanel name.
Type ePanel Type (Custom or Default).

Categories Chromatography category of the ePanel (IC, HPLC, or GC).

Module Types Module type for which the ePanel was designed.

Module ID Module ID.

Date Modified Date last updated.

Visible To Chromeleon users with access to view ePanel.

Send To Exports selected ePanel.

Import From Imports ePanel.

3.2.1.2 ePanel Set M anager

The ePanel Set Manager manages all custom ePanel sets. The follow ing columns are available:

Option Description
Name ePanel Set name.

ePanels Lists the ePanels includes in the ePanel Set.

Associated With Select instruments to be associated with ePanel set.

Preferred On Preferred instrument for ePanel set.

3.2.1.3 ePanel Editor

ePanels are graphical representations of the instruments that they are connected to. The ePanel editor allow s for creating
new ePanels or modifying existing ones. Figure 4 below show s the ePanel editor.

Figure 4: ePanel Editor

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A. Toolbox – Contains a list of the controls that can be included on the ePanel (see section 0.0.1959744544.27).
B. ePanel Organizer – Displays the name of the ePanel currently being edited. If the ePanel includes sub ePanels, they
are listed below the main ePanel name.
C. Design Surface – Displays the ePanel currently being edited.
D. Properties pane – Enables selecting characteristics of the control currently selected on the Design Surface (see section
0).

Toolbox
The follow ing controls can be displayed on an ePanel.
CM Controls:

Toolbox Control Description

Groups controls into a single box. When controls are in a group box it is possible to move or modify
them as a group.

Groups related controls into a single container. The group box provides a caption.

Organizes groups of controls on tabbed pages.

Organizes groups of controls into a container with two sections separated (horizontally or vertically) by a
bar.

Indicates the status of the device property linked to the color box. It can be linked to any instrument
property that can have only two values. The color box can display a different background and text color
for each value.

Adds the list of properties and commands for the Instrument.

Adds a Web browser for accessing information on the World Wide Web or on a local area network. It is
possible to specify the URL to display when the ePanel is opened, and to prohibit browsing.

Adds an Instrument Audit Trail. For more details see section Error! Reference source not found..

Adds a plot for displaying current signal data. Additionally, the gradient plots can be shown on this plot.

Adds a mass spectral plot.

Graphically displays a data point in a data range. It is also possible to add sliders. These are used to set
the instrument property.

Displays the current value of a property and selects a new value by either typing or selecting from a
drop-down list. If the control is linked to a property that has only discrete values, the field cannot be
edited. The value must be selected from the list.

Displays the current value of a property and selects a new value by either typing the value or selecting
from a list.

Identifies another control or when linked to a device property displays the property value.

Selects among two or more property states.

Toggles between two property states.

Executes a command, property or series of commands and properties.

Launches a definable application with optional parameters.

Groups sub ePanels into container and displays them vertically or horizontally separated.

Adds table to ePanel.

Provides embedded PDF content viewing using the installed Adobe PDF reader application.

Displays a list of the contents of a sub-folder of /InstrumentData/ for the current instrument

Third Party Controls:

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Chromeleon 7

Toolbox Control Description

Displays the Agilent ICF panel control if the Agilent Instru me nt Co nt rol Fra me work (I CF) i s
installed.
Displays the Agilent ICF configuration control if the Agilent Instrument Control Framework (ICF) i s
installed.

Displays any custom driver-specific information which may be implemented in t he in st ru men t

driver
Displays the Waters Acquity Console if the Water Acquity UPLC System Instrument Driver
Software is installed.
Displays the Trace 1300 command dialog.

Displays the TriPlus RSH status panel.

Displays the TriPlus RSH command dialog.

Displays TriPlus 100 LS status panel.

Displays TriPlus 100 LS command dialog.

Note: Each object can be moved and resized on-screen. When relevant fonts and colors can be set in the properties
pane.

ePanel Organizer
The ePanel Organizer gives an overview of the main ePanel and subpanels available in the main ePanel. It displays the
name of the ePanel currently being edited. If the ePanel includes sub ePanels, they are listed below the main ePanel name.
The ePanel Organizer allow s the follow ing actions:

Action Description
New Sub ePanel Creates a new (blank) sub ePanel.

Delete (Available only if a sub ePanel is selected) Deletes the selected sub ePanel.
Rename (Available only if a sub ePanel is selected) Renames the selected sub ePanel.

Save As If the main ePanel is selected, Save As saves the main ePanel and its sub ePanels to a new name. I f a su b
ePanel is selected, Save As saves the sub ePanel to a new name. The sub eP ane l will b e a vailab le f o r
selection in the ePanel Manager.
Add Adds an existing ePanel as a sub ePanel.

Test Tests the ePanel in a test window.

Properties Pane
The Properties pane on the ePanel Editor lets you select characteristics of the control currently selected on the Design
Surface. The available properties depend on the type of the selected control. To see a brief description of a property, click its
name. The description appears at the bottom of the Properties pane. The properties pane is divided in categories, available
depending in the control:
• Appearance (see 0.0.1959744544.27)
• Behavior (see 0.0.1959744544.27)
• Data (see 0.0.1959744544.27)
• Layout (see 0.0.1959744544.27)
• Axis / Decoration (see 0.0.1959744544.27).
• Current Zoom (see 0.0.1959744544.27).

• Default Scales (see 0.0.1959744544.27).

• Gradient Plot (see 0.0.1959744544.27).
• Tube Stripes (see 0.0.1959744544.27).
• Scale (see 0.0.1959744544.27).

Appearance

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The appearance category allow s changing the appearance of the selected control. The options depend on the type of
control selected. The appearance category is not available for the Web Brow ser control. It is possible to change:
• Color (Color, Fore Color, Back Color, Collection)
Three color palettes are available:
The Custom palette contains the available custom colors.
The Web palette contains the standard Web-safe colors.
The System palette contains the standard colors provided by the operating system.
• Font (Typeface, Text Color, Text Alignment)
• Image (Not available for all controls)

Behavior
The behavior category allow s setting the behavior of the selected control, for example, in this category it is possible to set
the “Show If” and “Enable If” properties and determine if dialog should be modeless.
The behavior category is not available for the Command List control.

Data
To enable the intended function of a control that you have added to an ePanel in the ePanel Editor, you must link the control
to a device property or command. This is done in the Data category.
The data category is not available for the Container, Tab Container, Split Container, Command List, Audit Trail, Web
Brow ser, and Signal Plot controls.
For the controls Color Box, DropDow n List (only Link), Edit Field (Only Link), Gauge (Only Link), Group Box, Label, Radio
Buttons, and Sw itch are the follow ing tw o properties available:
• Link – Links the control to an instrument property

• Caption – Adds a caption to the control. This caption can contain text and device properties.
For the Button the follow ing options are available:
• Caption – Add a caption to the button. This caption can contain text and device properties.
• Command – Select action to perform w hen the button is clicked (none, run script).
• Script – Possibility to enter the command, property, or series of commands and properties to be executed w hen the
button is clicked.

Layout
The layout category can define the size of the selected control; it’s location on the canvas and autosize properties. This
category is available for all controls.

Axis / Decoration
The axis / decoration category allow s setting all default axis and decoration parameters for the Signal Plot.

Current Zoom
The current zoom category allow s setting the default axis in the zoom box in the Signal Plot.

Default Scales
The default scales allow setting the signal and time range defaults of the Signal Plot w hen the instrument is idle.

Gradient Plot
The Gradient Plot category allow s show ing the gradients used on these instruments (Eluent Composition, Flow , Eluent
Generator). The follow ing options can be set:
Dw ell Time – Specifies dw ell time in minutes
Gradient Label – Show s labels in gradient plots
Gradient Label Font – Defines the font for the gradient labels
Gradient Line Style – Defines the gradient line style
Gradient Line Width – Defines the gradient line w idth

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Chromeleon 7

Gradient Overlay – Indicates w hether the gradient overlay is visible

Time Marker – Defines w hether the time marker is visible

Tube Stripes
The Tube Stripes parameter for the Signal Plot allow s defining for fraction collection w hich channel to use for delay time
correction and w hether tube stripe overlays should be visually represented on the plot.

Scale
The scales allow setting the intensity and mass ranges and autoscaling of the Mass Spectral Plot.

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3.2.2 Instrument Queue

The instrument queue show s a list of all sequences that are scheduled to be run on an instrument (see Figure 5 below ).

Figure 5: Instrument Queue

The Queue tab has tw o sections, an upper and a low er:

View Description
Current and Pending Displays the queue and the status of each sequence (see section 3.2.2.1).
Recent Displays items that have been removed from the queue within the last week (see section 3.2.2.3).

3.2.2.1 Queue – Current and Pending View

The Current view of the Queue list contains the follow ing columns:

Function Sub Function Description

Startup N/A Indicates if SmartStartup runs before starting this sequence.

Name N/A Displays the sequence name and location.

Status Pending Sequence has not been started.

Running Wake-up Wake-up conditions are running.

Running Smart Startup Smart Startup conditions are running.

Running Sequence is running.

Waiting for Start Sequence with delayed start time has started, b ut e arlie st
allowable start time has not been reached.
Incomplete Sequence contains unacquired injections but is not currently
in an active part of the queue, pending acquisition.

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Chromeleon 7

Function Sub Function Description

Cancelled Queue was stopped while sequence was running (user
interaction)
Failed A module reported an error, or running sequence f a iled t o
communicate with instrument.
Finished All injections in the sequence are completed.

Start after N/A Indicated earliest allowable start time.

Other options on the Queue tab in the current view :

Function Sub Function Description

Add N/A Add a sequence to the queue.

Remove N/A Removes a sequence from the queue.

Manual Upload Only available if the automatic upload of a remote sequence

failed. Allows the user to manually upload the sequ ence t o
the remote Data Vault.
Manual Move Only available if the automatic upload of a remote sequence
failed. Allows the user to manually move the sequence t o a
new location on the remote Data V a ult (ke e pin g t h e o ld
sequence, e.g. because of conflicts that could not be
resolved).
Retry Only available if the automatic upload of a remote sequence
failed. Allows the user to retry the automatic upload.
Cancel Cancels the remove operation and closes the dialog

Move Up N/A Move the sequence one place up in the queue.

Move Down N/A Move the sequence one place down in the queue.

Postpone N/A Moves a Pending sequence to the inactive p o rti on o f t he

queue, changing its status to Incomplete.
Reactivate N/A Moves an Incomplete sequence to the active portion o f t h e
queue, changing its status to Pending.
Properties N/A Opens the sequence properties dialog b o x, wh ere a ut o-
report options can be configured, for the sequence currently
selected in the queue. (see 4.3.2).
Start N/A Starts the queue.
Stop N/A Stops the queue.

Ready Check N/A Performs a ready check for the queue.

Options N/A Displays the Queue Options dialog

3.2.2.2 Queue Options dialog

Function Sub Function Description

After running the queue N/A Defines action when queue is finished.

Keep instrument ready Instrument keeps running, using last conditions.

Run Smart Shutdown Instrument shuts down.

Run Smart Standby Instrument goes in standby mode.

Emergency Instrument Method N/A Defines which Instrument Method to u se wh e n a n A b ort
error occurs in the queue.

3.2.2.3 Queue – Recent View

The Recent view displays items that have been removed from the queue w ithin the last w eek. This view is divided w ith a
splitter into a grid of sequences (on top) and an injection list (read-only sequence display) below . Double-clicking a
sequence or an injection opens the Chromatography Studio.

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3.2.3 Instrument Audit Trail

The audit trail records all commands executed on an instrument and all errors and w arnings that occur. A separate audit trail
file is created each day. The details recorded in the audit trail are dependent on the commands that can be executed on an
Instrument. The audit trail is recorded automatically and cannot be disabled by users (including system administrators).
Figure 6 below show s some of the details commonly recorded in the audit trail.

Figure 6: Instrument Audit Trail

The instrument audit trail offers the following top-level functions:

Function Description
Copy Copies selected audit trail entries to the clipboard.

Report Creates a printable HTML file of the instrument audit trail.

Filtering Provides a filtering option for each of the columns in the audit trail.
Grouping Allows the audit trail to be grouped by any of the columns available.

Display Offers 4 options:

All: Shows all audit trail entries
Run Only: Shows audit trail entries related t o e ven ts t h a t o ccu r wh ile a
sequence is running
Preconditions only: Shows audit trail entries related to system status prior t o
an injection
Errors and Warnings: Shows only errors and warnings
Level Offers 3 options:
Normal: Only shows audit trail entries for normal user level.
Advanced: Shows audit trail entries for normal and advanced user level.
Expert: Shows audit trail entries up to expert user level.
Next Day Shows audit trail entries for the next day.

Previous Day Shows audit trail entries for the previous day.
Search Box Allows entry of text for search purposes.

Find Next Finds the next audit trail entry that meets the search criteria.
Find Previous Finds the previous audit trail entry that meets the search criteria.

The audit trail also offers some functionality that can be accessed by right clicking on any one of the column headers:

Function Description
Table Columns Allows definition of which columns should be displayed and in which order.

Fill Last Column Ensures that the last column is extended to fill an empty space.

Show Group Area Activates the grouping option.

Show Tool Strip Shows/hides the tool strip.

Finally, right clicking on any one of the audit trail entries show s in addition to the functionality described above some
additional functionality:

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Chromeleon 7

Function Description
Select All Selects all audit trail entries.
Scale Columns to Fit Page Ensures that the audit trail columns are sized to fit the screen view.

3.2.4 Instrument Overview Grid

Selecting the Overview option in the Instruments navigation pane displays the Instruments Overview grid. The instruments
displayed in the grid are appropriate to the selected context (Global, Local, Favorites) for the Instrument section.

Figure 7: Instrument Overview grid

The Instrument Overview grid pane offers the follow ing top-level functions:

Function Description
Launch eWorkflow Opens a dropdown containing a list of all the eWorkflows that the current use r c a n
run on the currently selected instrument.
View Instrument Opens the ePanel for the currently selected instrument.
View Queue Opens the Queue of the currently selected instrument.

Stop Queue Stops the Queue of the currently selected instrument

Start Queue Starts the Queue of the currently selected instrument

Resume Queue Resumes the Queue of the currently selected instrument (only displayed when t h e
queue has been stopped and has items remaining).
Filtering Provides a filtering option for each of the columns in the audit trail.

Grouping Allows the list of instruments to be grouped by any of the columns available.

Detach View Detaches the Instrument Overview pane from the Chromeleon co n so le Wi nd ow
and displays it in its own separate Window.

The Instrument Overview grid offers the follow ing content:

Function Description
Instrument Name The name of the instrument

Instrument Status The current status of the instrument

Controller The name of the IPC to which the instrument is connected

Sequence The name of the currently acquiring Sequence

Injection The number of the currently acquiring Injection, out of total number of Injectio ns i n
the Sequence, and the name of the currently acquiring injection
Queued By The name of the user who added the currently acquiring Sequence to the Queue
Queue Status Contains details of the instrument queue, including a n y re main ing P e nd ing o r
Cancelled Sequences.

The Instrument Overview grid also offers some functionality that can be accessed by right clicking on any one of the
instrument row s:

Function Description
Launch eWorkflow Opens a sub-menu containing a list of all the eWorkflows that the current user ca n
run on the currently selected instrument.
View Instrument Opens the ePanel for the currently selected instrument.

View Queue Opens the Queue of the currently selected instrument.

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Function Description

Stop Queue Stops the Queue of the currently selected instrument.

Start Queue Starts the Queue of the currently selected instrument

Resume Queue Resumes the Queue of the currently selected instrument (only displayed when t h e
queue has been stopped and has items remaining).

3.3 Data Category

Selecting the data category bar changes the contents in the navigation area to a list of all Data Vaults registered on the
discovery server. The w ork area displays the contents of the selected object (see Figure 8 below ).

Figure 8: Data Category

The data category provides access to the follow ing object types:

• Data Vaults (see section 4.1)

• Folders (see section 4.2)
• Sequences (see section 4.3)
• Injection Query (see section 4.4)
• Data Audit Trail Query (see section 4.5)

• Instrument Audit Trail Query (see section 0)

• Administration Audit Trail Query (see section 4.7)
• Instrument Audit Trail (see section 3.2.3)
• Instrument Method (see section 4.9)
• Processing Method (see section 5.3)
• View Settings (see section 5.4)
• Report Templates (see section 5.7)
• Electronic Reports (see section 5.9)
• Spectral Library (see section 5.10)
• MS Spectral Library (see section 5.11)

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Chromeleon 7

• Data Audit Trail (see section 5.12)

• Deleted Items (see section 4.8)

3.3.1 Sequence Status Bar

Depending on the status of the sequence the function changes from start or stop a sequence run or resume an interrupted
sequence. Submit/Review /Approve a finished sequence (only available if electronic signatures are enabled for the
sequence). The follow ing functions are offered for all sequences in the status bar:

Function Sub Function Description

Start N/A Start the current sequence

Start with Smart Startup Start the current sequence using Smart Start up t o
perform instrument equilibration prior to starting
Smart Startup Run Smart Startup based on the settings in the
Instrument Method for the first injection
Add to Queue Add the sequence to the Queue without starting
Submit Electronically submit the sequence

Resume N/A Restart the sequence at the first idle injection in the
list
Remove Remove the sequence from the Queue

View Queue Opens the Instrument ePanel

Stop N/A Stop the running sequence. The option to stop
immediately, after the current injection or aft er t h e
current sequence will be offered.
Remove N/A Removes a sequence from the queue.

Manual Upload Only available if the automatic upload of a re mot e

sequence failed. Allows the user to manually
upload the sequence to the remote Data Vault.
Manual Move Only available if the automatic upload of a re mot e
sequence failed. Allows the user to manually move
the sequence to a new location on the remote Data
Vault (keeping the old sequence, e.g. be ca use o f
conflicts that could not be resolved).
Retry Only available if the automatic upload of a re mot e
sequence failed. Allows the user to retry the
automatic upload.
Cancel Cancels the remove operation and closes the
dialog
Submit N/A Apply an Electronic signature to the se q uen ce a t
the submit level
Review N/A Apply an Electronic signature to the se q uen ce a t
the review level
Remove Submit Completely remove the electronic signature

Approve N/A Apply an Electronic signature to the se q uen ce a t

the approve level
Remove Submit Completely remove the electronic signature
Remove Submit N/A Completely remove the electronic signature

Convert N/A Converts non-Chromeleon data and enables d a t a

processing by Chromeleon.
Instrument button Open Instrument… Open a detached ePanel for the currently displayed
instrument (default action of main button)
Assign Instrument… Assign the sequence to a different instrument

Command Instrument… Opens the Command dialog and issue a command

to the instrument

3.3.2 Sequence Toolbar

The follow ing functions are offered for all sequences in the Sequence Toolbar:

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Function Sub Function Description

Save N/A Save any pending changes to the sequence
Studio N/A Open the currently selected injection in the Chromato gra phy
Studio.
Print Report Print a report based on the settings i n a Re po rt T emp lat e
(default action of main button)
Injection List Print the sequence table.
Up N/A Moves to the next level directory above the current sel e ct ion
in the navigation pane.
Insert Row N/A Insert one row into the Sequence table immediately above the
currently selected line/cell
3 Insert three rows into the Sequence table immediately ab ove
the currently selected line/cell
5 Insert five rows into the Sequence table immedia te ly a b ove
the currently selected line/cell
10 Insert ten rows into the Sequence table immed iat ely a bo ve
the currently selected line/cell
Fill Down N/A Copy the contents of the current cell se l ect ion t o a ll ce lls
below in the same column.
Injection Locking Lock Lock the selected finished injections

Unlock Unlock the selected finished injections

Filtering N/A Display the filter bar at the top of the sequence table

Grouping N/A Display the grouping bar at the top of the sequence table

Custom Columns Insert Result Formula Opens the Result Formula Wizard. Use the wizard t o e it her
create a new result formula or to import a result formula f ro m
an existing sequence.
Insert Custom Variable Opens the Custom Variables Wizard. Use the wizard to either
create a new custom injection variable o r i mp ort a cu st om
injection variable that is already available in an existing Da ta
Vault or Sequence.
Edit Opens the Table Columns dialog with the prope rt ies o f t h e
selected custom variable or result formula displayed.
Delete Removes the selected custom variable or result formula f rom
the table.
Text box N/A Text to find using the Find Next button
Find Next N/A Find the next occurrence of the text entered i n t h e t e xt b ox
within the sequence injection list
Find Previous Find the previous occurrence of the text entere d i n t h e t e xt
box within the sequence injection list

3.3.3 Sequence Table Context Menu

The follow ing context menu operations are also available:

Function Sub Function Description

Open Instrument Method Opens the instrument method associated with the sel ecte d
injection in the Studio window.
Injection Audit Trail Opens the injection audit trail in a new audit trail window.

Processing Method Opens the Studio window with the Data Processing category
selected. If the view setting does not contain the processing
method pane, no processing method will be visible.
All Channels Opens the Studio window with the Data Processing category
selected and all acquired channels pinned.

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Chromeleon 7

Function Sub Function Description

<Channel> Opens the Studio window with the Data Processing category
and chosen channel selected. The default channel is bolded
in the list. Selection of non-default channel will override t h e
default selection.
Open raw file with <Registered Software Application> Opens the injection MS raw file in th e se l ect ed so f t wa re
application. The function is visible only when the in jecti on
has MS data in Xcalibur raw file format. The su b f un ctio ns
are visible only if software applications are registered und er
the Operating System with the *.raw extension.
Copy N/A Copies data selected in the sequence editor to memory.
Paste N/A Pastes data in memory to the sequence. If an injection with
raw data was copied, the raw data will also be copied over.
Insert N/A Inserts an empty injection before the se l ect ed lin e i n t h e
sequence.
Delete N/A Deletes the selected line(s) in the sequence editor.

Fill Down N/A Auto-populates the selected ranges of cells in the sequence
editor with the first line of the column. In the case the Name
column of the sequence is selected, a wizard to dynamically
create names will appear.
Injection Locking Lock Locks the selected finished injections.

Unlock Unlocks the selected finished injections.

Undo N/A Steps backwards through all the actions taken in the
sequence since opening.
Redo N/A Steps forwards through all actions undone.
Print… N/A Opens the Print dialogue.

Export… N/A Opens the Export dialogue for export in various formats.
Show Data Audit Trail… N/A Opens the data audit trail in a new audit trail window.

3.3.4 Sequence Context Menu

The follow ing context menu operations are also available:

Function Description
Cut Cut selected sequence to memory.
Copy Copies selected sequence to memory.

Paste Pastes sequence in memory to specified location.

Rename Renames the selected sequence.

Delete Deletes the selected sequence.

Delete Raw Data Opens Delete Raw Data dialog providing options to delete All raw data or Selected raw data.
Print Report Defines report template and print setting for printing.

Export Opens the Export dialog. For a description of each option, refer to section 5.8.26.2.

Convert to Chromeleon Processing Converts non-Chromeleon 7 data and enables data processing by Chromeleon 7.
Read-Only Indicates if the sequence is read-only or not. Read-only sequences cannot be modified.

Send To Opens the Send to dialog for export in various formats. For a description of each option , re f er t o
section 5.3.9.
Show Data Audit Trail… Opens the sequence audit trail in a new audit trail window.

Properties For a description of each option, refer to section 4.3.2.

3.3.5 Associated Items

The Associated items tab displays all items associated w ith the selected Sequence. The follow ing information is provided
for each item:

Function Description

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Name Name of the associated item

Type Type of associated item.

Includes: Instrument Method, Processing Method, Report Template, View Settings, Attachment.
Date Modified The date of the last modification (or creation) of the Associated Item
Comment User text relating to the Associated Item
Associated Items (e.g Documents, Images, SOPs) can be added using the Add Attachment option in the context menu.

3.3.6 Custom Sequence Variables

The Custom Sequence Variables tab displays Custom Sequence Variables associated w ith the Sequence.

Function Description
Name Name of the Custom Sequence Variable

Value Value of the Custom Sequence Variable

Description Description of the Custom Sequence Variable

Custom Sequence Variables can be added by selecting the “Click here to add a custom sequence variable” option in the
grid.

3.3.7 Custom Formulas

The Custom Formulas tab displays Custom Formulas associated w ith the Sequence.

Function Description
Name Name of the Custom Formula
Formula Details of the Custom Formula

Description Description of the Custom Formula

Custom Formulas can be added by selecting the “Click here to add a new custom formula” option in the grid.

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Chromeleon 7

3.4 eWorkflows Category

Selecting the eWorkflow s category bar changes the contents in the navigation area to a list of all eWorkflow s available in all
Data Vaults (see Figure 9 below ). The w ork area displays details about the eWorkflow , a list of associated files (if any are
provided), and a list of all instruments capable of running the eWorkflow .

Figure 9: eWorkflow Category

The list of eWorkflow s in the navigation area can be grouped and filtered. The section “More filters“can be expanded and
offers additional filtering functionality. The follow ing options are available:

Function Sub Function Description

Grouping N/A Allows the list of eWorkflows to be grouped by

Data Vault
State
Tag
Type
More filters Data Vault Allows the list of eWorkflows to be filtered by Data Vault.
State Allows the list of eWorkflows to be filtered by State.

Tag Allows the list of eWorkflows to be filtered by Tag.

Type Allows the list of eWorkflows to be filtered by Type.

It is possible to startup an instrument using Smart Startup by selecting the Smart Startup option from the context menu.

3.4.1 Editing an eWorkflow

The edit screen for eWorkflow s offers three tabs:

• eWorkflow General – used to define the general settings

for the eWorkflow

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• Sequence General – used to define the general settings

for the sequence that w ill be created from the eWorkflow

• Sequence Layout – used to define the injection list layout

that w ill be provided in the sequence generated by the
eWorkflow .

3.4.1.1 eWorkflow General

The follow ing options are available:

Function Sub Function Description

State N/A Allows the user to define the state of the eWorkflow. Choices
are:
• In Development
• Ready
• Approved
• Retired

General eWorkflow Type Allows the user to define a type for the eWorkflow. Ch oices
are:
• GC
• HPLC
• IC
• None

eWorkflow Tags Allows the user to mark the eWorkflow with Tags. Tags a re
defined in the administration console.
Show Description at Launch When enabled the description of the eWorkflow is shown i n
the first page of the wizard when launching the eWorkflow.

Allow Sequence Edits in eWorkflow When enabled the user launching the eWorkflow is allo wed
Wizard to modify any Sequence field within the Wizard. All edits are
applied to the created sequence.
eWorkflow Description A description of the eWorkflow.
Associated Items Instruments Instruments that are capable of running the eWorkfl ow ca n
be added here. If no instrument is added, the eWorkflow will
offer all instruments in the laboratory to the user.
Methods Chromeleon methods can be added here. If one of the
following methods is not added, the user will be prompted to
supply one when running the eWorkflow:
Instrument Method
Processing Method
View Settings
Report Template
Methods can either be added directly to the e Workf l ow o r
added as a link.
Attachments Any file type (e.g. Microsoft Word, Adobe Acrob at ) ca n b e
added here. These can either be added directly to the
eWorkflow or added as a link.

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Chromeleon 7

Figure 10: eWorkflow General Settings

3.4.1.2 Associated Items context menu

The follow ing options are available in the context menu for Associated Items:

Function Description

Open Opens the selected Associated Item.

Remove Removes the selected Associated Item from the eWorkflow.

Link (only for Instruments) Links together two instruments to enable dual-inlet sequence creation.
Unlink (only for Instruments) Removes the link between two linked instruments.

3.4.1.3 Default Assignments

The follow ing options are available:

Function Sub Function Description

Default Values Report Template Defines either that a single default report templa te wi ll b e
used for all sequences that will be created by the eWorkflow
or that Report Templates will be selected for each
instrument using the <Defined per instrument> option.

Save only a link to the selected When checked only a link to the selected report at its current
Report Template(s) location will be saved to the sequence. This is only available
if the report has been added as a link on the eWorkflow
General page.
Channel Defines either that a single default channel will be u se d f o r
all sequences that will be created by the eWorkflow or that a
Channel will be selected for each instrument using the
<Defined per instrument> option.

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Function Sub Function Description

View Settings Defines the default view setting for the sequence that will be
created by the eWorkflow. The list contains all View Settings
added to the Methods section of the eWorkflow General tab,
and also an option to choose tha t V ie w S et tin gs wi l l b e
selected for each instrument (<Defined per instrument>).
Save only a link to the selected When checked only a link to the selected view settings file at
View Settings its current location will be saved to the se q u en ce . T his i s
only available if the view settings file has been a d ded a s a
link on the eWorkflow General page.
Run Sequence after creation When checked all Sequences created by the eWorkflow will
be automatically added to the instrument Queue and started
immediately following creation.
Copy Options Instrument Method Defines which associated items will be copied into the
sequence that will be created by the eWorkf l ow. T he list
contains three options: “Copy all items of this typ e ”, “Co py
only Selected Items”, “Copy all instrument methods f o r t h e
selected instrument”
Report Template Defines which associated items will be copied into the
sequence that will be created by the eWorkf l ow. T he list
contains two options: “Copy all items of t hi s t yp e”, “Co py
only Selected items”
Processing Method Defines which associated items will be copied into the
sequence that will be created by the eWorkf l ow. T he list
contains two options: “Copy all items of t hi s t yp e”, “Co py
only Selected items”
View Settings Defines which associated items will be copied into the
sequence that will be created by the eWorkf l ow. T he list
contains two options: “Copy all items of t hi s t yp e”, “Co py
only Selected items”
Default Assignments grid Instrument Name Contains one row per instrument defined in the Instrume nt s
section of the eWorkflow General tab.
Instrument Method Allows selection, for each instrument, of the default
Instrument Method for the Sequence that will be created b y
the eWorkflow. Contains a list of all the Instrument Methods
defined in the Methods section of the eWorkf l ow G e nera l
tab, filtered for this instrument.
Processing Method Allows selection, for each instrument, of the default
Processing Method for the Sequence that will be created b y
the eWorkflow. Contains a list of all the Processing Methods
defined in the Methods section of the eWorkf l ow G e nera l
tab.
Report Template Allows selection, for each instrument, of the default Re port
Template for the Sequence that will be created by the
eWorkflow. Contains a list of all the Report Templates
defined in the Methods section of the eWorkf l ow G e nera l
tab.
View Setting Allows selection, for each instrument, of t he d e fa ult V iew
Setting for the Sequence that will be created by the
eWorkflow. Contains a list of all the View Settings defined in
the Methods section of the eWorkflow General tab.
Channel Allows selection, for each instrument, of the default Channel
for the Sequence that will be creat ed b y t h e e Wo rkf lo w.
Contains a list of all the Channels defined in all the
Instrument Methods in the Methods section of the eWorkflow
General tab.
Autosampler Tray Sharing Allows selection, for linked instruments, of the range of
autosampler positions that will be used to populate the
sequence for each of the linked instruments. There are five
options: “Independent Carousel”, “Tray 1 st Half ”, “T ra y 2 n d
Half”, “Tray Odd Numbers”, “Tray Even Numbers”.

3.4.1.4 Sequence General

The follow ing options are available:

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Chromeleon 7

Function Sub Function Description

Sequence General Sequence Name Provides the default sequence name. Formulas can also be added from the following
report variable categories
• Global Functions – 7.1

• General – 7.2
• eWorkflow - 7.42
If this field is left blank, users will be prompted to supply a se q ue nce n a me wh en
running the eWorkflow
Data Vault Specifies the data vault that the sequence will be created in.

Path Provides the default sequence path. Formulas can also be added from the follo wing
report variable categories
• Global Functions – 7.1

• General – 7.2
• eWorkflow - 7.42
If this field is left blank, users will be prompted to su p p ly a se q ue nce p a th wh en
running the eWorkflow
Comment A free text entry for further information to be ad ded t o t h e se q u ence com ment .
Formulas can also be added from the following report variable categories
• Global Functions – 7.1
• General – 7.2
• eWorkflow - 7.42

Append injection(s) if Check box to allow the injections created by the eWorkflow to b e a ppe nd ed t o a n
sequence already exists existing sequence. The option to include all/any of the following blocks is provided:
• Header Block
• Bracket Block
• Footer Block

Auto-reporting Configure auto reporting… Opens the Auto reporting settings dialog (see 3.4.1.4)
Settings

Notification Enable Notifications Enables configuration of notifications for sequences created by the eWorkflow.
Settings
Configure notifications Opens the Configure notifications dialog (see 3.4.1.5)

Electronic N/A Check box options to define the levels of signature required for sequen ce . O p t ions
Signature are;
• Submit
• Review
• Approve

Queue Settings Enable Smart Startup when Automatically run a Smart Startup procedure wh e n a se q ue nce cre a te d b y t he
adding the sequence to the eWorkflow is added to the queue.
queue
Features Update Visible Views For For MS data, provides an option to defer auto-processing and updating of view panes
MS Data in the Studio

NTMS New Peak Detection Determines the algorithm to be used when performing NTM S (M AM ) a nalysi s o f
Algorithm peptides. Choose from BioPharma Finder (the default) or SIEVE (the original
algorithm)
Peptide Display Mode When working with peptides in the Studio, this option controls whether th e o nly t h e
master (composite) peptide, only the charge state peptides or both are shown.
Custom Variables N/A Allows custom sequence variables and custom formulas to be added. See 3. 1. 3 f o r
and Formulas more details on custom sequence variables. See 3.1.4 for more deta ils o n cu st om
formulas.

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3.4.1.5 Auto reporting settings dialog

Function Sub Function Description

Auto-reporting Settings Perform NTMS preprocessing When checked for NTMS sequences, NTMS processing
(and reporting) will automatically be performed a ft er e a ch
injection.
Note: this option is only supported for the BioPharma Finder
NTMS algorithm,
Save Electronic Report A report will be automatically created and saved for all
sequences created by the eWorkflow (can be enfo rce d f o r
an instrument in Instrument Configuration Manager)
Print report A report will be automatically created a n d p rin ted f or a l l
sequences created by the eWorkflow
Export report A report will be automatically created and expo rte d f o r a ll
sequences created by the eWorkflow
Print/Export report Determines when report will be generated. Options are:
After whole sequence (default)
After each injection
Printer Allows a printer to be selected. This printer will become t he
default printer for any report generated for a n y S equ en ce
created from this eWorkflow.

3.4.1.6 Configure notifications dialog

Function Sub Function Description

Notification Settings Enable Notifications Enables configuration of notifications for sequences created
by the eWorkflow.

Send notification email when Checking the box will cause an email to be sen t wh en t he
sequence finishes normally last injection of the sequence completes t o t h e sp e cif ied
email addresses (or Chromeleon usernames)

Send notification email when Checking the box will cause an email to be sent to the
sequence is aborted by the specified email addresses (or Chromeleon usernames) if the
instrument sequence aborted by the instrument

Send notification email when Checking the box will cause an email to be sent to the
sequence is cancelled by a user specified email addresses (or Chromeleon usernames) i f a
user aborts the sequence

Include the user who started the If enabled, the user who submitted t he se q u en ce t o t h e
sequence instrument will be notified, in addition to the other recipie nt s
specified above

Include the user who crea te d t h e If enabled, the user who created the sequence will be
sequence notified, in addition to the other recipients specified above

Include the user who crea te d t h e If enabled, the user who created the sequence will be
sequence notified, in addition to the other recipients specified above

3.4.1.7 Sequence Layout

The follow ing options are available for defining the structure of the sequence layout. Note that in this section it is possible to
define the default values for each injection (e.g. name, injection volume), the column layout (order of columns and w hich
columns are visible or not), and w hich custom injection variables are available.

Function Description
Sequence Header Defines injections that must be performed at the start of the sequence. Th is se ct i on can b e l ef t
empty if required.
Sample Block Defines the injections that must be performed for each physical sample. For example, t h is c a n b e
duplicate or triplicate injections, or unspiked and spiked injections.

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Bracket Defines the injections that must be performed for each Bra cke t . Th e f re que ncy o f b ra cke ti ng
injections in defined by the “Max. Samples per Bracket” optio n (se e t a ble b elow). A lt ern at ing
brackets are supported by the “No. of alternate brackets” option (see table below).
This section can be left empty if required.
Sequence Footer Defines injections that must be performed at the end of the sequence. This section can be left empty
if required.

When left empty, the default setting for position is to automatically determine the vial position w hen the eWorkflow is
launched. Additionally, it is possible to enter valid sampler positions such as “RA1” and numbered positions (1, 2, 3,…)
w hich are converted to valid sampler positions w hen the eWorkflow is launched.
The follow ing options are available for defining constraints for the sequence layout:

Function Description
Max. Samples per Bracket Defines the maximum number of sample blocks that can run between bracketed standards

Max. Brackets per Sequence Defines the maximum number of brackets that are allowed in the sequence.
No. of alternate Brackets Defines the number of alternate brackets. A value of zero provides 1 bracket (no alternates), a value
of 1 provides 2 brackets (1 set of alternating brackets), and so on.

Use Bracket Block after Seque nc e Defines if the first bracket block begins after the sequence header or not.
Header
Use Bracket Block before Sequence Defines if the final bracket block finishes before the sequence footer or not.
Footer

The bottom half of the w indow provides a preview for the sequence.
The follow ing options are available w ithin the preview :

Function Sub Function Description

Number of Samples N/A Mimics the number of samples as entered by the user
when launching the eWorkflow.
(Instrument Selection) <No Instrument Selected> Mimics the instrument as selected by the user when
Drop list with instruments launching the eWorkflow.

Sampler start position N/A Mimics the sampler start position as entered b y t h e u se r
when launching the eWorkflow.
Try Launch N/A Allows to test run the eWorkflow wizard.

3.5 Command Line Parameters

Chromeleon offers a number of command line parameters to activate Chromeleon from an external program. The follow ing
options are available:

Function Command Line Syntax Description

Import Chromele on d a ta Chromeleon.exe <file path> Imports data from a single CMBX file.
backup file (.CMBX)

Import Chromeleon Chromeleon.exe <file path> Imports an eWorkflow from a single EWBX file.
eWorkflow backup file
(.EWBX)

Import one or more Chromeleon.exe <file path> [file path2...] Imports ePanels from one or more PANX files.
Chromeleon ePanel
backup files (.PANX)

Import Chromele on X M L Chromeleon.exe <file path> Creates a sequence as defined by t he imp ort ed WL EX
worklist file (.WLEX) worklist file.

Import Chromele on CS V Chromeleon.exe <file path> Creates a sequence as defined by the imported CSV
worklist file (.CSV++) worklist file.
Unattended Mode Unattended Optional parameter to start Chromeleon without user
interface (only available for worklist import).

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Login credentials /user:<Chromeleon user> and Optional parameter to provide login credentials.
/password:<user password>

Open Chromeleon data Chromeleon.exe <URL> Opens the specified data item in the Console.
item
Open Chromeleon Studio Chromeleon.exe [/open studio] Opens the specified data items (sequence, injection) and in
[/channel=channel name] <url1> [url2...] the Studio.
Show help Chromeleon.exe [/h|?|help] Shows the online help about command line parameters.

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Chromeleon 7

4 Objects in the Data Category

The follow ing objects are available in the Data Category:
• Data Vaults (see section 4.1)
• Folders (see section 4.2)

• Sequences (see section 4.3)

• Instrument Audit Trail (see section 4.4)
• Instrument Method (see section 4.9)
• Processing Method (see section 5)
• View Settings (see section 5.4)

• Report Templates (see section 5.7)

• Electronic Reports (see section 5.9)
• Spectral Library (see section 5.10)
• MS Spectral Library (see section 5.11)
• Injection Query (see section 4.4)
• Data Audit Trail Query (see section 4.5)
• Instrument Audit Trail Query (see section 4.6)
• Administration Audit Trail Query (see section 4.7)
• Deleted Items (see section 4.8)
• Data Audit Trail (see section 5.12)
This section provides details of all these objects.

4.1 Data Vaults

Data Vaults are the root directory for all Chromeleon files and directories. It is possible to connect to more than one Data
Vault. Data Vaults are based on a database container and a file system. Chromeleon supports the use of MS SQL Express,
MS SQL Server databases, and Oracle databases. Data Vaults can be located on the hard disk of a standalone PC or on a
netw ork server and can be connected from any PC w ith a netw ork link to the host server.

4.1.1 Data Vault Properties

Global policies for the data vault are defined in this section.

4.1.2 General
Function Description
Read-Only Defines if a Data Vault is read-only or not.
Enable versioning and data audit trails Enables/Disables versioning (see section 6 for more details).

Enable privileged actions Enforces privileged actions for the data vault (see section 11.4.12 for more details).

Enable audit trail events If this function is enabled all audit trail events which a re e nab led in t he g loba l
policies (see section 11.4.17 for more details) a re c o p ied in to n ewly c re at ed
sequences.

4.1.3 Access Control

Function Description
Add User or Group Allows specific users or groups to be allowed access to a Data Vault.

Roles Allows specific roles to be assigned to users or groups when working with ob ject s
within the Data Vault. These roles may differ from the login role of the user

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4.1.4 Downtime
Function Sub Function Description

Specify a period during which the Data Vault is always up Specifies that the data vault is always available.
data vault is planned to be down.
Daily downtime Specifies that the data vault is unavailable for a f ixed t i me
period every day from x to y for a duration of z.
Weekly downtime Specifies that the data vault is unavailable for a f ixed t i me
period once per week on a specified day from x t o y f o r a
duration of z.

4.1.5 Database Statistics

This tab contains a pie chart show ing the used and total capacity for the database part of the Data Vault. This is only
relevant for Microsoft SQL Express based Data Vaults.

4.1.6 Raw Data Statistics

This tab contains tw o pie charts for the raw data part of the Data Vault. The first show s statistics for the hard drive w here the
Data Vault resides and the second a breakdow n of the raw data in the Data Vault.

4.2 Folders
An unlimited number of folders can be created in a Chromeleon Data Vault. The follow ing options are available in the folder
properties:

4.2.1 General
Function Description
Read-Only Defines if a folder is read-only or not

A table show s the number of each object type in the folder and any subfolders.

4.2.2 Access Control

Function Description
Add User or Group Allows specific users or groups to be allowed access to a Data Vault.
Roles Allows specific roles to be assigned to users or groups when working with o b ject s
within the Data Vault. These roles may differ from the login role of the user

4.2.3 Raw Data Statistics

This tab contains a pie chart show ing the breakdow n of data contained w ithin the folder and any subfolders.

4.3 Sequences
A sequence is a list of injections that shall be processed and/or have already been analyzed. The sequence summarizes all
injection data, for example, name, injection volume, dilution, etc.
A sequence consists of three parts; the injection list, the associated items, and the custom variables. The associated items
section stores all files associated w ith the sequence (e.g. instrument methods, processing methods, etc.). The custom
variables section stores all custom variables associated w ith the sequence.
All data entry values are checked against the allow ed values. Any invalid data entries are not accepted by Chromeleon.
Figure 11 below show s a typical sequence.

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Chromeleon 7

Figure 11: Typical Sequence

4.3.1 Injection List

The injection list consists of the sample list. An unlimited number of injections can be created in the list. The user can define
the order in w hich the table columns can be displayed as w ell as w hich columns they w ish to view . The follow ing options are
available.

Parameter Sub Parameter Description

Chromatogram N/A Shows the MiniPlot™ of the chromatogram. Different
channels can be selected.
Name N/A The injection name
Cell (only available for ASE 350) N/A The cell position

Type Unknown The injection type

Blank
Check Standard

Calibration Standard

Matrix
Spiked

Unspiked
Level N/A Defines the calibration level. Can only be used with inj ectio n
types Check Standard, Calibration Sta nda rd, S pike d , a n d
Unspiked.
Position N/A The injection vial position in the autosampler.

Volume N/A The injection volume of the injection.

Vial (only available for ASE 350) N/A The vial position

Instrument Method N/A The instrument method used to acquire the injection
chromatogram.

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Parameter Sub Parameter Description

Processing Method N/A The processing method file used to process the injection.

Extract Time (only available for ASE N/A The time stamp of the successful injection.
350)
Status Idle This is the status if the injection has not been run.
Finished All injections are automatically assigned the status Fi n ish e d
after successfully running.
Interrupted If an injection stops before the end of the designated run time
it is automatically assigned the status Interrupted.
Running This is the status while the injection is running.

Inject Time N/A The date and time of the injection.

Lock Status N/A Indicates the Lock Status of the Injection

Weight N/A The weight used to calculate the content - normalized t o t h e
basic unit - of a substance in an injection. For example, i f t he
calculated concentrations should always be valid for 1 m g o f
an injection, the actual weight is entered; for example, 124.0 8
mg. Chromeleon will then divide all calculated concentratio ns
by 124.08.
Dilution N/A A correction value for amount calculation formulae.

IntStd N/A The Injection Variable IntStd Amount is only re qu ired f or a

calibration based on a variable Internal Standard (intern al o r
internal/external). In this case, the column serves in the
sample list for entering the amount va lues o f t h e in te rna l
standards used for the different samples.
Replicate ID N/A Used to mark samples as Replicates.
Comment N/A A comment about the sample.

Spike Group N/A Associates unknown (unspiked) injections with spiked

injections.
Re-injections N/A Indicates the number of re-injections made by Intelligent Ru n
Control (IRC).
GUID N/A The globally unique identifier that was assigned to this
injection.
Autodilution Ratio N/A The sample-to-diluent ratio.

Retention Time Standard N/A Used to assign a Retention Time Standard.

Target Formula or Mass N/A Allows specification of the target detection m ass, e i t he r b y
entering the m/z value or by typing the chemical formula
Target Negative Adducts N/A Allows selection of one or more negatively charged MS
adducts from a dropdown list. User-defined entries a re a lso
supported
Target Positive Adducts N/A Allows selection of one or more positively charged MS
adducts from a dropdown list. User-defined entries a re a lso
supported

Additional columns can also be seen in the sequence table:

- Custom Injection Variables (see section 3.1.3).

Parameter Sub Parameter Description

Frozen Columns N/A Enter the number of columns to freeze. Frozen columns
remain in view when you scroll the injection list horizontally.

Show Result Formula Statistics N/A Displays statistical data for all result formulas included in t he
Pane injection list.
Manage Order N/A Manages the order of table columns.
Move Up Moves the currently selected column up in the list.

Move Down Moves the currently selected column down in the list.

Custom Columns N/A Manages custom columns.

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Parameter Sub Parameter Description

Add Custom Variable… Opens the Custom Variables Wizard. Use the wizard to either
create a new variable or import a va ria ble t hat i s a l read y
available for the current Data Vault.
Add Result Formula… Opens the Result Formula Wizard. Use the wizard t o e it her
create a new result formula or to import a result formula f ro m
an existing sequence.
Remove Removes the selected custom variable or result formula f rom
the table.
Column Properties N/A Shows/hides column properties

Hide Properties Collapses the column properties dialog box.

In the column properties dialog, there are several options depending on the selected column:

Parameter Description
Format Shows the formatting properties of the column, such as the font and alignment.

Type Shows the properties of the column.

Custom Variable Shows the properties of the Custom Variable.

Result Formula Shows the properties of the Result Formula.

Statistics Shows the statistical properties of the Result Formula.

4.3.1.1 Reserved Injection Custom Variable „CM7: IntStd_Levels”

An injection custom variable w ith the name “CM7:IntStd_Levels” is reserved for CM internal use. If this custom variable of
type Text or List is present in the sequence, the evaluation of the Variable Internal Standard Method w ill use this column
instead of the IntStd column (see also 5.3.2.6 Standard Method).

4.3.2 Sequence Properties

Sequence properties are defined in this area.

4.3.2.1 General

Parameter Description
Comment The comment for the sequence.
Instrument The instrument associated with the sequence.

Report Template Default report template to be used with sequence

View Settings Default view settings to be used with sequence

Channel Default data channel to be used with sequence

Read-Only Indicates if the sequence is read-only or not. Read-only se q u enc e s c a n not b e

modified.

4.3.2.2 Features

Function Description
Update Visible Views For MS Data For MS data, provides an option to defer auto-processing and u pd at ing o f vi ew
panes in the Studio
NTMS New Peak Detection Algorithm Determines the algorithm to be used when performing NTMS (MAM) a nalysi s o f
peptides. Choose from BioPharma Finder (the default) o r S I E VE (t he o rigin al
algorithm)
Peptide Display Mode When working with peptides in the Studio, this option controls whether the only the
master (composite) peptide, only the charge state peptides or both are shown.

4.3.2.3 Locks

Function Description
Revoke locks Allows specific users to revoke all locks of objects that are being modified.

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4.3.2.4 Signature

Function Description
Signature Check box options to define the levels of signature required for sequence. Options
are;
Submit
Review
Approve

4.3.2.5 Auto Reporting

Function Description

Perform NTMS preprocessing When checked for NTMS sequences, NTMS processing (and reporting) will
automatically be performed after each injection.
Note: this option is only supported for the BioPharma Finder NTMS algorithm,
Save Electronic Report A report will be automatically created and saved to the sequence (can be enforced
for an instrument in Instrument Configuration Ma nag er, o r i nhe rite d f ro m t h e
eWorkflow definition if sequence was created from an eWorkflow)
Print report A report will be automatically created and exported f o r t he se q ue nce (ca n b e
enforced for an instrument in Instrument Configuration Manager, or inherited f ro m
the eWorkflow definition if sequence was created from an eWorkflow)
Export report A report will be automatically created and exported f o r t he se q ue nce (ca n b e
enforced for an instrument in Instrument Configuration Manager, or inherited f ro m
the eWorkflow definition if sequence was created from an eWorkflow)
Print/Export report Determines when report will be generated. Options are:
After whole sequence (default)
After each injection
Printer Allows a printer to be selected. This printer will be the default printer for any report
generated for this Sequence.

4.3.2.6 Notifications
This tab is used to enable email notification of events related to this sequence

Function Sub function Description

Send notification email wh e n (Checkbox) Checking the box will cause an email to be sent when the last injection of th e
sequence finishes normally sequence completes
Mail recipient(s) Specifies the email addresses (or Chromeleon u se rn ames) t o wh o m t h e
notification will be sent

Send notification email wh e n (Checkbox) Checking the box will cause an email to be sent if the sequence is aborted by
sequence is aborted by the the instrument
instrument
Mail recipient(s) Specifies the email addresses (or Chromeleon u se rn ames) t o wh o m t h e
notification will be sent

Send notification email wh e n (Checkbox) Checking the box will cause an email to be sent if someone aborts the
sequence is cancelled by a sequence before it completes
user
Mail recipient(s) Specifies the email addresses (or Chromeleon u se rn ames) t o wh o m t h e
notification will be sent

Include the user who If enabled, the user who cancelled the sequence will be notified, in addition to
cancelled the sequence the other recipients specified above

Include the user who sta rt ed If enabled, the user who submitted the sequence to the inst ru me nt will be
the sequence notified, in addition to the other recipients specified above
Include the user who create d If enabled, the user who created the sequence will be notified, in addit ion t o
the sequence the other recipients specified above

4.3.2.7 Raw Data Statistics

This tab contains a pie chart show ing the breakdow n of raw data contained w ithin the sequence.

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4.3.3 Injection Rack View

The injection rack view provides a graphical display of the injection vial positions for the current sequence in the assigned
instruments autosampler. The follow ing options are available.

Function Description

Copy to Clipboard Copies the current rack image to the clipboard.

Full Size Scale the rack view to full size.

Zoom in (+) Zoom into the rack view.

Zoom out (-) Zoom out of the rack view.

In the rack view properties dialog, there are several options:

Parameter Sub Parameter Description

Visible Trays Show all trays Shows all configured trays for the select ed a ut osa mp ler i f
supported.
Hide inactive tray Hides trays that are configured but do not contain any
injections (i.e. are not used) in the current sequence.
Show Overview Displays the rack overview in the top right corner of t he ra ck
view.
Positions Displays the vial positions in the rack view. (Only visible when
zoom allows.)
Tray name Displays the tray names on the rack view.
Interactions Enable scaling Disables zooming of the rack view.

Enable rotation Disables rotation of the rack view.

4.4 Injection Query

Injection Queries are used to search for injections and/or sequences. When creating a new Injection Query or opening an
already existing one a dedicated Injection Query Window is opened.

Figure 12 - Injection Query Window

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Injection Queries are split into four major parts:

• Quick Search Criteria: Search criteria for injection and sequence properties w hich can be executed by corresponding
database queries.

• Com puted Criteria: Searches for values which are calculated by Chromeleon. Searches based on these criteria take
longer to perform.

• Query Result Table: A table listing the resulting injection records after executing the query.
• Associated Items: A liist of associated data items w hich are stored together w ith the injection query.
Via the Save / Save As button the corresponding query settings are saved to the already existing or a new injection query
object in the datavault. Via the Query Now button the query is executed and the found injection records are listed in the
query result table below the Computed Search Criteria section.
Both the quick search and the computed criteria of an injection / sequence record have to be fulfilled to get an injection
record listed in the query result table.

4.4.1 Quick Search Criteria

The quick search criteria refer to injection and sequence properties w here the query can be executed via a dedicated
database query.

Search Criteria Sub Parameter Description

Match All The query will only return injection records which fulfil all condit ions i n
the Quick Search Criteria section.
Any The query will only return injection records which f u lfil at l east o n e
condition in the Quick Search Criteria section.
Search Data Vault Current Data Vault The query is executed on the same data vault where the injection query
data object is stored.
<Data Vault Name> Name of the data vault where the injection query is executed.

Sequence Comment The user comment for the sequence.

Controller The computer name where the sequence is supposed to run or did run.

Instrument The instrument name which is or has been used for the sequence run.

Default Channel The default channel property of the sequence.

Name The name of the sequence of the sequence.

Creation Date & Time The date/time when the sequence has been created.

Created By The user name which created the sequence.

Last Update Date & Time The date/time when the sequence has been modified the last time.

Last Updated By The user name which modified the sequence the last time.
Default Report The default report property of the sequence.

Default View Settings The default view settings property of the sequence.

Path The folder path of the sequence relative to the root of the data vault.
Signature Status The signature status of the sequence (None, Submitted, etc…)

Signature Steps The required signature steps for the sequence.

Submitted By The user name who executed the submit signature for the sequence.
Submitted Date & Time The date/time of the submit signature.

Reviewed By The user name who executed the review signature for the sequence.
Review Date & Time The date/time of the review signature.

Approved By The user name who executed the approve signature for the sequence.

Approve Date & Time The date/time of the approve signature

eWorkflow Name The name of the eWorkflow if a sequence h a s b e en cre a te d b y a n
eWorkflow run.
Read-Only The read-only property of the sequence.

*<Custom Variable Name> The name of a sequence custom variable prefixed by a ‘*’.

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Chromeleon 7

Search Criteria Sub Parameter Description

Injection Comment The user comment property of the injection.
Level The calibration level property of the injection.

Type The injection type.

Status The status of the injection.

Position The vial position property of the injection.

Volume The injection volume property of the injection.

Inject Time The injection date & time.

Weight The sample weight property of the injection.

IntStd The IntStd property of the injection.

Dilution The dilution property of the injection.

Spike Group The spike group property of the injection.

Replicate ID The replicate ID property of the injection.

Number The injection number.

Name The injection name.

Processing Method The processing method name of the injection record.

Instrument Method The instrument method name of the injection record.

Locked The injection lock status (Unlocked, Locked) of the injection record.
Lock Operator The operator who executed the injection lock.

Lock Date & Time The date & time when the injection lock happened.

GUID The injection GUID property.

Re-injections The number of re-injections triggered by an IRC step.

Identification The injection ID property.

*<Custom Variable Name> Name of the injection custom variable prefixed by a ‘*’.

4.4.2 Computed Criteria

In the computed criteria section any formula can be entered w hich can be evaluated for an injection or sequence record.

Search Criteria Sub Parameter Description

Match All The query will only return injection records which fulfil all condit ions i n
the Computed Criteria section.
Any The query will only return injection records which f u lfil at l east o n e
condition in the Computed Criteria section.
Formula N/A Result formula which can be evaluated in the context of an injection o r
sequence record.

4.4.3 Query Result Table

After executing the query the query result table is filled w ith the injection records fulfilling the quick search and computed
criteria. The follow ing injection / sequence properties are offered as result table columns.

Column Name Description

<Default From Sequence> Shows the MiniPlot™ of the chromatogram for the default channel of the corresponding sequence
Injection Name The name of the injection.

Injection # The injection number in the sequence.

Path The folder path of the sequence relative to the root of the data vault.
Sequence Name The name of the sequence.

Instrument The instrument name which is or has been used for the sequence run.

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Column Name Description

Type The injection type.
Position The vial position property of the injection.

Volume The injection volume property of the injection.

Instrument Method The instrument method name of the injection record.

Processing Method The processing method name of the injection record.

Status The status of the injection.

Inject Time The injection date & time.

Weight The sample weight property of the injection.

Dilution The dilution property of the injection.

IntStd The IntStd property of the injection.

ID The injection ID property.

Replicated ID The replicate ID property of the injection.

Comment The user comment property of the injection.

Level The calibration level property of the injection.

Spike Group The spike group property of the injection.

GUID The injection GUID property.

Re-injections The number of re-injections triggered by an IRC step.

*<Custom Variable Name> Name of the injection custom variable with a *-prefix.

#<Result Formula Header> The header of the result formula with a #-prefix.

Triggered by the command “Table Columns…” in the context menu of the query result table header the visibility and order of
these columns can be edited.
The follow ing functions are offered for the query result table in the toolbar above the query result table.

Function Sub Function Description

Print Report Print a report for all injections in the query result table b a se d
on the settings in a Report Template.
Injection List Print the injection query result list.
Studio N/A Opens a Studio window for the currently sel ect ed i nje ctio n
record in the result table. The studio window will be built for all
injections of the query result table.
Save As … N/A Opens a dialog to save the injection list of t h e q u ery re su lt
table into a new sequence incl. the corresponding raw data.
Filtering N/A Display the filter bar at the top of the query result table

Grouping N/A Display the grouping bar at the top of the query result table
Result Formula Insert Opens the Result Formula Wizard. Use the wizard t o e it her
create a new result formula or to import a result formula f ro m
an existing sequence. The new result formula will be
evaluated in a new column of the query result table.
Edit Opens the Table Columns dialog with the prope rt ies o f t h e
currently selected result formula column displayed.
Delete Removes the selected result formula column from th e q u ery
result table.
Text box N/A Text to find using the Find Next button
Find Next N/A Find the next occurrence of the text entered i n t h e t e xt b ox
within the query result table.
Find Previous N/A Find the previous occurrence of the text entere d i n t h e t e x t
box within the query result table.

The context menu in the query result table offers the follow ing additional functions:

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Chromeleon 7

Function Description
Open Query ... Opens a Studio window for the currently selected injection record in the result table. The
studio window will be built for all injections of the query result table.

Open Sequence ... Opens a Studio window for the currently selected injection record in the result table. The
studio window will be built by all injections of the corresponding sequence.

Goto Sequence Selects the corresponding sequence in the console window.

Copy Copies the currently selected records of the query result table to the clipboard.

4.4.4 Associated Items

The Associated Items tab in the low er part of the injection query w indows allows to add report templates and view settings to
the injection query. These data objects are used w hen a studio w indow is opened for the query result table. Via the “Add
Attachment …” in the context menu one can also any attachments (e.g Documents, Images, SOPs) to the injection query.
The table of the associated items provide the same functionality as the corresponding area in the sequence (see section
3.3.4 for details.

4.4.5 Custom Formulas

The Custom Formulas tab is filled w ith all custom formulas associated w ith all the report templates and/or view settings
associated w ith the injection query. The table offers the same functionality as the corresponding area in the sequenc e ( s ee
section 3.3.7 for details).

4.4.6 Properties Dialog

Via the “Properties…” command in the context menu of the console w indow the properties dialog for an injection query is
opened. There you can edit the follow ing parameters:

Parameter Description
Report Template Default report template to be used when a studio window is opened for th e q u ery
result table.
View Settings Default view settings to be used when a studio window is opene d f o r t he q uery
result table.
Channel Default data channel to be when a studio window is opened for th e q u ery re su lt
table.

4.5 Data Audit Trail Query

Data Audit Trail Queries are used to search for data audit trail records of a datavault or a specific folder in a datavault incl. all
subfolders. When creating a new Data Audit Trail Query or opening an already existing one a dedicated Data Audit Trail
Query w indow is opened.

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Figure 13 - Data Audit Trail Query Window

The w indow is separated in 3 sections containing the basic search criteria, the advanced search criteria and the query result
table. Via the Save / Save As button the corresponding settings are saved to the already existing or a new data audit trail
query object in the datavault. Via the Query Now button the query is executed and the found data audit trail records are
listed in the query result table at the bottom of the w indow .
Both the basic and the advanced search criteria of a data audit trail record have to be fulfilled to get a record listed in the
query result table.

4.5.1 Basic Search Criteria

The basic search criteria refer to the location in a datavault (incl. its root folder) and a corresponding date range.

Search Criteria Sub Parameter Description

Root Folder N/A With the Browse-button the Root Folder for the query is selected. When
executing the query only those data audit trail records are co n si dere d
which refer to this folder, any data item in this folder, any subfolder a nd
any data item in any subfolder incl. sequences.
Date Restriction None No date restriction for the data audit trail query.

Specific Dates Specifies the fixed time range for the data audit trail query. O nly d a ta
audit trail records with a date/time stamp in this time range are
considered.
Relative Date In this case the time range for the data audit trail query depends on the
time when the query is executed. You can specify the number of
recent days / months with the option to include the current day / month

4.5.2 Advanced Search Criteria

The advanced search criteria can be both defined for either properties of the data audit record or properties of an associated
audit trail event.

Search Criteria Sub Parameter Description

Match All The query will only return data audit trail records which fulfil all
conditions in the Advanced Search Criteria section.
Any The query will only return data audit trail records which fulfil at least one
condition in the Advanced Search Criteria section.
Data Audit Trail Type Allows to define a search condition for the type of the da ta a udit t ra il
record.

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Search Criteria Sub Parameter Description

Operation Allows to define a search condition for the operation of the d at a a u dit
trail record.
Operator Allows to define a search condition for the operator of the data audit trail
record.
Role Allows to define a search condition for the role of the o pe rat or o f t h e
data audit trail record.
Comment Allows to define a search condition for the comment of the d at a a u dit
trail record
Audit Trail Event Name Allows to define a search condition for the name of an audit trail e vent
which is linked to the audit trail record. At least one a ud it t ra il e vent
records needs to fulfil the condition.
Event Type Allows to define a search condition for the event type of an a ud it t ra il
event which is linked to the audit trail record. At lea st o n e a ud it t ra il
event records needs to fulfil the condition.
Operator Allows to define a search condition for the operat or o f a n a u dit t rail
event which is linked to the audit trail record. At lea st o n e a ud it t ra il
event records needs to fulfil the condition.
Role Allows to define a search condition for the role of t h e o pe rat or o f a n
audit trail event which is linked to the audit trail record. At least one audit
trail event records needs to fulfil the condition
Description Allows to define a search condition for the description of an a ud it t ra il
event which is linked to the audit trail record. At lea st o n e a ud it t ra il
event records needs to fulfil the condition.

4.5.3 Query Result Table

The query result table in the low er part of the data audit trail query w indow is built by the same columns and data audit trail
properties as the data audit trail w indow (see section Error! Reference source not found. for details) and additionally a
path column containing the full datavault path of the data object referring the data audit trail record. Above the query result
table header there is a toolbar w ith the follow ing top-level functions:

Function Description
Report Creates a HTML report of the data audit trail query results.
Show Changes Opens a new window showing the changes of the data object in re sp ect o f t h e
selected data audit trail record.
Restore Restores the version of the data object which refers t o t h e se le c te d a ud it t ra il
record. The new version will not overwrite the current version but is a version on i ts
own and is only persisted when saved by the user.
Studio Opens a read-only Chromatography Studio window of the currently selec te d d a ta
object and the corresponding version. If the data object (e.g. Processing Method) is
located in a sequence the corresponding sequence version is opened in the re ad -
only window.
Filtering Provides a filtering option for each of the columns in the query result table.

Grouping Allows the query result tablel to be grouped by any of the columns available.

Search Box Allows entry of text for search purposes.

Find Next Finds the next data audit trail entry that meets the search criteria.

Find Previous Finds the previous data audit trail entry that meets the search criteria.

By right clicking on any one of the data audit trail entries in the query result table the follow ing commands can be invoked:

Function Description
Show Changes Opens a new window showing the changes of the data object in re sp ect o f t h e
selected data audit trail record.
Restore Restores the version of the data object which refers to t h e se le c te d a ud it t ra il
record. The new version will not overwrite the current version but is a version on its
own and is only persisted when saved by the user.

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Function Description
Studio Opens a read-only Chromatography Studio window of the currently selected d a ta
object and the corresponding version. If the data object (e.g. Processing Method) is
located in a sequence the corresponding sequence version is opened in the re ad -
only window.
Show Data Audit Trail… Shows the data audit trail of the selected data object in a n ew d at a a u dit t rail
window.

For data audit trail records w ith linked audit trail events a yellow flash icon ( ) is show n in the corresponding column. If
such an audit trail record is selected the low er part of the query result table show s the corresponding list of audit trail events.
See section Error! Reference source not found. for details.

4.6 Instrument Audit Trail Query

Instrument Audit Trail Queries are used to search for instrument audit trail records in instrument audit trails. When creating a
new Instrument Audit Trail Query or opening an already existing one a dedicated Instrument Audit Trail Query w indow is
opened.

Figure 14 - Instrument Audit Trail Query Window

The w indow is separated in 3 sections containing the basic search criteria, the advanced search criteria and the query result
table. Via the Save / Save As button the corresponding settings are saved to the already existing or a new instrument audit
trail query object in the datavault. Via the Query Now button the query is executed and the found instrument audit trail
records are listed in the query result table at the bottom of the w indow .
Both the basic and the advanced search criteria of an instrument audit trail record have to be fulfilled to get a record listed in
the query result table.

4.6.1 Basic Search Criteria

The basic search criteria refer to the location w here to look for instrument audit trails and a corresponding date range.

Search Criteria Sub Parameter Description

Audit Trail Source Folder With the Browse-button the Root Folder for t h e q ue ry is se l e ct ed.
When executing the query only those instrument audit trails are
considered which are located in this folder or any subfolder.

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Search Criteria Sub Parameter Description

Instrument With the Browse-button an Instrument in the Chromeleo n d oma in i s
selected. When executing the query the instrument cont rolle r o n t h e
computer which is connected to the select ed in st ru men t h as t o b e
running. The query is restricted to the local datavault and folder wh e re
the instrument controller is storing the instrume nt a udit t ra ils o f t h e
selected instrument,
Date Restriction None No date restriction for the instrument audit trail query.

Specific Dates Specifies the fixed time range for the instrument audit trail query . O n ly
instrument audit trail records with a date/time stamp in this time ra n ge
are considered.
Relative Date In this case the time range for the instrument audit trail query dep end s
on the time when the query is executed. You can specify the number of
recent days / months with the option to include the current day / month

4.6.2 Advanced Search Criteria

Search Criteria Sub Parameter Description
Match All The query will only return instrument audit trail records whi ch f u lfil a ll
conditions in the Advanced Search Criteria section.
Any The query will only return instrument audit trail records wh i ch f u lfil a t
least one condition in the Advanced Search Criteria section.
Date/Time Allows to define date/time range condition beyond the corre sp on din g
basic search criteria,
Retention Time Allows to restrict the instrument audit trail records for a certain retention
time range.
Device Allows to restrict the instrument audit trail records wh e re t h e De vice
property fulfils certain condition.
Message Allows to restrict the instrument audit trail records where the M essa g e
property fulfils a certain condition.
Category Allows to restrict the instrument audit trail records where the Ca t eg ory
property is equal or not equal to either:
• Information or
• Warning or
• Error

4.6.3 Query Result Table

The query result table in the low er part of the instrument audit trail query w indow is built by the same columns and properties
as the instrument audit trail (see section 3.2.3 for details). Above the query result table header there is a toolbar w ith the
follow ing top-level functions:

Function Description
Report Creates a HTML report of the query result table.

Filtering Provides a filtering option for each of the columns in the query result table.
Grouping Allows the query result table to be grouped by any of the columns available.

Display Offers the following filter options:

• All: Shows all query result records.
• Run Only: Shows query result records which occurred while a sequence was
running.
• Preconditions Only: Shows only the query result records which were initially
written when the corresponding instrument audit trail has been created.
• Errors and Warnings: Shows only query result records which category Error
or Warning.

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Function Description
Level Offers the following filter options:
• Normal: Shows only instrument audit trail records for normal user level.
• Adv anced: Shows only instrument audit trail records for normal or advanced
user level.
• Expert: Shows instrument audit trail records up to the expert user level.
Search Box Allows entry of text for search purposes.
Find Next Finds the next query result record that meets the search criteria.

Find Previous Finds the previous query result record that meets the search criteria.

The query result table also offers some functionality that can be accessed by right clicking in anyone of the column headers:

Function Description
Table Columns Allows definition of which columns should be displayed and in which order.
Fill Last Column Ensures that the last column is extended to fill an empty space.

Show Group Area Activates the grouping option.

Show Tool Strip Shows/hides the tool strip.

Right clicking on any one of the instrument audit trail records show s in addition to the functionality described above some
additional functionality:

Function Description
Copy Copies selected instrument trail records to the clipboard.

Select All Selects all records in the query result table.

Scale Columns to Fit Page Ensures that the columns of the query result table are sized to fit the screen view.

4.7 Administration Audit Trail Query

Administration Audit Trail Queries are used to search for certain events in the administration audit trail. When creating a new
Administration Audit Trail Query or opening an already existing one a dedicated Administration Audit Trail Query w indow is
opened.

Figure 15 - Administration Audit Trail Query Window

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Chromeleon 7

The w indow is separated in 3 sections containing the basic search criteria, the advanced search criteria and the query result
table. Via the Save / Save As button the corresponding settings are saved to the already existing or a new administration
audit trail query object in the datavault. Via the Query Now button the query is executed on the Chromeleon Domain
Controller computer.
Both the basic and the advanced search criteria of an administration audit trail record have to be fulfilled to get a record
listed in the query result table.

4.7.1 Basic Search Criteria

With the basic search criteria you can restrict the date/time range of the administration audit trail records and also filter for
the category property.

Search Criteria Sub Parameter Description

Date Restriction None No date restriction for the administration audit trail query.

Specific Dates Specifies the fixed time range for the administration audit t rail qu ery.
Only administration audit trail records with a date/time stamp in this time
range are considered.
Relative Date In this case the time range for the administration audit trail query
depends on the time when the query is executed. You can specify t h e
number of recent days / months with the option to include the cu rren t
day / month
Audit Trail Categories Select one or multiple categories from a list. Only those administra tio n
audit trail records are considered which have one of the selected
category property.

4.7.2 Advanced Search Criteria

Search Criteria Sub Parameter Description
Match All The query will only return administration audit trail records which fulfil all
conditions in the Advanced Search Criteria section.
Any The query will only return administration audit trail records which fulfil at
least one condition in the Advanced Search Criteria section.
Operator Name Filters the query results reg. the Operator Property.
Object Name Filters the query results reg. the Object Property.

Host Name Filters the query results reg. the Host Name Property..
Operation Filters the query results reg. the Operation Property.

User Comment Filters the query results reg. the Comment Property.

Additional Information Filters the query results reg. the Additional Information Property.
Computer Name Filters the query results reg. the Computer Name Property.

Application Name Filters the query results reg. the Application Property.

Application Version Filters the query results reg. the Application Version Property.

4.7.3 Query Result Table

The query result table in the low er part of the administration audit trail query w indow is built by the Date/Time property of
the administration audit trail record and – except for the Host Name – by the same columns and properties w hich can be
filtered in Advanced Search Criteria (see previous section 4.7.2). If multiple categories are selected in the Basic Search
Criteria (see section 4.7.1) a Category column also appears in the query result table.
Above the query result table header there is a toolbar w ith the follow ing top-level functions:

Function Description
Reexecutes the query.
Reload
Report Creates a HTML report of the query result table.

Show Changes Opens a new window showing the changes of the administration object in re sp ect
of the selected administration audit trail record.
Filtering Provides a filtering option for each of the columns in the query result table.

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Function Description
Grouping Allows the query result table to be grouped by any of the columns available.

4.8 Deleted Items

Deleted Items is a special folder in each data vault in the Data category in the Chromeleon Console. It provides temporary
storage for any deleted data objects. It is possible to brow se the Deleted Items contents and restore data objects that w ere
deleted by mistake or delete them permanently.
Any folder, sequence, or injection query can be moved to the Deleted Items folder. The follow ing types of data can be
moved to the Deleted Items folder only w hen they are standalone items in a folder: instrument method, processing method,
report template, view settings, spectral library, and electronic report. If they are not standalone items, they w ill be
permanently deleted.

4.9 Instrument Method

The instrument method contains the instrument commands that w ill be executed for a sample analysis. All data entry values
are checked against the allow ed values. Any invalid data entries are highlighted.
The same common commands can be used for different instruments from different vendors (e.g. Flow , Inject, Wavelength,
etc.). How ever, many instruments have commands that are specific to them and cannot be executed on different
instruments.
The commands available depend on the instrument that the program file is connected to. The list below show s some
commands that are applicable to the UltiMate 3000 DAD-3000(RS) detector.

4.9.1 DAD-3000(RS)
Variable Description
UV.3DFIELD.MaxWavelength The maximum wavelength of the 3D Field.
UV.3DFIELD.MinWavelength The minimum wavelength of the 3D Field.

UV.3DFIELD.BunchWidth The bunch width of the diode group.

UV.UV_VIS_1.Wavelength The wavelength setting of a single acquisition channel

UV.UV_VIS_1.Bandwidth The bandwidth setting of a single acquisition channel

UV.UV_VIS_1.RefWavelength The reference wavelength of a single acquisition channel

UV.UV_VIS_1.RefBandwidth The reference bandwidth of the 3D field

A typical program has tw o different views depending on the type of instrument that is connected - a script view and a dev ic e
view . The script view (see Figure 16 below ) show s a list of all the instrument commands w hereas the device view (see
Figure 17 below ) displays only the commands for the relevant device in a more graphically orientated aw ay.

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Figure 16: Instrument Method Script Editor View

The script editor breaks dow n the instrument commands into 8 blocks:

Block Description
Instrument Setup All commands in this section are executed before the instrument is m a de re ady f o r
performing an injection.
Equilibration Equilibration commands.
Inject Preparation Commands in this section are used to ensure that the instrument is ready to make a n
injection.
Inject Contains all commands required as part of the inject process.
Start Run Contains the commands that will be executed on receiving the inject signal.

Run Contains the timed events that must occur during a run (e.g. gradient steps).
Stop Run Contains the commands that will be executed in order to stop the run.

Post Run Contains commands required for post-run equilibration of the co lumn; i nclud es a l l
commands in the method script that are executed after Stop Run.

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Figure 17: Instrument Method Device View (WPS-3000 Autosampler)

4.9.2 Mass Spectrometers

Supported Thermo Scientific mass spectrometers use the same instrument drivers as those used by the Xcalibur
application. As such, Chromeleon allow s for instrument method editing and review using the same interface in the
Instrument Method data object as seen in Figure 18 . Please consult the manuals for the respective mass spectrometers for
further information on functionality. Please consult the List of Supported Instruments for a list of supported mass
spectrometers.

Figure 18: Instrument Method Device View (Mass Spectrometer)

4.9.3 Startup / Shutdown

The instrument method also contains the instrument commands that w ill be executed w hen starting up the instrument using
Smart Startup and shutting dow n the instrument, or putting it in standby mode, using Smart Shutdow n.

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Figure 19: Smart Startup Settings in the Instrument Method

Smart Startup and Smart Shutdow n can be activated manually using the toolbar in the Instruments category, or
automatically using the Queue Settings (see section 3.2.2). Smart Startup can be manually activated from the eWorkflow s
category (see section 3.4).

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5 Chromatography Studio
The chromatography studio is a user interface that provides access to all information related to a sequence. It is designed to
look like Microsoft Outlook. Figure 20 show s an example of the Chromatography Studio.

Figure 20: Overview of the Chromatography Studio

1. Category Bars, providing access to:
a. Injection List (see section 4.3).
b. Instrument Method (see section 4.9).
c. Data Processing (see sections 5.4), and providing access to:
i. Processing Method (see section 5.3).
ii. View Settings (see section 5.2).
d. Non-Targeted MS Processing (see sections 5.5, 5.6)
e. Intact Protein Deconvolution (See section 5.7)
f. Report Designer (see section 5.8).
g. Electronic Reports (see section 5.9)
h. Spectral Library (see section 5.10).
2. Navigation Pane - Area in w hich you can navigate through the objects available in the selected category.
3. Work Area - The content changes according to the selected category.
4. Ribbon - Menu tool for main actions in the studio. Depending on the category or the selected pane, different
Ribbon tabs are available.
5. Studio Button - The location for commands related to general tasks (see section 5.1).

5.1 Studio Button

The Application Menu is the location for commands related to general tasks, like printing, exporting, saving, etc. The
follow ing options are available in the Application Menu:

Parameter Sub Parameter Description

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Parameter Sub Parameter Description

New Instrument Method Creates a new Instrument Method in the current sequence.
Processing Method Creates a new Processing Method in the current sequence.

View Settings Creates new View Settings in the current sequence.

Report Template Creates a new Report Template in the current sequence.

Spectral Library Creates a new Spectral Library in the current sequence.

Open N/A Opens a sequence in a new Chromatography Studio

Add Instrument Method Adds an existing Instrument Method to the current sequence.
Processing Method Adds an existing Processing Method to the current sequence.

View Settings Adds existing View Settings to the current sequence.

Report Template Adds an existing Report Template to the current sequence.

Spectral Library Adds an existing Spectral Library to the current sequence.

Save Save Opens the save dialog with the possibility to choose data
objects to save.
Save All Immediately saves all modified objects in current sequence.
Save Sequence As Save a copy of the current sequence with a different name o r
at a different location.
Save As Save a copy of the currently selected data object with a
different name at a different location.
Print Print Opens the print dialog.
Quick Print Immediately prints the currently sel ect ed d o cu men t t o t he
default printer.
Print Preview Opens the print preview window.

Export N/A Opens the export dialog.

Convert N/A Converts non-Chromeleon data and enables data processi n g

by Chromeleon.
Close N/A Closes the chromatography studio.

5.2 View Settings

The View Settings stores all aspects of the data visualization of the sequence w ithin the Chromatography Studio.
The view settings include the follow ing settings:
• Selection of visible panes (dependent on license options).
• All visual aspects of chromatogram, calibration, spectral contour and 3D plots, such as line colors, labels to be show n,
etc.
• Selection and layout of the interactive results tables.

• The size, location and layout of the MS ‘Find in Library’ w indow (see section 5.4.12.9)
In addition, the pane “Presets” allow s to activate a task oriented predefined pane layout w ith a single click. The follow ing
presets are available:

Short name Pane selection

Results Chromatogram plot, Interactive Results Tables

Calib. & PM Chromatogram plot, Calibration plot, Processing Method

Contour & Res. Chromatogram plot, Peak properties, UV-Vis Contour plot, Interactive Results Tables
Proc. Method Chromatogram plot, Processing Method

Res & Charts Chromatogram plot, Interactive Results Tables, Interactive Charts
Calib. & Results Chromatogram plot, Calibration plot, Interactive Results Tables

Contour/3D Chromatogram plot, Peak properties, Contour plot

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PM & Results Chromatogram plot, Processing Method, Interactive Results Tables

Calibration Chromatogram plot, Peak properties, Calibration plot

UV-Vis & Res. i Chromatogram plot, Spectral plot, Interactive Results Tables

FL & Results Chromatogram plot, Fluorescence spectral plot, Interactive Results Table
MS & Results Chromatogram plot, Mass Spectrum Plot, Interactive Results Tables

MS Components MS Components plot, Mass Spectra plot, Interactive Results Table

I-t & Results Chromatogram plot, I-t plot, Interactive Results Table

Inj. Rack View Chromatogram plot, Interactive Results Tables, Injection rack view

Frac. Tray View Chromatogram plot, Interactive Results Tables, Autosampler’s fraction tray view
Atlas Chromat. Atlas orientation of Interactive Results Tables, Chromatogram plot, Processing Method

Atlas Calib. Atlas orientation of interactive Results Tables, Calibration plot, Processing Method

Atlas Spectral Atlas orientation of Spectral plot, Calibration plot, Chromatogram plot, interactive Results Tables
HRAM Quan MS Components plot, Calibration Plot, Mass Spectra plot, Processing Method, Interactive Results Table

SRM Quan MS Components plot, Calibration Plot, Interactive Charts, Processing Method, Interactive Results Table
Xcalibur Qual Chromatogram plot, Mass Spectra plot

MS Comp & PM MS Components plot, Processing Method

The “Data Processing Home” ribbon also offers cut, copy and paste operations and buttons for navigating to the
next/previous Injection, Channel and Component. All options available in each pane are listed in subsequent chapters.

5.3 Processing Method

The processing method contains all the data processing instructions (e.g. detection parameters, peak names, etc.). All the
parameters are separated out into 10 main areas, as detailed below .

Note: The layout of the processing method can be changed. The description below is based on the “Advanced” Layout.
Options can be found on different processing method tabs, depending on the selected layout. For a description of the
layouts, see section 5.3.20.

All data entry values are checked against the allow ed values. Any invalid data entries are not accepted by Chromeleon.
Figure 21 below show s a typical processing method using the “Advanced” layout.

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Figure 21: A Typical Processing Method

5.3.1 Detection
The “Detection” tab holds all detection parameters for the processing method. An unlimited number of parameters can be
entered in the table. Each parameter can be activated either at the same time or at different times. Detection parameters
can be assigned to specific channels (or all channels) and to specific injection types (or all types).
Chromeleon 7 has three detection algorithms:
• Chrom eleon 6: This is the detection algorithm from Thermo Scientific Chromeleon 6 CDS. Details of this algorithm
are provided in the Chromeleon 6.8 functional specification
• Cobra: This is the default algorithm for Chromeleon 7. Details of the Cobra Algorithm detection parameters are
provided in section 5.3.1.1 below .
• Atlas: This is the detection algorithm from Thermo Scientific Atlas CDS. Details of this algorithm are provided in
section 5.3.1.2 below .

5.3.1.1 Cobra detection algorithm

Baseline Noise
The “Auto Range” option automatically determines a suitable time range by searching the signal for a baseline segment w ith
low deviation from a line.
In addition, the Start and End Times can be used to define a fixed range that is used for computing the noise in the signal for
automatic thresholds of minimum area/height detection parameters and the curvature noise for the peak and baseline
detection thresholds.

Cobra Smoothing Width

Determines the w idth (= time span) from w hich several successive data points are interpreted as peak or as noise.

Consider Void Peak

Use this parameter to hide a negative peak at the chromatogram start. This is especially useful for the negative w ater peak
in ion chromatography. If Consider Void Peak is set to On, peak detection is disabled for the range of the negative w ater
peak.
The system searches for the negative w ater peak in the retention time range betw een Consider Void Peak = On and
Consider Void Peak = Off. The negative w ater peak is the peak w ith the low est signal at the retention time. Peak
suppression is enabled for the time betw een Consider Void Peak = On and the end of the negative w ater peak. The
chromatogram is recorded, but it is not integrated. (This corresponds to Inhibit Integration = On.) Peak detection is enabled
again only after the peak end of the negative w ater peak has been detected. (This corresponds to Inhibit Integration = Off.)

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Baseline Point
The Baseline Point detection parameter defines a baseline point at the indicated time.

Baseline Type
Baseline Type offers various options for defining the baseline:

Valley to Valley Enables baseline treatment from valley-to-valley, that is, from peak minimum to peak minimum, in a series o f
non-resolved peaks.

Drop Perpendicular This is the default value. In case of non-resolved peaks, the baseline is not pulled up to the relat ive m inima
(valleys). The baseline connects the start of the first with the end of the last non-resolved peak.

If one of the valleys in-between is located below the baseline, the baseline is connected with this minimum t o
avoid cutting off a peak foot. The Valley-to-Valley parameter is not effective.
Lock at current level The baseline is fixed at the current signal level and is extrapolated horizontally to the right . The V alle y -to -
Valley parameter will not take effect.
Lock at global minimum Chromeleon searches to the right for the next absolute minimum. The search is performed either to the end of
the chromatogram or to the next Lock Baseline. Within this interval, the base l ine i s l o cke d o n t h e f o un d
minimum and is horizontal. The Valley-to-Valley parameter is not effective.

Detect Negative Peaks

The Detect Negative Peaks parameter enables and disables detection of negative peaks. When turned on, negative as w ell
as positive peaks are detected. An additional option is offered - “On Don’t Label”. This option should be used to correct the
baseline w ithout labeling the peaks or including peaks in the peak list.

Detect Shoulder Peaks

The Detect Shoulder Peaks parameter rejects a peak if it is a shoulder.
First, the average baseline curvature is determined for the entire chromatogram. The curvature threshold value is the
product of the average baseline curvature and the threshold value.
Detected peak shoulders w ith a maximum curvature above this threshold value are not considered. Select the Sensitivity
detection parameter to influence the determination of the average baseline curvature. Higher sensitivity results in a smaller
average baseline curvature and thus affects peak shoulder recognition.

Fixed Baseline
The Fixed Baseline parameter defines the start and the end of a straight baseline betw een tw o data points of the
chromatogram. Start and end time of this baseline section are determined by the retention time of the corresponding Fixed
baseline detection parameter pair, i.e. Fixed Baseline = Start and Fixed Baseline = End.

Fronting Sensitivity Factor

This detection parameter is an implicit threshold for setting the peak start.
When set to Off (=0), the peak start is moved on the time axis until the slopes of the chromatogram and of the baseline
correspond in the peak start.
When set betw een 1 - 100 the follow ing process is used:
First, the time for the peak start is determined as described above for Off (=0), and then the right baseline w idth is
determined, using the Baseline Level parameter of the Right Width peak variable or (0)). The value, w hich is the upper limit
for the distance betw een the peak retention time and the peak end, is peak.right_w idth multiplied by the Fronting sensitivity
factor. If this limit is exceeded, the peak start is corrected and reset accordingly.

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Inhibit Integration
If the value is set to On before the first peak to inhibit, peak detection w ill not take place until the parameter is disabled (Off);
that is, no peaks are recognized in this area. The chromatogram is displayed on screen, but it is not integrated.

Maximum Rider Ratio

If one or several peaks (h1 to h4) are above the Rider Threshold in a series of non-resolved peaks, Chromeleon determines
via the Maximum Rider Ratio detection parameter, w hether a peak is classified as main peak or Rider.
For this, the height of the peak to classify is put in relation to the height of the greatest peak in the series (reference peak).

Figure 22: Rider Detection Parameters

As can be seen in Figure 22, not the "real" peak height of the peak to be classified is evaluated but the distance betw een the
peak maximum and the skimming tangent. If the ratio h/b multiplied by 100 percent produces a value larger than the one
defined as maximum rider ratio, the peak is a main peak. If the ratio h/b multiplied by 100 percent produces a value smaller
than the one defined as maximum rider ratio, the peak is a rider peak. Starting w ith the largest peak in the series (reference
peak), all adjacent peaks are then classified. As soon as another main peak is recognized, this peak automatically becomes
the new reference peak (b´). The maximum rider ratio is recalculated considering b´. The remaining peaks are classified
again. The process is continued until all peaks of the series are classified.

Maximum Width
The Maximum Width detection parameter defines the maximum w idth above w hich peaks are ignored during peak
detection. The peak w idth is measured on the baseline. For peaks that do not reach the baseline, the w idth is extrapolated.

Minimum Area
The Minimum Area detection parameter is used as a minimum criterion determining the area threshold below w hich peaks
are not integrated.

Minimum Baseline Box Width

Determines the size of the box used to search time ranges w ith a low curvature for the algorithm that is used to identify
peaks of the chromatogram w here the baseline is measured directly (outside of a peak).

Minimum Height
The Minimum Height detection parameter is used as a minimum criterion determining the height threshold below w hich
peaks are not integrated.

Minimum Relative Area

Peaks are rejected if their relative area is below a given threshold.

Minimum Relative Height

Peaks are rejected if their relative height is below a given threshold.

Minimum Rider Ratio

Rejects the identification of a peak as rider if its height is below the given fraction of the height of the largest peak in the
group of neighboring unresolved peaks. See maximum rider ratio for more details.

Minimum Signal to Noise Ratio

Sets the signal-to-noise ratio for the limit of detection threshold if Minimum Area or Minimum Height are set to Auto.

Minimum Width
The Minimum Width detection parameter is used as a minimum criterion defining the minimum w idth below w hich peaks are
ignored during peak detection. Peak w idth is measured on the baseline. In the case of peaks not reaching the baseline, the
w idth is extrapolated

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Peak Group Start/End

Select the Peak Group Start and Peak Group End detection parameters to identify several successive peaks as one peak
group. A peak group that has been defined in such a w ay is treated as one single peak. The peak maximum of the largest
peak becomes the peak maximum of the entire group.
Tw o options are available – “Auto” selects the group start/end automatically, and “Fixed” uses the defined retention times for
the group start/end.

Rider Detection
This parameter defines if riders w ill be detected or not (On/Off). When turned On, both fronting and tailing riders are
detected. This can be further controlled by selecting either “Front Only” if only riders on the peak front should be detected,
and “Tail Only” if only riders on the peak tail should be detected.

Rider Skimming
This parameter indicates how Rider Peaks are skimmed.
• Tangential at low er peak end: For ascending rider peaks, the peak start, and for descending rider peaks, the peak end
is defined in such a w ay that rider skimming is tangential to the chromatogram.
• Tangential at both peak ends (default and the common skimming method): Peak start and peak end are determined
so that rider skimming is tangential at both ends of the chromatogram.
Exponential: The chromatogram is approximated by an exponential function, so that the slope of the chromatogram and the
exponential function correspond at the peak start and the peak end of the rider peak. This option clearly distinguishes from
the tw o others. In most cases, Exponential maps the actual course of the curve very accurately. With this option, the rider
peak w ill usually receive a more realistic larger area. You can use this option only if a sufficient number of data points are
available.

Snap Baseline
By default, Cobra w ill use the raw data baseline as the detected baseline. In many cases this w ill be the correctly defined
baseline, but if this is not the case, turning off the “Snap Baseline” option w ill allow Cobra to detect a baseline separated
from the raw data baseline.

Tailing Sensitivity Factor

This detection parameter is an implicit threshold for setting the peak end.
When set to Off (=0), the peak end is moved on the time axis until the slopes of the chromatogram and of the baseline
correspond in the peak end.
When set betw een 1 - 100 and follow ing process is used:
First, the time for the peak end is determined as described above for Off (=0), and then the right baseline w idth is
determined, using the Baseline Level parameter of the Right Width peak variable or peak.right_w idth(0)). The value, w hich
is the upper limit for the distance betw een the peak retention time and the peak end, is multiplied by the Fronting sensitivity
factor. If this limit is exceeded, the peak end is corrected and reset accordingly.

5.3.1.2 Atlas detection algorithm

The Atlas detection algorithm provides a new option for peak detection in Chromeleon. This algorithm w as previously
available only in Thermo Scientific Atlas CDS. With this option, Chromeleon provides access to the full set of Detection
(Integration) events available in Atlas and, w hen selected, Chromeleon uses the same set of processes used in Atlas to
detect the start, end, area and height of a peak.
This option can be used for new , existing or imported data.

Bunch Size
Data bunching averages data points together and smooths over-sampled data. The number of data points that can be
amalgamated into a single point lies in the range 0-50. The optimum number of data points over the half height of a peak
should be in the range 10–20.

Start Threshold / Threshold

Start Threshold determines how sensitive Chromeleon is to detecting the start of a peak. Raising the Start Threshold
decreases the number of peaks detected. Low ering the Start Threshold increases the number of peaks detected. Enter a
value in the range 0.0001-10000.0000.

End Threshold

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End Threshold determines how sensitive Chromeleon is to detecting the end of a peak. Low ering the End Threshold value
makes peak end harder to find. Increasing the End Threshold value decreases the sensitivity, i.e. few er peak ends are
detected.
By default, the End Threshold is set to half the Start Threshold value. In most cases this provides an adequate baseline.
How ever, the value can be modified independently of the Start Threshold value.
Enter a value in the range 0.0001-10000.0000.

Start Trend
Start Trend w orks in conjunction w ith the Threshold events to determine the position of peak start. Increasing the Start
Trend value causes peak start to occur later: decreasing the value causes peak start to occur earlier. The Start Trend v alue
defaults to 2, but can accept a value in the range 1 - 5. Normally, this event need only be modified if correct peak start
positions cannot be achieved using the Threshold parameter.

End Trend
End Trend w orks in conjunction w ith the End Threshold parameter to determine the peak end positions. Increasing the End
Trend value causes peak end to occur later in the peak: decreasing the value causes peak end to occur earlier in the peak.
This parameter defaults to 11, but can accept a value in the range 1-100. Normally, this event need only be modified if
correct peak end positions cannot be achieved using the End Threshold parameter

Force Baseline
During integration, Chromeleon splits each peak group by dropping a perpendicular to the baseline at each valley point. If
required, the baseline can be forced to meet the data at all valley points w ithin a peak group using the Force Baseline event.
.Setting Force Baseline to On forces the baseline to meet the raw data at valley points in the data.

Minimum Area
Small peaks, for example those due to noise, can be rejected during the final pass of integration if they fail to exceed a user-
defined area, height or w idth. Minimum Area specifies an area threshold. Any peaks w ith an area below the area thres hold
w ill be rejected during integration.

Minimum Height
Small peaks, for example those due to noise, can be rejected during the final pass of integration if they fail to exceed a user-
defined area, height or w idth. Minimum Height specifies a height threshold. Any peaks w ith a height below the height
threshold w ill be rejected during integration.

Minimum Width
Small peaks, for example those due to noise, can be rejected during the final pass of integration if they fail to exceed a user-
defined area, height or w idth. Minimum Width specifies a w idth threshold. Any peaks w ith a w idth below the w idth threshold
w ill be rejected during integration.

Negative Peaks
During integration, Chromeleon determines the presence of positive peaks in a chromatogram. The presence of negative
peaks in the data can result in incorrect baselines being applied. The Negative Peak event prompts Chromeleon to detect
the presence of both positive and negative peaks. Select the Negative Peaks On event prior to the start of a region
containing any negative peaks. Select the Negative Peaks Off event at the end of a region containing negative peaks.

Shoulder Sensitivity
When tw o or more peaks elute at similar retention times they may merge to such an extent that no valley occurs betw een
them: the only indication that more than one peak exists is the presence of a shoulder on the merged peak. The Shoulder
Sensitivity event enables Chromeleon to separate the merged peaks by dropping a perpendicular to the baseline at each
shoulder. Chromeleon detects a shoulder as a point of inflection in the second derivative of the raw data. The Shoulder
Sensitivity event accepts a value betw een 0 and 1, w here 0 detects no shoulders and 1 provides the maximum shoulder
detection sensitivity. The closer the Shoulder Sensitivity gets to 1, the greater the likelihood that shoulders w ill be detected.

Skim Sensitivity
When tw o peaks elute at similar retention times, one of the peaks, know n as the rider, may elute on the front or tail of the
other peak, as show n in the figure below :

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Figure 23: Parent and Rider peaks

Normally, Chromeleon splits the parent and rider by dropping a perpendicular at the valley point betw een the peaks. If
required, a rider peak may be skimmed from the parent peak using the Skim Sensitivity event.
The Skim Sensitivity event specifies w hether the rider is skimmed, based on a height ratio betw een the parent and rider
peaks:

Height rider peak / Height parent peak ≤ Skim Sensitivity value

The Skim Sensitivity value has a range betw een 0 and 1, inclusively, w here a value of 0 skims no rider peaks and a value of
1, the maximum, skims all rider peaks w ith a height less than or equal to the height of the parent peak. A rider peak that is
taller than the parent peak cannot be skimmed. In this event, the parent peak becomes the rider and w ill be skimmed
accordingly.

Suppress
You can prevent integration of unw anted sections of the chromatogram.

• The Suppress Immediately event begins suppressing integration at the exact time specified, and is commonly used for
suppressing a solvent front at the beginning of a chromatogram.

• The Suppress Next Group event delays suppressing integration until the beginning of the next peak. This event is
commonly used to suppress selected peaks w ithin a peak group.
• The Suppress Off event sw itches off the Suppress Immediately and Suppress Next Group events

5.3.2 Component Table

The “Component Table” tab is the area w here all information relating to expected peaks are entered. An unlimited number of
components can be added to the table.
Right-clicking on a cell in the table exposes the follow ing options

Menu item Description

Copy Copies the values in the highlighted cell(s) to the Windows Clipboard
Paste Pastes the values in the Windows Clipboard to the highlighted cell(s)

Fill down When multiple cells are highlighted, copies the value in the first highlighted ce ll t o
all of the other highlighted cell(s)
Get Current Retention Times Updates the retention times of the highlighted cell(s) based on the actual retention
times of the currently selected chromatogram and channel.

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Edit Peptide Name (Appears only when the component table contains peptides). Displays an
interactive dialog for editing the peptide name. Modifications are highlig ht ed a n d
may be updated by selecting from a list. When the dialog is closed, the syn t a x o f
the edited name is validated.
Adjust Retention Times Adjusts all of the retention times in the table by a fixed amount or a fixed
percentage
Add Confirming Peak (MS Only) Creates an additional confirming peak column in the component t ab le.
Note that you must still manually add the masses, filters and so on.
Remove Confirming Peak (MS Only) Removes a confirming peak column from the component t a ble. No t e
that if the column contains an actual peak definition, that information will be lost.
Add Quantitation Peak (MS Only) Creates a quantitation peak column in the component table if one d o es
not already exist. Note that you must still manually add the masses, filters a n d so
on.
Remove Quantitation Peak (MS Only) Removes the quantitation peak settings for all components.

Remove Selected Peak (MS Only) Clears the settings of the quantitation or co nf irmat ion p eak f o r t h e
component of the currently selected cell.

For each component, the follow ing information can be entered:

5.3.2.1 Name
The name of the peak.

5.3.2.2 Retention Time

The expected retention time of the peak. The follow ing options are available:

Parameter Description
Use this component as reference component Defines if this component is a reference component for relative retention times.

Absolute Time The expected retention time of the peak in minutes.

Time distance The time distance from a user specified reference peak. Value can be negative o r
positive.
Time ratio The time ratio (%) of a user specified reference peak.

Retention Time Standard Peak Area Ratio Expected retention time is dynamically determined from a valid re te nt ion t ime
standard using the component predefined peak area ratio.

5.3.2.3 Window
The Window parameter defines a tolerance interval w ithin w hich the peak is expected. The start and end times of the
retention w indow result from adding the w indow value to and subtracting it from the retention time (retention time +/- w indow
value); that is, the w indow width is alw ays twice as wide as the value. A peak outside this w indow is not identified.

Parameter Sub Parameter Description

Window Interpretation Absolute The window value is treated as an absolute time.

Relative The window value entered is treated as a percenta ge o f t h e

expected retention time – the higher the re te nt ion t ime t h e
larger the window.
Component Match

Algorithm Retention Time The component match is only based on the expected
retention window.
Retention Time & Peak Height The component match is based on the exp ecte d re t en tio n
window and the peak height.
Retention Time & Peak Area The component match is based on the exp ecte d re t en tio n
window and the peak area.
UV Spectrum Match The component match is based on the comparison of the UV
spectrum of the peak and the UV reference spectru m o f t h e
component.
MS Spectrum Match The component match is based on the comparison of the M S
spectrum of the peak and the MS reference spectru m o f t h e
component.

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Parameter Sub Parameter Description

Algorithm = Retention Time Nearest If more than 1 peak is located within the expecte d re t en tio n
time window, the peak nearest to the expected retention t ime
in the window is assigned to the component.
First If more than 1 peak is located within the expecte d re t en tio n
time window, the first peak in the window is assigned t o t h e
component.
The 2 nd peak in the window If more than 1 peak is located within the expecte d re t en tio n
time window, the second peak in the window is assi g n ed t o
the component.
The 3 rd peak in the window If more than 2 peaks are located within the expected retention
time window, the third peak in the window is assigned to t he
component.
The 4 th peak in the window If more than 3 peaks are located within the expected retention
time window, the fourth peak in the window is assigned to the
component.

Algorithm = Retention Time & P eak Greatest If more than 1 peak is located within the expecte d re t en tio n
Height time window, the greatest peak reg. the pe ak h e ig ht i n t h e
window is assigned to the component.

The 2 nd greatest peak in the If more than 1 peak is located within the expecte d re t en tio n
window time window, the second greatest peak in the window is
assigned to the component.
The 3 rd greatest peak in the If more than 2 peaks are located within the expected retention
window time window, the third greatest peak in the window is assigned
to the component.

The 4 th greatest peak in the If more than 3 peaks are located within the expected retention
window time window, the fourth greatest peak in the window is
assigned to the component.
Algorithm = Retention Time & P eak The largest peak in the window If more than 1 peak is located within the expecte d re t en tio n
Area time window, the largest peak reg. the peak area in the
window is assigned to the component.
The 2 nd largest peak in the window If more than 1 peak is located within the expecte d re t en tio n
time window, the second largest peak in the window is
assigned to the component.
The 3 rd largest peak in the window If more than 2 peaks are located within the expected retention
time window, the third largest peak in the window is assign ed
to the component.
The 4 th largest peak in the window If more than 3 peaks are located within the expected retention
time window, the fourth largest peak in the window is assigned
to the component.
Algorithm = UV Spectrum Match Consider only peaks inside the Computes the comparison value for all peaks in the
window = Off chromatogram against the UV reference spectrum of the
component and assigns the peak with the greatest mat ch ing
value.

Consider only peaks inside the Computes the comparison value only the p ea ks i n si d e t h e
window = On expected retention window of the component and assigns th e
peak with the greatest matching value.
Algorithm = MS Spectrum Match Consider only peaks inside the Computes the comparison value for all peaks in the
window = Off chromatogram against the MS reference spectrum of the
component and assigns the peak with the greatest mat ch ing
value.

Consider only peaks inside the Computes the comparison value only the p ea ks i n si d e t h e
window = On expected retention window of the component and assigns th e
peak with the greatest matching value.

For the component match options referring to a 2nd, 3rd or 4th peak the number of peaks in the expected retention time
w indow has to greater or equal to the corresponding option (i.e. 2, 3 or 4). Otherw ise the component is not assigned to any
peak at all.

5.3.2.4 Channel
This defines the channel that the peak details are assigned against. The choices are “All Channels” or specific channels.

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Chromeleon 7

5.3.2.5 Evaluation Type

This parameter defines the peak value that is used for the quantitative analysis of the peak. The follow ing options are
available:

Parameter Sub Parameter Description

Area N/A The quantitative analysis is performed using the peak area.
Height N/A The quantitative analysis is performed using the peak height.

Relative Area All Components The quantitative analysis is performed using the peak rela tive
area (calculated using the areas of all peaks).
Identified Components Only The quantitative analysis is performed using the peak rela tive
area (calculated using the areas of all identified peaks).
Exclude ISTD Components The quantitative analysis is performed using the peak rela tive
area (calculated using the areas of all peaks e xc e p t f o r a ny
peaks defined as ISTD peaks).
Relative Height All Components The quantitative analysis is performed using the peak rela tive
height (calculated using the heights of all peaks).
Identified Peaks Components The quantitative analysis is performed using the peak rela tive
height (calculated using the heights of all identified peaks).
Exclude ISTD Components The quantitative analysis is performed using the peak rela tive
heights (calculated using the heights of all pe aks e xce p t f or
any peaks defined as ISTD peaks).
CE Area N/A Integration type for capillary electrophoresis.
CE-Area = Area / Ret. Time

5.3.2.6 Standard Method

The Standard parameter indicates the standard method to be used for calibration. The follow ing options are available:

Parameter Description
External The calibration curve determines the area/amount ratio.
Internal Calibration corresponds to the External Standard method. In addition, a n I n te rna l
Standard is added. The internal standard itself is calibra t ed a s a l l o t her p e aks.
When performing the integration, the calculated amounts of the re m aini ng p e aks
are corrected by the nominal/actual ratio of the intern al st a n da rd. Ch rome leo n
recognizes any number of internal standards. Theoretically, each peak may have its
own internal standard!
Internal/External When calibrating with an internal standard, calculation is wi t h a rea a nd a mo un t
ratios instead of absolute areas and amounts. During integration, the area ra t io is
inserted into the saved calibration function to calculate the amount ratio. The resu l t
is the amount in relation to its reference peak. Each peak can have its own internal
standard.
Use Channel For internal and internal/external standard calibrations it is optional to sp e cify t h e
channel used during calibration,
Use this component as Internal Standard (ISTD) Defines the component as an Internal Standard.

Use sample amount as reference (Variable I nt ern al Uses the amount value defined in the sequence table rather than the amount value
Standard) defined in the Amount table.
If the custom variable with the reserved name “CM7:IntStd_Levels” is defined in the
sequence the amount value for the Internal Standard is picked from the
concentration level in the processing method given by the v a lue o f t h is c u st o m
variable property of the injection.

Generally components w hich are used as ISTD cannot refer to another ISTD component. Yet if the custom variable
“CM7:SyringeStandard” is defined in the processing method such a reference is possible. The value of the custom variable
has to be set to an appropriate component name w hich is an ISTD as w ell. In this case the ISTD is calibrated and evaluated
against the other ISTD w hich is defined via the custom variable “CM7:SyringeStandard”.

5.3.2.7 Calibration Type

The Calibration Type parameter determines the Calibration Function and the Weights. The follow ing options are available:

No Calibration

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When selecting “No Calibration”, the peak is not quantified.

Automatic Calibration
Use this option to calibrate using a calibration function. With this option enabled, you can also define the w eighting and
averaging of calibration values. The follow ing settings are possible:

Parameter Sub Parameter Description

Curve Fit Type Linear The calibration curve is a straight line.

Quadratic The calibration curve is a quadratic curve.

Cubic The calibration curve is a cubic curve.

Polynomial The calibration curve is a polynomial curve (m aximu m o f 7

orders).
Power The calibration curve is a power curve.

Average Calibration Factor (AvCF) The calibration curve is a straight line through the origin . T he
slope is determined by taking the average response for eve ry
different calibration level and th en a v erag e t h e re sp o nse
factors for the different levels.
Point to Point (P-P) The calibration curve is polygon, that is, a linear interpolat ion
between two calibration points. If there are several replicate s
of a calibration level, they are averaged before interpolation.
Base Function x Uses x as base function for polynomial curve fit.
(Available only if Polynomial is √x Uses √x as base function for polynomial curve fit.
selected under Curve Fit Type)
2
x Uses x2 as base function for polynomial curve fit.
log(x+1) Uses log(x+1) as base function for polynomial curve fit.

Weighting No Weighting Higher weighting of higher amounts.

1/Amount Nearly cancels out the weighting of higher amounts.

2
1/Amount Causes over-proportional weighting of smaller amounts.

1/Response Nearly cancels out the weighting of higher signal va lu es. I n

this case, the Y-values (dependent signal values) of the
calibration points are used as weight factors instead of the X -
values (nominal amounts).
1/Response 2 Causes over-proportional weighting of smaller signal valu es.
In this case, the Y-values (dependent signal va lues) o f t h e
calibration points are used as weight factors instead of the X -
values (nominal amounts).
1/Rel.Std.Dev. Each average level is weighted reciprocally with the
corresponding relative standard deviation.
Note: Is only available if the o pt ion “A ve rag e Ca libra t ion
Levels before Curve Fitting” is enabled.
1/Rel.Std.Dev.2 Each average level is weighted reciprocally with the
corresponding square of the relative standard deviation.
Note: Is only available if the o pt ion “A ve rag e Ca libra t ion
Levels before Curve Fitting” is enabled.
1/Log (Amount) Very strong weighting of smaller amounts in proportion to high
amounts. This function is not suitable for amount values < 1.
1/Log 2 (Amount) Extremely strong weighting of smaller amounts in prop ort ion
to high amounts. This function is n o t su i t able f or a m oun t
values < 1.
1/Log (Response) Very strong weighting of smaller signal values in proportion to
high signal values. The Y-values (dependent signal values) o f
the calibration points are used as weight factors instead of the
X-values (nominal amounts). This function is not suitab le f o r
signal values < 1.

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Chromeleon 7

Parameter Sub Parameter Description

2
1/Log (Response) Extremely strong weighting of smaller signal values in
proportion to high signal values. The Y-va lues (d e p e nde nt
signal values) of the calibration points a re u se d a s we i gh t
factors instead of the X-values (nominal amounts). This
function is not suitable for signal values < 1.
Ignore Origin (With Offset) N/A Does not force the curve through the origin.

Force Through Origin N/A Forces the curve through the origin.

Compute with Origin (Add Zero) N/A Includes the (0,0) value when calculating the curve fitting.

Average all response values of each N/A Averages all measuring points of one calibration level b ef ore
calibration level before curve fitt ing calculating the calibration curve from the averaged values.
(Avg)

Calibration of other component or peak group

This option uses the calibration curve for the selected component. The component can be selected using a drop-dow n box
w hich lists all components from the component table. A relative Response Factor can be entered.

Manual Calibration
This option allows the manual definition of the calibration curve. The following formula can be defined:
f(x) = C0 + C1x + C2x2 + C3x3
w here C0 to C3 are user definable values

5.3.2.8 Concentration Levels

Parameter Description

Calibration Levels The amount for the relevant calibration level (as defined in the “Level” injection field,
section 4.3.1)
Tolerance [%] The allowable deviation (Calibration Level ± Tolerance [%]) for pass or fail results

5.3.2.9 Conc. Unit

The concentration unit for the component.

5.3.2.10 Factor
The Factor is a component-specific, multiplicative factor w ithout dimension to correct the actually measured peak area on
the basis of estimated effects.

5.3.2.11 Peak Type

The Type parameter determines the type of baseline contact and the separation of other, non-resolved peaks. The follow ing
options are available:

Parameter Description
Autodetect The peak type is determined via an algorithm, or via detection parameters.

Rider (R) The peak is integrated as a rider.

Main (M) The peak is integrated as a main peak without baseline contact.
Baseline-Main (B-M) The peak is integrated as a main peak with right bilateral baseline contact.

Main-Baseline (M-B) The peak is integrated as a main peak with left bilateral baseline contact.
Baseline-Main-Baseline The peak is integrated as a main peak with left and right baseline contact.

Note: When Chromeleon reports the peak type, the follow ing distinctions are made:
• In the case of rider peaks, an ascending edge is reported as “u” (u = up) and a descending edge is reported as “d” (d =
dow n).
• In the case of a main peak direct baseline contact on the left and/or right side is indicated by a capital B. If the baseline
below non-resolved peaks is draw n from minimum to minimum (Valley to Valley), that is from peak end to peak end,
this type of baseline contact is characterized by a small b (Figure 24).

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 Chromeleon 7

Figure 24: Explanation of different Peak Types

5.3.2.12 Peak Group(s)

Peaks may be grouped and then be calibrated and integrated together. Peak groups are defined in the peak group table.
Any peak group of type ‚Named Group‘ (see 5.3.4 for details) can be entered for a component. Multiple assignments are
also possible.

5.3.2.13 Comment
The comment for the peak.

5.3.2.14 Left/Right Limit

Normally, peak integration is performed automatically. It is possible to limit or extend integration on the left, right, or on both
sides w ith the appropriate parameters. This may be done in the component table via a left and/or a right limit.
The peak is integrated betw een left and right limit, that is, betw een:
t - LL ... t + RL
Where:
t = Retention Time
LL = Left Limit
RL = Right Limit.

5.3.2.15 Retention Index

Linear retention indexes are defined for programmed GC as w ell as for HPLC. On the basis of the values defined in the
component table, Chromeleon calculates the retention index for the remaining components.

5.3.2.16 Upper / Lower Confidence Probability

The confidence interval describes the range in w hich the "true" calibration curve w ill be found w ith a given probability. Use
the Upper and Low er Confidence Probability columns to define the component probability limits.

5.3.2.17 Previous Retention

Dialog box to define w hether the retention time stored in the component table (nominal time) is used to identify a peak or
w hether the detected retention time of a peak in a previous injection is used. The follow ing settings are available:
Parameter Sub Parameter Description

Use recently detected retention All Injections Select if retention times of all injections are to be used.
times of
Calibration Standards Only Select if retention times of standard injections are to be used.

Set Reference Time to Last value Use the retention time of the last injection or calibration
standard.
Average of last <n> values Average the actual retention times of the last n inject ion s f o r
the newly set retention time. n can be any valu e b e twe en 2
and 99.
Global average Use the averaged retention times of all i nject ions a ct u ally
processed as the new set retention time.

5.3.2.18 Custom Component Variables

Custom Component variables can be created for processing methods. For details refer to section 3.1.3.

5.3.2.19 Reference UV Spectrum Settings

UV Reference spectra are used for substance identification. A UV reference spectrum can be chosen for each peak. The
reference spectra can be obtained from either a spectra library or from the apex spectrum of any peak in any sequence.

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Chromeleon 7

Check Extrema
The parameter indicates w hether the spectra search compares the number of extrema in the reference spectrum w ith the
ones in the peak spectrum.

Match Criterion
The match criterion defines the mathematical method w ith w hich tw o standardized spectra are compared w ith each other.
The signal deviation, that is, the difference betw een the UV spectrum and a reference spectrum at defined w avelength, is
checked (∆1, ∆2, ...) (Figure 25). Since the square of the deviations is calculated as w ell, the direction of the subtraction
does not matter.

Figure 25: Check Signal Deviation to determine Match Factor

The method provides a value of similarity (match) betw een completely different (= 0) and identical (= 1000). The follow ing
mathematical methods are available in Chromeleon:

Parameter Description
Least Square Forms the sum of the squared signal deviations at each wavelength and
determines the average square deviation between two spectra.
Weighted Least Square Analogous to Least Square; the squared deviations are weighte d b y t h e si g na l
height (for spectra extracted close to the detection limit).
Correlation Usual match criterion in statistics if a linear correlat ion b e twe en t wo cu rves i s
presumed (similar to Least Square; usually provides the same result).

Relative Maximum Deviation

The Relative Maximum Deviation column allow s you to enter the maximum permissible deviation of the w avelength maxima
of the reference spectra from the maximum of the current peak spectrum.

Spectrum Derivative
This provides the follow ing options for spectra comparison:

Parameter Description
Off Compares the curve shape of the spectra themselves.
st
1 Derivative Compares the curve shape of the 1 st derivative of the spectra.

2 nd Derivative Compares the curve shape of the 2 nd derivative of the spectra.

Threshold
This parameter defines the threshold of the Match Factor above w hich tw o spectra may be accepted as matching.

Wavelength Range
The low er and upper w avelengths used for the spectra comparison.

5.3.2.20 Reference M ass Spectrum Settings

MS Reference spectra are used for substance identification. An MS reference spectrum can be chosen for each peak. The
reference spectra can be obtained from either a spectra library or from the apex spectrum of any peak in any sequence.

Peak Mass Spec Filter

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This parameter Indicates the scan filter used w hen evaluating the peak mass spectrum in the component match.

Ref Mass Spec Settings

These parameters define the mathematical method w ith w hich the two mass spectra are compared.
Selecting the corresponding check box w ill cause these parameters to be extracted from the MS Library Screening tab of
the processing method.
To use custom library search settings, the check box should be cleared. One may then specify the search parameters

Parameter Sub Parameter Description

Search Type Identity Three options are available:
Normal: Uses a standard pre-screen search filter. This is the default search type.
Quick: Uses a fast pre-screen search filter.
Penalize Rare Compounds: Limits the impact of rare compounds by reducing t h eir
match factors. This option is effective only when you have selecte d a NI S T Ma ss
Spectral Library (such as mainlib). It has no effect o n sp e ct ra i n i nt ern al NI S T
libraries or other commercial libraries.
Each reference spectrum in a NIST Mass Spectral Library contains a record of other
commercial libraries containing information about the compound. A c o mp ou nd i s
considered 'rare' if it is present in a limited number of these libraries.
Similarity Simple: Finds a large set of spectra to compare with the submitted spectru m. T his
search option is generally slower than an identity search.
Hybrid: Uses a combination of the Simple and Neutral Loss sea rch t yp e s. Wh e n
Hybrid is selected, the Search with Mol. Weight edit box under Search O pt ion s i s
enabled. Enter an estimate of the submitted spectrum's molecular weight.
Neutral Loss: Compares neutral losses of the submitted spectrum with spectra in the
library data. The neutral losses in a spectrum are the mass differences between the
molecular ion and other major ions in the spectrum. For certain classes of
compounds, neutral losses can be a very characteristic spectral feature. In a Neutral
Loss search, Chromeleon identifies the molecular ion of the submitted spectrum and
includes the molecular ion in the search, along with the spectrum. Significant neutral
losses of the submitted spectrum are calculated and compared with the library data.
Hits are returned according to matches of the molecular ion and its neutra l l osse s.
When Neutral Loss is selected, the Search with Mol. Weight edit box under Search
Options is enabled. Enter an estimate of the submitted spectrum's molecular

Search options Search with Molecular Wt When a value is supplied, searches will be restricted t o l ibra ry e nt ries wi t h t he
indicated molecular weight.
Reverse Search When checked, this parameter indicates that a reverse search wi ll b e p e rfo rme d
instead of a standard search
Thresholds Match Factor Defines the minimum match factor below which matches will not be reported

Reverse Match Factor Defines the minimum reverse match factor below which matches will not be reported

5.3.2.21 Extracted Ion Chromatograms

The parameters used to extract ion chromatograms from mass spectrometry (MS) raw data in a sequence. Extracted ion
chromatogram (XIC) definitions for one quantitation peak and multiple confirming peaks can be created for each component
in the component table.

Data Range for Extracted Ion Chromatograms

When MS Detection is combined w ith Extracted Ion Chromatogram parameters from the Component table, in some
situations, a partial XIC is created for peak detection and integration. The extraction w indow is a minimum of +/- 0.5min or is
determined by the formulas:
extraction start time = retention time – display w indow *10
extraction end time = retention time + display w indow * 10

Display Range
The retention time range the extracted ion chromatogram for MS components w ill be displayed.

Function Description

Use Retention Time Use the retention time assigned to the component in the component table.

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Chromeleon 7

Function Description

Specify Time Specify a mid-point time that is not tied to the retention time.
Use Retention Window Use the retention time window assigned to the component in the component table.

Specify Window Specify a display window that is not tied to the retention time.

XICs
This function opens the Update XICs w indow.

Function Sub Function Description

Update… N/A Opens the Update XICs window

Update XICs Window

This function enables automated ion ratio calculations and bulk-apply of ratio tolerances and peak coelution settings.

Function Sub Function Description

Target Components For all components Enables automated ion ratio calculations and/or bulk-apply o f
ratio tolerances and peak coelution settings for all components.
For selected components Enables automated ion ratio calculations and/or bulk-apply o f
ratio tolerances and peak coelution settings for a limited subset
of components.
<Component Names> Selection defines components where ion ratios are
automatically calculated or ratio tolerances and peak coelution
settings are applied.

Confirming Peak Ratio Calcula tio n Calculate Ion Ratios Enables automated calculation of ion ratios
Settings
Use average of selected injections Uses user-selected injections to determine the ion ratios

Use average of all calibration Uses the average ion ratios from all calibration standards in the
standards sequence.

Use average of all calibration Uses the average ion ratios from all calibration standards o f a
standards at level single level from the sequence.
<Level ID> Defines the level ID (number or name) from which the average
ion ratio is calculated from.
Ratio Tolerances and Coelution Window Type Enables bulk-apply of the Window Type parameter
Settings
<Relative / Absolute> Defines whether the Window value is interpreted as a relat ive
or absolute window around the target ion ratio.
Window +/- Enables bulk-apply of the Window parameter.

<Value (%)> Defines the pass/fail tolerance window around the t arg et io n
ratio.
Ion Coelution Enables bulk-apply of the Ion Coelution parameter.

<Value (min)> Defines the maximum retention time deviation a confirm at ion
peak may have against the quantitation peak. T hi s va lu e i s
always absolute.
Update ‘Include in Calibration’ to Enables bulk-apply of the ‘Include in Calibration’ option

<Option> Include / Don’t Include

Smoothing Method Enables bulk-apply of the smoothing parameters

<Method Type> Digital filter (smoothing algorit hm) t o a pply t o t he d at a t o
reduce signal noise (or select None).
Smoothing points Number of points in smoothing block

Signal Filter Settings Update filters for all ions Enables bulk-update of filters

Select best match from f ilt ers i n Bulk-update of filters by selecting the best matching filter f ro m
current injection those available in the current injection
Use this filter Bulk-update of filters to a specific filter name
<Filter> Select the acquisition filter from which the chromatogram will
be extracted or enter a custom filter.

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Extracted Ion Chromatogram

Show s each XIC definition on a separate tab page. There can be one XIC definition designated the MS Quantitation Peak
and multiple MS Confirming Peak definitions.

Function Sub Function Description

chromatogram plot preview N/A Displays a preview of the XIC plot.

Signal N/A Defines the signal parameters to use for performing the
extraction:
Type Type of extraction performed
- TIC (Total Ion Current): All ions matching the filter entered i n
the Filter list will be extracted from the raw data.
- Base Peak: Base peak ions that match the filter e nt ere d i n
the Filter list and/or the mass range entered in the Mass
Range(s) field will be extracted from the raw data.
- Mass Range: Ions that match the filter entered in the Filter list
and with a mass that matches the mass or mass range
entered in the XIC Mass(es) or Range(s) box will be extracte d
from the raw data.
Precursor Mass Mass of the first precursor of the MS trace, if a p recu rso r i s
defined by the filter.
XIC Mass(es) or Range(s) Mass or mass range to limit the data extracted to ions from the
selected filter that match the masses entered.

Filter Select the acquisition filter from which the chromatogram will
be extracted or enter a custom filter.
Smoothing Digital filter (smoothing algorit hm) t o a pply t o t he d at a t o
reduce signal noise (or select None).
Calibration Include in Calibration (Confirming peaks only) When selected, the response o f t his
peak is added to that of the quantitation peak for purp ose s o f
calibration
Ratio N/A Enables options to compare the confirming ion's response as a
ratio of the quantitation ion's response.
Target Ratio Target ratio of the confirming ion's response to the quantitation
ion's response.
Window type Type of calculation (Absolute or Relative) used to determine a
range of ratios in which the target ratio is considered
acceptable.
Window +/- Ion ratio percent (%) to be added before and after t h e t a rge t
ratio.
Ion Coelution Maximum acceptable difference in re te nt ion t ime (i n m in )
between a confirming peak and a quantitation peak.
Use default MS Detection settings N/A Select this check box to use the default settings defined on the
MS Detection Settings page of the processing method.
Clear this check box to enter custom MS detect ion se t t ings.
For a description of each option, refer to section 5.3.9.
Spectral plot preview N/A Shows the spectrum for the selected filter that is n e are st t h e
extraction time and is within the extraction window.

5.3.2.22 M ol. Mass

The molecular mass of the component. It is only used for reporting purposes.

5.3.2.23 CAS
Chemical Abstracts Service (CAS) registry number of the component, only used for reporting purposes.

5.3.2.24 Chem. Formula

Chemical structure of the component represented by text (letters and numbers), only used for reporting purposes.

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Chromeleon 7

5.3.2.25 Peptide Group

An optional numeric value w hich may be used to group components w hich represent the same peptide but w ith different
modifications. It is only used for reporting purposes.

5.3.2.26 M ass Tolerance

Specifies the mass tolerance value to be used in calculations related to this component that require a mass tolerance be
specified.
The units of the value correspond to the units defined on the MS Settings tab of the Processing method. (See 5.3.11) The
cells in this column are only enabled if the ‘Specify Mass Tolerance per Component’ option is enabled on the MS Settings
tab.

5.3.2.27 RTS Ratio Standard

The tolerance (%) that defines a range of acceptable peak area ratio values. Used to confirm a match w ith a component
w hen using a Retention Time Standard Processing Method.

5.3.3 Calibration
The “Calibration” tab is the area that show s all the global calibration settings and the list of calibration standards that are
used to quantify the peaks in the currently active chromatogram. In this tab it is possible to disable/enable the calibration
points for specific peaks/channels. Additional options available are:

Function Sub Function Description

Mode Fixed The calibration standards from a selected sequence are u se d
for calibration. The other sequence is copied to the calibratio n
table in the processing method. You can update the calibration
any time, for example, after the oth er se q u en ce h as b e e n
updated.
Total Calibration is performed using all valid calib rat ion st a nd ard
samples of the sequence.
Additional For calibrating a sample, all calibration standard injections that
are listed before this sample in the sample list are used.
Group The calibration of a sample series from t h e sa m ple list (f o r
example, samples 3 to 50) is performed based on the
calibrations standards listed directly before this series; for
example, no. 1 and 2. If this sample list includes further
standards, as for instance, no. 51 and 52, the following
samples, for example, 53 to 100, will be evaluated b a se d o n
these. The standard samples in lines 1 and 2 will no longer b e
considered.
Bracketed Samples are evaluated based on all calib rat ion st a nd ard s
immediately surrounding. In case of a list containing two
samples, two calibration standards, two samples, two
calibration standards and so on, samples 1 and 2, lo ca te d a t
positions 3 and 4, are evaluated with standards 1, 2, 3, and 4 ,
located at positions 1, 2, 5, and 6. Samples 3 and 4 are
evaluated using the standards 3, 4, 5, and 6, located at
positions 5, 6, 9, and 10.
Standard Addition Calibration is performed using spiked and unspiked injections.

Curve Fitting Normal Selects normal dependent and i nd ep end ent va riab les f o r
calibration i.e. x-axis = amount, y-axis = measured value.
Inverted Selects inverted dependent and indepe nde nt vari able s f o r
calibration i.e. x-axis = measured value, y-axis = amount.
Dual-Column Separate Calibration N/A When this function is enabled it is possi b le t o u se o n ly t he
standards for the active column in tandem mode.
Concentration Level Tolerances N/A When this function is enabled, it is possible to define %
tolerances on a level-by-level and component-by-co mpo nen t
basis and allows for visualization of results on the ca libra t ion
plot.

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Function Sub Function Description

Amount Ratio for Variable I nt ern al Selecting this check box when performing va riab le i nt ern al
Standard standard calibration will plot the response ra t io a g ain st t h e
amount ratio on the calibration curve and adjust the resp on se
factors accordingly.
This check box is selected by default for new processing
methods created using Chromeleon 7.2.6 and later versions. It
is unselected by default for processing methods created using
a previous version of Chromeleon.

Origin of Standards for Fixed N/A Allows the user to select an external sequence for calibrat ion.
Calibration On selection, all standards in the external sequence are copied
into the current sequence.

5.3.4 Peak Group Table

This section is used to define the naming and quantitation options for peak groups. For every peak group record the
follow ing options are available:

Function Description

Name The name of the peak group.

Group Type Two peak group types are available:
Timed Group: Defines a peak group which spans over a certain time interval in the chroma to gram
allowing to incorporate also unidentified peaks in a peak group. The time interval is d e f ine d b y t he
Start/End Time properties (see below).
Named Group: So-called named peak groups can be selected in t he co mpon en t t a ble . E very
component can be assigned to 1 or more named peak groups.
Start Time The start time for the peak groups of type ‘Timed Group’.

End Time The end time for the peak groups of type ‘Timed Group’.
Channel The assigned channel for the peak group. Similar to components peak groups can be assigned to ‘All
Channels’ or to single ones.
Group Evaluation Three evaluation types are available:
None: there is no group evaluation at all. This type e.g. can be used to combine m u ltip le d isj un ct
timed groups together to a single name group.
Reporting: results of peak groups (e.g. group area) can be reported in a dedicated report table.
Calibration: this type also contains the reporting capabilities but beyond that such a peak group ca n
be also calibrated. A component record can refer to such a peak group when setting the calibra tio n
type to ‘Calibration of other component or peak group’ (see 0.0.1959744544.27 Calibration o f o t her
component or peak group).
Evaluation Type Evaluation Type for quantitating the peak group. Same as for the Evaluation Type in the compon en t
table (see section 5.3.2.5 for details).
Standard Method Similar to the standard method field of the component table a peak g ro u p h a s i t s o wn st a n da rd
method. Possible values are External and Internal referring to an associated ISTD component.
A peak group can never be specified as an ISTD itself.
Calibration Type Calibration Type for quantitating the peak group. Same as for the Calibration Type in the component
table (see section 5.3.2.7 for more details). This property is only available for peak groups with group
evaluation ‘Calibration’.
Peak Group(s) Timed peak groups can be assigned to named groups thus extending the scope of name d g rou ps.
For named peak groups such an assignment is not available.
Include Identified Peaks Via this property the identified peaks in the time windo w (S ta rt/ E nd T ime) ca n b e i nclud ed i n
corresponding timed group.
Factor Multiplicative factor without dimension to correct the actually measured peak are a o n t h e b asi s o f
estimated effects.
Comment Arbitrary user comment

Calibration Level(s) Similar to the calibration levels of the component table the calibra tio n l evel i s u se d t o e nt er t o
reference amount of a peak group. If this value is empty and the group type is ‚Na m ed G ro up ’ t he
calibration level values of all component records which are member of this peak group are su m med
up to give the reference amount of such a named peak group.

Analogue to the component table custom variables can be added to the peak group table as w ell.

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Chromeleon 7

5.3.5 Chromatogram Subtraction

This tab defines any baseline subtractions performed.

Function Description
No Subtraction Blank run subtraction is not performed.

Subtract recent Blank Run injection in correspondin g The blank run in the corresponding sequence is subtracted point by point fro m a ll
sequence injections for which the same processing method is assigned. For t h e b lan k ru n
injection itself the subtraction is not applied in any case.
Subtract a fixed injection Allows the user to select a blank run or any chromatogram fro m a ny se q u ence .
This chromatogram is subtracted point by point from all injections in the sequen ce
for which the same processing method is assigned. For the fixed blank run
injection itself the subtraction is not applied.

5.3.6 UV Spectral Library Screening

To identify substances, UV spectra can be compared to library spectra. The spectra search can be performed via the
Spectra Library Screening tab of the Processing Method. The follow ing options are available:

Parameter Sub Parameter Description

Spectral libraries to be searched in N/A The spectral libraries to be searched in.

Compare Conditions Match Criterion As per 0.0.1959744544.27.

Hit Threshold As per 0.0.1959744544.27.

Use Spectrum Derivative As per 0.0.1959744544.27.

Wavelength Range As per 0.0.1959744544.27.

Library Spectral Filter N/A Defines additional conditions for spectra matches.

Match XXX of the following rules ALL is equivalent to the AND logical operator. Finds injections
with variable values that match all of the criteria sp e cifie d i n
the rules that are assigned the AND logical operator.
ANY is equivalent to the OR logical operator. Finds injection s
with variable values that match any of the criteria specifie d i n
the rules that are assigned the OR logical operator.
Variable Selects a hit spectrum variable from the list.
Comparison operator Select the operator to be used for comparing variable values:
= (is equal to)
<> (is not equal to)
< (is less than)
<= (is less than or equal to)
> (is greater than)
>= (is greater than or equal to)
is between
is not between
is during previous
is not during previous
is like (use with wildcards) (for Quick Search only)
is not like (use with wildcards) (for Quick Search only)
contains
does not contain
starts with
does not start with
ends with
does not end with
is any
is not any
is empty
is not empty
Value Select the compare value.

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5.3.6.1 UV Spectra
For a better comparability of UV spectra, it is useful to subtract the baseline spectrum (of the solvent). Chromeleon performs
this automatically using the follow ing algorithm:
• The baseline spectra are determined for both peak ends. At both peak ends, several UV spectra can be averaged over
a specified range.

• The baseline peak spectrum (usually at the peak maximum) is determined via linear interpolation of these tw o baseline
spectra and subtracted from the single spectrum (usually of the peak maximum).

Parameter Description
Peak Spectrum Bunch Number of single spectra to be bunched to form the spectrum at the peak
maximum.
No Baseline Correction. Baseline correction is disabled.

Peak Dependent Correction Allows automatic background subtraction for each peak. In the edit fields under left
region bunch and right region bunch the number of spectra to be used for formin g
the two background spectra can be entered.
Fixed Correction Defines two fixed ranges for background subtraction for the entire chromatogram.

This section also contains default settings for UV Spectra Comparison:

Parameter Description
Match Criterion As per 0.0.1959744544.27.

Use Spectrum Derivative As per 0.0.1959744544.27.

Restrict Wavelength Range As per 0.0.1959744544.27.

Peak Purity Threshold A limit for the signal height above which spectra comparison is performed f o r t h e
UV spectra.

5.3.7 SST/IRC
As defined in cooperation w ith EURACHEM, System Suitability Checking (SSC) or System Suitability Test (SST) is "a series
of tests to check the performance of a measuring process" [P. Bedson and M. Sargent, Accred. Qual. Assur. (1996) 1, 265-
274]. The aim and objective of System Suitability Testing is to ensure the performance of the operating system and the
system. To this has been added Intelligent Run Control (IRC) w hich enables the user to perform further actions based on
the results of the System Suitability Test Case. Different actions can be set for a passed and a failed test case. It is also
possible to create an Unconditional Test Case w hereby the desired actions are performed for every injection w hich satisfies
an injection condition. When creating a new test case, it is now possible to copy an existing test case. It is also possible to
associate more than one IRC action to a given test case.

5.3.7.1 Test Cases

The follow ing templates are available w hen creating a new system suitability test case.

Parameter Description
Custom Test Blank test case with no conditions defined.
Autodilution (Large/Small Loop) Determines peak amount for a particular component based on the null and
maximum amounts defined by the calibration levels and is designed to work with a
Large/Small Loop Autodilution setup.
Autodilution (Partial Loop) Determines peak amount for a particular component based on the null and
maximum amounts defined by the calibration levels and is designed to work with a
Partial Loop Autodilution setup.
Autodilution (Vial to Vial) Determines peak amount for a particular component based on the null and
maximum amounts defined by the calibration levels and is designed to work with a
Vial to Vial Autodilution setup.
Autodilution (Amount Limits) Determines peak amount for a particular component to null and maximum amounts
defined in calibration levels.
Peak Amount Limits Compares the calculated peak amount for a particular component to the minimu m
and maximum amounts defined in calibration levels.
Peak Asymmetry Determines the peak asymmetry and ensures it is less than or equal to a specified
value.

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Chromeleon 7

Parameter Description
Peak Width (5%) Determines the peak width at 5% of the peak height and ensures it is less th a n o r
equal to a specified value.
Peak Width (10%) Determines the peak width at 10% of the peak height and ensures it is less than or
equal to a specified value.
Peak Width (50%) Determines the peak width at 50% of the peak height and ensures it is less than or
equal to a specified value.
Peak Width (baseline) Determines the peak width at baseline level and ensures it is less than or equal t o
a specified value.
Resolution (EP) Using EP formula, resolution is calculated against the next peak in the
chromatogram and evaluated so that it is greater than or equal to a specified value.
Resolution (USP) Using USP formula, resolution is calculated against the next peak in the
chromatogram and evaluated so that it is greater than or equal to a specified value.
Retention Time Checks that the detected retention time of a peak is great er t h an o r e q ua l t o a
specified value.
RSD of Peak Areas Determines relative standard deviation of the pea k a re a f o r b et wee n 2 a nd 6
injections and evaluates that the result is less than a specified value.
RSD of Peak Retention Times Determines relative standard deviation of the peak retention time f o r b et wee n 2
and 6 injections and evaluates that the result is less than a specified value.
RSD of Peak Heights Determines relative standard deviation of the peak height f o r b et wee n 2 a nd 6
injections and evaluates that the result is less than a specified value.
Signal Noise Checks that the chromatogram noise across the time range used for peak
detection is less than or equal to a specified value.
Signal / Noise Ratio Checks that the signal to noise ratio is greater than or equal to a specified value.

Theoretical Plates (EP) Using EP formula, theoretical plates are evaluated so that the result is greater than
or equal to a specified value.
Theoretical Plates (JP) Using JP formula, theoretical plates are evaluated so that the result is greater tha n
or equal to a specified value.
Theoretical Plates (USP) Using USP formula, theoretical plates are evaluated so that the resu l t i s g re at er
than or equal to a specified value.

5.3.7.2 SST/IRC Conditions

This tab page lists test cases and their defined test conditions.

Parameter Sub Parameter Description

Name N/A Gives a description of the test case.

Statistics None No statistical evaluation is performed.

Average Average value of the aggregated injections.

Maximum Maximum value of the aggregated injections.

Minimum Minimum value of the aggregated injections.

Range Result range of the aggregated injections.

Relative Range Relative result range of the aggregated injections.

Relative Standard Deviation Relative standard deviation of the aggregated injections.

Standard Deviation Standard deviation of the aggregated injections.

Statistics Condition N/A Defines which injection results will be included in the statistical
calculations.

Include at least n an d a t mo st n Defines the minimum and maximum number of injectio ns t o

injections (incl. current injection) use for the statistics calculations.

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 Chromeleon 7

Parameter Sub Parameter Description

Only include injections with The statistics calculation will only be applied to injections t h a t
fulfill the specified rules. Any variable from the “Inject ion” l ist
(see sections 0) can be selected. The user enters a value and
then selects one of the following restriction options: -
=
<>
>
<
>=
<=
contains
doesn’t contain
starts with
doesn’t start with
ends with
doesn’t end with
The compare value is typed or selected from the list . M o re
than one value may be required, depending on the se le cted
comparison operator.
Evaluation Formula N/A The formula can be based on variables f ro m a ll t he a rea s
detailed in section 7.
Operator = Restricts the data points shown based on comparing the
selected variable with a user-defined va lu e a nd u sin g t h e
<> following logical arguments:
<= Is equal to

< Is not equal to

Is smaller than or equal to
>=
Is smaller than
> Is larger than or equal to
contains Is larger than
Contains
doesn’t contain
Does not contain
starts with Starts with
doesn’t start with Does not start with
Ends with
ends with
Does not end with
doesn’t end with
Is between
between Is not between
not between

Reference Value 1 N/A The Reference Value variable returns the ref ere nce valu es
that are compared against the evaluation value. The fo rmula
can be based on variables from all the areas detailed in
section 7.
Reference Value 2 N/A Second Reference Value available when operat or i s se t t o
between or not between.
Channel Default channel Sequence default channel (if one is selected).

Channel name List of available channels acquired during sample run.

Peak All components Applies the test for all identified peaks (components).
Component name Applies the test to the specified peak (component).

Detected peak number Applies the test to the peak with the specified peak number.
Detected peak with The peak with the lowest/highest value for the variable
selected for this option. Variables can be select ed f rom t h e
“Peak Results”, “Peak Calibration”, and “Peak Purity and
Identification” variable groups (see sections 7.10, 7.12, 7.13).
N.A. Failed Details the result reported if the test cannot be evaluated. Can
be set to either “Passed” or “Failed”.
Passed

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Chromeleon 7

Parameter Sub Parameter Description

Fail Action Continue Details the actions that CHROMELEON must take if t he t e st
fails. Can be set to either “None” or “Abort queue”.
Abort queue

Injection Condition Apply to all injections Applies the test for all types of injections.

Injection type Applies test for the selected injection type only (se e se ct io n
4.3.1).
Injection property The test will be run only for injections that fulfill the sp e cif ied
rules. Any variable from the “Injection” or “Sequence” lists (see
sections 0, 7.3) can be selected. The user enters a value a nd
then selects one of the following restriction options: -
=
<>
>
<
>=
<=
contains
doesn’t contain
starts with
doesn’t start with
ends with
doesn’t end with
The compare value is typed or selected from the list . M o re
than one value may be required, depending on the se le cted
comparison operator.
Custom condition Applies the test to the injections corresponding to t h e f re ely
selectable injection condition.
Result N/A Result of the system suitability test case.

SST Message N/A Additional information about the performed the SST test case.

Pass Action Abort Details the actions that CHROMELEON must take if t he t e st
passes. This can be set to Abort, Arithmet ic Co mbin at ion,
Arithmetic Combination Autodilution, Copy Channel, Derivative, Extract from 3D
Autodilution Channel, Extract MS Channel(s), Extract Opt. In t . Ch a nne l,
Insert Injection, Pause, Power Law, Re-inject or Smooth
Copy Channel Channel.

Derivative
In the case of an unconditional test case, t h e p a ss a ct i ons
Extract from 3D Channel detail the actions that CHROMELEON must t a ke f or e ve ry
injection which meets the injection condition.
Extract MS Channel(s)

Extract Opt. Int. Channel

Insert Injection
Pause

Power Law
Re-inject

Smooth Channel

Fail Action Abort Details the actions that CHROMELEON must take if t he t e st
fails. This can be set to Abort, Arithmetic Combination,
Arithmetic Combination Autodilution, Copy Channel, Derivative, Extract from 3D
Autodilution Channel, Extract MS Channel(s), Extract Opt. In t . Ch a nne l,
Insert Injection, Pause, Power Law, Re-inject or Smooth
Copy Channel Channel.

Derivative
Extract from 3D Channel
Extract MS Channel(s)

Extract Opt. Int. Channel

Insert Injection

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 Chromeleon 7

Parameter Sub Parameter Description

Power Law
Re-inject

Smooth Channel

Abort N/A Aborts the queue

Arithmetic Combination Channel A Defines the channel from the current injection to b e u se d i n
the combination.
Factor A Determines the multiplying factor to be applied to Cha nn el A
before combining it with Channel B.
Channel B Defines the second channel for the combination.
Factor B Determines the multiplying factor to be applied to Cha nn el B
before combining it with Channel A.
Operation Defines the arithmetic operation to be performed o n t he t wo
channels selected. The following optio ns a re a va ilab le: +
(addition), - (subtraction), * (multiplication) and / (division).
Result channel Defines the name for the result channel

Autodilution Processing Method Assigns processing method to be used.

Instrument Method Assigns instrument method to be used.

Injection Volume Defines injection volume in microliters (µl).

Weight Defines weight correction variable.

Internal Standard Amount Defines quantity of internal standard added to t h e a na lyze d

sample.
Dilution Factor Defines the value of dilution, where a value of 1 indicates that
there was no dilution.
Comment Allows a user-defined comment to be added.

Replicate ID Defines the replicate ID.

Type Defines the injection type.

Concentration Level Defines the concentration level.

Position Defines the position on the autosampler rack from whi ch t he

sample is to be injected.
Spike Group Defines a spike group for the injection. This allows unsp i ke d
(unknown) injections to be associated with spiked injections.
Max. no of re-injections Defines maximum number of re-injections to be carried out.

Copy Channel Original channel Defines the channel from the current injection to be copied.
Result channel Defines the name for the result channel

Derivative Original channel Defines the channel from the current injection to be derived.

Derivative The derivative level is selected here. This can be set to first or
second
Result channel Defines the name for the result channel
Extract from 3D Channel Source 3D field Defines the 3D field to be extracted.

Wavelength Defines the wavelength at which the extraction sh o uld t ake

place
Use interpolation Defines whether the resulting chromatogram retention t imes
should be interpolated to 1 second intervals.
Bandwidth Defines the bandwidth for the extraction.

Result channel Defines the name for the result channel

Units Selects the units to be used for the extracted chan ne l. T h is
can be set to AU, mAU, μAU.

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Chromeleon 7

Parameter Sub Parameter Description

Extract MS Channel(s) Trace Specify the chromatogram trace type to be extracted:
TIC (Total Ion Current)—all ions matching the filter entered in
the Filter list will be extracted from the raw data.
Base Peak—base peak ions that match the filter e nt ere d i n
the Filter list will be extracted from the raw data.
Mass Range—ions that match the filter entered in the Filter list
and with a mass that matches the mass or mass range
entered in the Mass range(s) box will be extracted f ro m t he
raw data.
Precursor Defines the precursor ion mass to reduce the list of f ilt ers i n
the Filter list to only those filters with a matching precursor ion
mass.
Mass ranges Defines the mass, mass range, or a set of mass ranges to b e
extracted
Filter Specifies the acquisition filter from which the chroma to gra m
will be extracted
Channel Name Defines the label that will be used to identify this extracted ion
chromatogram in the channels list
Smoothing Specifies the type of smoothing to be performed on the
chromatogram data when it is extracted.
Pts. Defines the number of data points for smoothing.
Extract Opt. Int. Channel Source 3D field Defines the 3D field to be integrated.

Original channel Defines the original channel

Bandwidth The bandwidth for the integration is specified here

Result channel Defines the name for the result channel

Insert Injection Source injection The injection to be inserted is selected here.

Max. no of insertions The maximum number of times to perfo rm t h e i nse rt ion is

determined here. Range is from 1 to 9999.
Power Law Original channel Defines the channel to which the power factor should be
applied
Power factor The power factor to be applied is selected here. Range is from
1.0 to 2.0.
Result channel Defines the name for the result channel

Re-inject Current injection Allows the user to re-inject the current injection
Completed injections Allows the user to restart the sequence

From most recent Allows the user to select anywhere else in the sequence fro m
which to re-inject
Max. no of re-injections The maximum number of times to perform the re-injectio n i s
determined here. Range is from 1 to 9999.
Smooth Channel Original channel Defines the channel to be smoothed

Filter type Defines the smoothing algorithm to be used. Four options are
available: Savitzky-Golay, Moving A ve rage , O l ym pic a nd
Gaussian.
Filter size Defines the number of data points use d t o g en era te e ach
output data point in the smoothed chromatogram. Th is i s a n
odd number between 3 and 999.
Result channel Defines the name for the result channel

If an action fails to execute Continue to the next action Determines what CHROMELEON should do if an action from
a test case cannot be executed.
Continue to the next test case

Continue to the next injection

Pause the queue

Abort the queue

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 Chromeleon 7

Parameter Sub Parameter Description

Rounding N/A The values for the evaluation result and reference va lue a re
rounded to the specified decimal places.

5.3.8 Advanced Settings

On this tab it is possible to specify some more advanced settings.

Parameter Sub Parameter Description

Comment N/A Gives a description of the processing method.

Amount Interpretation: Re fe ren ce Use inject volume of first standard Uses the injection volume of the first standard as basis for a l l
Inject Volume amount calculations.
Fixed Uses a fixed injection volume, entered in the box on the righ t,
as basis for all amount calculations.
Retention Time Settings Use absolute greatest signal value Uses the retention time of the absolute greatest signal value.

Use relative greatest signal va lu e Uses the retention time of the signal value that is relatively the
over the baseline greatest value over the baseline.
Dead/Delay Time(s) Dead Time Specifies the dead time of the method.
nd
2 Detector Specifies the delay time of the second detector.
rd
3 Detector Specifies the delay time of the third detector.

Matrix Correction Enable Matrix Correction Enables matrix correction, where peak areas (or heights) from
matrix blank injections are subtracted from the other injections
in the sequence.

5.3.9 Composite Scoring

This tab allow s users to set up pass / indeterminate / fail levels, select specific criteria to test components against, and set
tolerances for certain criteria.

Parameter Sub Parameter Description

Pass score if at least <number> N/A Minimum number of passing criteria required for a component
criteria passed to pass scoring. If number of criteria passed are greater th a n
the failure requirement and less than the pass re q u ire men t,
the score will be indeterminate.

Fail score if less than <number> N/A Maximum number of failing criteria required for a compo nen t
criteria passed to fail scoring. If number of criteria passed are gre at er t h an
the failure requirement and less than the pass re q u ire men t,
the score will be indeterminate.

Amount based peak identity (Checkbox) Enables scoring criteria based on calibrated amounts between
verification user-selected channels with user-defined tolerances.
Disabled by default.
Reference Channel Defines the reference channel for amount-based compo nen t
verification. Confirmation channel to reference channel ra t io
approaches 100% as calculated amounts for e a ch ch an nel
approach unity.
Confirmation Channel Defines the confirmation channel for amount-based
component verification. Confirmation channel t o re f ere nce
channel ratio approaches 100% as calculat ed a mou nt s f o r
each channel approach unity.
Tolerance Maximum deviation allowed between reference and
confirmation channel for a passing result. Allowable range o f
0.1 to 50%.
Confirming ion ratio passed (Checkbox) Enables scoring based on confirmation ion ratio and ion
coelution criteria as defined by the specifications in
0.0.1959744544.27. Enabled by default.
Is Filter Isotopes Used Returns whether or not filtering of low abundance isoto pes i s
enabled

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Chromeleon 7

Parameter Sub Parameter Description

Filter Isotopes Reference Percent Returns an absolute height value or the percent of the he ight
of the TIC or BPC, which defines the low isoto pe t hre sh old
level. Returns n.a. when ‘Is Filter Isotopes Used’ I false or th e
reference type is height.
Filter Isotopes Reference Type Returns ‘%TIC’, ‘%BPC’ or ‘Height’, which wh en c om bine d
with the Filter Isotopes Reference Percent, d et erm ines t h e
value of the isotope abundance threshold
Filter Isotopes Reference Value Returns the effective value of the low abundance t h resh o ld.
Isotopes below this level are excluded from calculations
Isotopic dot product (Checkbox) Enables isotopic dot product scoring for specific imported data
types and raw data combinations. Disabled by default
(Number) Defines minimum pass criteria for imported d a ta t yp es a n d
raw data combinations.
Mass accuracy (Checkbox) Enables mass accuracy scoring for specifi c i mpo rt ed d a ta
types and raw data combinations. (Disabled by default)
(Number) Defines maximum deviation value from target mass of
component peaks.
(Dropdown) Defines deviation units for mass accuracy scoring.

Peak apex alignment (Checkbox) Enables peak apex alignment based on p e ak g ro u pin g f or
specific imported data types and raw data combinations.
Disabled by default
(Number) Defines allowable peak apex retention time standard deviation
across component peaks in a group.

5.3.10MS Detection
This “MS Detection” tab holds all MS component detection parameters for the processing method. A set of parameters can
be applied globally for all components, individually for select components, or individually for all components.

Chromeleon 7.2 supports 4 algorithms: Chromeleon 6, Cobra, Genesis, and ICIS. Details of the Chromeleon 6 algorithm
are provided in the Chromeleon 6.8 functional specification. Details of the Cobra algorithm detection parameters are
provided in section 5.3.1. Details of the Genesis and ICIS algorithms are provided in the follow ing subsections.

Parameter Sub Parameter Description

Extracted Ion Chromatogram MS Default Detection Settings Displays editable global MS component detection parameters
(Component Name) Displays editable component-specific MS component
detection parameters. If Use MS default detection setting s i s
enabled, the global MS component detection parameters wi l l
be displayed
Use MS default detection settings (Checkbox) Displays global MS component detection param ete rs wh e n
selected. Enabled only when Extracted Ion Ch rom at ogra m
sub-parameter selected is (Component Name)
Detection Algorithm Chromeleon 6 Chromeleon 6 detection algorithm. S e e Ch ro mele on 6 . 8
functional specifications for details
Cobra Cobra detection algorithm. See section 5.3.1for details

Genesis Genesis detection algorithm. See section 5.3.10.1 for details

ICIS ICIS detection algorithm. See section 5.3.10.3 for details

Run Cobra Wizard … (None) Starts the Cobra algorithm peak detection wizard. See
section 5.3.13 for details

5.3.10.1 Data Range for M S Components

When MS Detection is combined w ith Extracted Ion Chromatogram parameters from the Component table, in some
situations, a partial XIC is created for peak detection and integration. The extraction w indow is a minimum of +/- 0.5min or is
determined by the formulas:
extraction start time = retention time – display w indow *10
extraction end time = retention time + display w indow * 10

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 Chromeleon 7

5.3.10.2 Genesis Algorithm

This algorithm is recommended for processing data w ith noisy baselines such as full scan MS data acquisition

Parameter Sub Parameter Description

S/N threshold (None) Changes the threshold for detecting peak edges
Enable valley detection (Checkbox) Enabling this option allows the algorithm to drop a vertical line
from the local minima of the valley between unresolved peaks
to the baseline. The intersection of the vertica l lin e a n d t he
baseline defines the end of the first peak and the beginning of
the second peak.
Expected width (sec) (None) Enabled only if the Enable valle y d e te ct ion p ara met er i s
enabled. This value controls the minimum width that a peak is
expected to have if valley detection is selected.
Any valley points nearer than the expected width/2 to the t op
of the peak are ignored. If a valley point is found outsi d e t he
expected peak width, the algorithm terminates the peak at that
point. The algorithm always terminates a peak when the
signal reaches the baseline, independent of the value se t f o r
the expected peak width.
Constrain peak width (Checkbox) Enabling this option allows the algori th m t o l imit t he p eak
width of a component during peak integration.
Peak height (%) (None) Determines the peak height at which the peak width is tested

Tailing factor (None) Enabled only if the Constrain peak width parameter is
enabled. This value determines how the algorithm integrat es
the tail of a peak.
This factor is the maximum ratio of the tra iling e dge t o t h e
leading side of a constrained peak.
Peak S/N cutoff (None) Determines the signal-to-noise level the algorithm defin es a s
the peak start and end points.
Rise percentage (%) (None) Defines the percent value that a chromatogram can rise
above the baseline after passing through a minimum. Wh e n
the chromatogram exceeds this value, the algorithm applies a
valley detection peak integration criterion.
Valley depth (None) Determines the signal-to-noise ratio used for valley detection
Calculate noise as RMS Calculates noise as RMS

Peak to Peak Calculates noise as peak-to-peak

Baseline noise tolerance (None) Defines how the baseline is drawn in t he n o ise d at a. Th e
higher the baseline noise tolerance valu e, t he h ighe r t he
baseline is drawn through the noise data
Min scans in baseline (None) Defines the number of scans the algorithm uses to determin e
the baseline
Baseline noise rejection factor (None) Defines the width of the RMS noise band abo ve a nd be low
the peak detection baseline. This factor is applied to the ra w
RMS noise values to raise the effective RMS noise u se d b y
the algorithm. The algorithm responds by assign ing t h e l ef t
and right peak boundaries above the noise and closer t o t he
peak apex value in minutes. This action effectively raises t h e
peak integration baseline above the RMS noise level.

5.3.10.3 ICIS Algorithm

This algorithm is recommended for data w ith low noise or abstracted data such as SIM and SRM data acquisition as w ell as
XIC data

Parameter Sub Parameter Description

Area noise factor (None) Determines the noise level multiplier used to d et ermin e t h e
peak edge after the location of the possible peak
Peak noise factor (None) Determines the noise level used to determine t h e p o te nt ial
peak signal threshold
Baseline window (None) Determines the number of scans to review, looking for a local
minima, to determine the baseline

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Parameter Sub Parameter Description

Constrain peak width (Checkbox) Enabling this option allows the algori th m t o l imit t he p eak
width of a component during peak integration.
Peak height (%) (None) Determines the peak height at which the peak width is tested

Tailing factor (None) Enabled only if the Constrain peak width parameter is
enabled. This value determines how the algorithm integrat es
the tail of a peak.
This factor is the maximum ratio of the tra iling e dge t o t h e
leading side of a constrained peak.
Noise method Incos Forces algorithm to use a single pass to determine the n oise
level
Repetitive Forces algorithm to use multiple passe s t o d e t e rmine t he
noise level. Incurs a performance hit compared to Incos
Min peak width (None) Determines the minimum number of data points required for a
peak
Multiplet resolution (None) Determines the minimum number of scans required betwe en
apexes of two potential peaks to be considered resolved
Area tail extension (None) Determines the number of scans past the peak end to use i n
averaging the intensity
Area scan window (None) Determines the number of scans on each si d e o f t h e p e ak
apex to include in the area integer
RMS (Checkbox) Enabling this option allows the algorithm to calculate noise a s
RMS. When disabled, the algorithm uses peak-to-peak noise
calculation

5.3.11MS Settings
On this tab it is possible to specify baseline correction, noise reduction and smoothing parameters for mass spectra

Parameter Sub Parameter Description

MS Spectral Bunching Peak Spectral Bunch Defines the number of spectra to be bunched at the apex

No Baseline Correction No baseline correction calculations will be performed

Peak Dependent Correction Allows specification of the number of spectra to be b u nche d
before peak start and after peak end in performing the
baseline correction
Fixed Correction Allows specification of 2 baseline segments ind epe nd ent o f
the peak position to be used in the baseline correction
calculation
MS Noise Reduction Do Not Reduce Noise No noise reduction calculations will be performed

Relative Threshold Allows masses below a specified percentage of the base peak
to be ignored
Fixed Threshold Limits spectra to only N largest mass intensities for a peak

MS Chromatogram Settings Mass Precision Defines the number of decimal places displayed by
Chromeleon and usable by the user
Manually define Mass Tolerance When enabled, allows a user specified value to be used for
calculations that require a mass tolerance.
Otherwise a system default value of 500 MMU is used.
Units Defines the units of the manually entered mass tolerance
value (AMU, MMU, PPM). This field is only enabled if
manually defining mass tolerance (see above)

Specify mass tolerance per When enabled, a corresponding column in the MS

component Component Table is enabled, which allows mass tolerance
to be specified differently for each component if desired.
(See 5.3.2.26)
Global mass tolerance Specifies the mass tolerance to be used for component-
independent calculations such as XIC extraction.
Apply all Updates the Mass tolerance field for all the items in the MS
Components table to the global value (see above)

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Parameter Sub Parameter Description

Inhibit Integration for TIC Defines whether the TIC is integrated or not
Smoothing Defines the type and level of smoothing to be performed

5.3.12MS Library Screening

On this tab it is possible to specify default parameters that w ill be used for both ad hoc (on demand) library searches, as w ell
as automatic library searches performed as part of data processing.

Parameter Sub Parameter Description

MS libraries to be searched (Checkbox List of libraries) When the box is checked next to a library in this list, that
library will be used as searched when a library search is
invoked.
Search Type Identity Three options are available:
Normal: Uses a standard pre-screen search filter. This i s t h e
default search type.
Quick: Uses a fast pre-screen search filter.
Penalize Rare Compounds: Limits the impact of rare
compounds by reducing their match factors. T his o p t ion is
effective only when you have selected a NIST Mass Spect ra l
Library (such as, mainlib). It has no effect on spectra in
internal NIST libraries or other commercial libraries.
Each reference spectrum in a NIST Mass S p e ct ral Li brary
contains a record of other commercial libra ries co n t ain ing
information about the compound. A compound is consi dere d
'rare' if it is present in a limited number of these libraries.
Similarity Simple: Finds a large set of spectra to compare with the
submitted spectrum. This search option is generall y sl o we r
than an identity search.
Hybrid: Uses a combination of the Simple and Ne ut ral L oss
search types. When Hybrid is selected, the Search wit h M o l.
Weight edit box under Search Options is enabled . E n te r a n
estimate of the submitted spectrum's molecular weight.
Neutral Loss: Compares neutral losses of the submitted
spectrum with spectra in the library data. The neutral losses in
a spectrum are the mass differences between the mole cular
ion and other major ions in the spectrum. For certain cla sse s
of compounds, neutral losses can be a ve ry ch ara ct eri st ic
spectral feature. In a Neutral Loss search, Chromeleon
identifies the molecular ion of the submit te d sp e ctru m a nd
includes the molecular ion in the search, along with the
spectrum. Significant neutral losses of the submitted spectrum
are calculated and compared with the library d at a. Hi ts a re
returned according to matches of the molecu lar i on a nd i t s
neutral losses. When Neutral Loss is selecte d, t h e S ea rc h
with Mol. Weight edit box under Search Options i s e n a ble d.
Enter an estimate of the submitted spectrum's molecular

Search options Search with Molecular Wt When a value is supplied, searches will be restricted to library
entries with the indicated molecular weight.
Reverse Search When checked, this parameter indicates that a reverse search
will be performed instead of a standard search
Thresholds Match Factor Defines the minimum match factor below which matches wi ll
not be reported
Reverse Match Factor Defines the minimum reverse match factor below which
matches will not be reported
Probability Defines the minimum probably below which matches wil l n ot
be reported

5.3.13Peptide Table
Upon import of a Pinpoint w orkbook, the Peptide Table w ill be populated w hich is primarily read-only. The user has the
ability to delete an isotope of a peptide but cannot re-add deleted peptide isotopes. The fields displayed are described
below .

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Chromeleon 7

Name Description
Name Peptide sequence, including modifications. Duplicate names may exist if multiple charge states of the sa me
peptide sequence are imported.
RT Expected retention time of peptide

Charge Charge state of the peptide

Precursor Exact mass of the peptide assuming all atoms are of the most abundantly occurring isotope in nature

Isotope n Exact mass of isotopes from the monoisotopic mass to the least abundant mass. n is defined by the number
of isotopes for each peptide in the Pinpoint workbook.
Peptide Group An optional numeric value which may be used to group components which represent the same p ep tid e b ut
with different modifications. It is only used for reporting purposes.

5.3.14QD Calibration
The “QD Calibration” tab is the area that show s all the global calibration settings and the list of calibration standards that are
used to quantify the peaks in the currently active chromatogram w hen using a QD detector. In this tab it is possible to
disable/enable the calibration points for specific peaks/channels. Additional options available are:

Function Sub Function Description

Mode Fixed The calibration standards from a selected sequence are u se d
for calibration. The other sequence is copied to the calibratio n
table in the processing method. You can update the calibration
any time, for example, after the oth er se q u en ce h as b e e n
updated.
Total Calibration is performed using all valid calib rat ion st a nd ard
samples of the sequence.
Additional For calibrating a sample, all calibration standard injections that
are listed before this sample in the sample list are used.
Group The calibration of a sample series from t h e sa m ple list (f o r
example, samples 3 to 50) is performed based on the
calibrations standards listed directly before this series; for
example, no. 1 and 2. If this sample list includes further
standards, as for instance, no. 51 and 52, the following
samples, for example, 53 to 100, will be evaluated b a se d o n
these. The standard samples in lines 1 and 2 will no longer b e
considered.
Bracketed Samples are evaluated based on all calib rat ion st a nd ard s
immediately surrounding. In case of a list containing two
samples, two calibration standards, two samples, two
calibration standards and so on, samples 1 and 2, lo ca te d a t
positions 3 and 4, are evaluated with standards 1, 2, 3, and 4 ,
located at positions 1, 2, 5, and 6. Samples 3 and 4 are
evaluated using the standards 3, 4, 5, and 6, located at
positions 5, 6, 9, and 10.
Standard Addition Calibration is performed using spiked and unspiked injections.

Curve Fitting Normal Selects normal dependent and i nd ep end ent va riab les f o r
calibration i.e. x-axis = amount, y-axis = measured value.
Inverted Selects inverted dependent and indepe nde nt vari able s f o r
calibration i.e. x-axis = measured value, y-axis = amount.
Dual-Column Separate Mode N/A When this function is enabled it is possi b le t o u se o n ly t he
standards for the active column in tandem mode.

Origin of Standards for Fixed N/A Allows the user to select an external sequence for calibrat ion.
Calibration On selection, all standards in the external sequence are copied
into the current sequence.
Calibrate Using Normality N/A When enabled, the Concentration Unit (found on the
Component Table) is locked to the selected Normality unit.

5.3.15MS Component Table Import

It is possible to create a MS component table by importing file types or searching through libraries. The import dialogue can
be opened by selecting any of the Component Table variant tabs in the processing method, then clicking the Import button
in the Studio Ribbon on the Processing Method tab.

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The follow ing file types are available:

Type Description
MS Raw Data Xcalibur raw data format containing an acquisition list in the data file header generated by ISQ , T SQ -8 000 ,
and TSQ Quantum GC mass spectrometers and TSQ Quantiva and TSQ Endura LC mass spectrometers for
quantitative scan types.
Compound Data Store TraceFinder compound data store formats (Version 2, 3, 4 and 5)

NIST Library (See below)

Acquisition List Acquisition lists for quantitative scan types in the following formats:
ISQ and TSQ Series SQ and QqQ GCMS
TSQ Series LCMS
Exactive Series Inclusion/Exclusion lists

BioPharma Finder Peptide BioPharma Finder Peptide lists consisting of only one (1) protein and MS1 iso t op es a s we l l a s m u ltip le
List peptide and charge states can be imported into Chromeleon. Upon import, a compon en t g ro up f o r e ach
peptide consisting of a sum of all the peptide charge states and individual charge states will b e c re a te d. A
component will be created for each summed peptide and peptide charge state. At the same time, theoretica l
isotope distributions will be calculated and created for each charge state’s isotope. If t h e e nt ry in c lude s a
chemical formula, then the theoretical isotope distributions are computed using the formula ; o t he rwise t h e
name is used.
BioPharma Finder Peptide lists are generated by BioPharma Finder version 3.0 and earlier
BioPharma Finder BioPharma Finder Peptide lists consisting of only one (1) protein and MS1 iso t op es a s we l l a s m u ltip le
Workbook peptide and charge states can be imported into Chromeleon. Upon import, a compon en t g ro up f o r e ach
peptide consisting of a sum of all the peptide charge states and individual charge states will b e cre a te d. A
component will be created for each summed peptide and peptide charge state. At the same time, theoretica l
isotope distributions will be calculated and created for each charge state’s isotope. If t h e e nt ry in c lude s a
chemical formula, then the theoretical isotope distributions are computed using the formula ; o t he rwise t h e
name is used.
BioPharma Finder Peptide workbooks are generated by BioPharma Finder version 3.1 and later
Pinpoint Workbook Pinpoint workbooks consisting of only one (1) protein and MS1 isotopes as well a s m ult ipl e p ep tid e a nd
charge states can be imported into Chromeleon. Upon impo rt, a co mpo nen t g ro up f or e a ch p ep tid e
consisting of a sum of all the peptide charge states and individual charge states will be created. A component
will be created for each summed peptide and peptide charge state. At the same time, t he ore tical i so t op e
distributions will be calculated and created for each charge state’s isotope.

Further, NIST format library directories can be searched to create a component table. The search is applicable to the TIC
channel and is applicable to full-scan type data. Chromeleon w ill parse each peak apex spectrum and match based on
NIST search. The highest probability hit is used to create the component, quantitation peak, and 2 confirmation peaks
based on the base peak and second and third most intense mass peaks.

5.3.16MS Component Table Export

It is possible to export an MS component table into an acquisition table in the TSQ-8000 scan table and Exactive Series
inclusion/exclusion list format files for quantitative scan types. These files can then be opened for use in the TSQ-8000 and
Exactive Series MS method editor. The export dialog can be opened by selecting any of the Component Table variant tabs
in the processing method, then clicking the Export button in the Studio Ribbon on the Processing Method tab.
Data mapping is defined as follow s:

5.3.16.1 TSQ-8000

Scan Table Column Chromeleon Component Table Column Comments

Name Name
RT Retention Time

Ion Polarity Polarity Filter Will be exported as ‘Positive’ if the value is ‘+’ and as
‘Negative’ if the value is ‘- ‘
Window Window

Pre-width Window
Post-width Window

Mass Mass Range if Scan Type Filter (experiment type)

is SRM, otherwise Product Mass Range
Product Mass Product Mass Range if Scan Type Filter 25 is the default Product Mass value in the sca n t a ble t o
(experiment type) is SRM, otherwise 25. identify SIM experiment type

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Chromeleon 7

Collision Energy CID Filter if Scan Type Filter (experiment type) i s 8 is the default Collision Energy value in the scan table t o
SRM, Otherwise 8 identify SIM experiment type
Peak Width Will be exported with value 5 as 5 is the default Peak
Width value in the MS scan table.

5.3.16.2 ISQ

Scan Table Column CM component Mapping Translation

Name Name

RT Retention Time

Polarity Polarity Filter or Polarity from imported data if the Will be exported as ‘Positive’ if the value is ‘+’ and as
Polarity Filter doesn’t exist ‘Negative’ if the value is ‘- ‘
Window Window
Pre-width Pre-width from imported data (not visible from UI)

Post-width Post-width from imported data (not visi b le f ro m

UI)
Mass Product Mass (UI XIC Mass)

5.3.16.3 Exactive Series – SIM mode only

Inclusion List Column Chromeleon Component Table Column Comments

Mass[m/z] XIC Mass

Formula [M] Chemical Formula Will be exported as null if charge is null

Formula type N/A

Species N/A

CS [z] Charge

Polarity Polarity Filter Will be exported as ‘Positive’ if the value is ‘+’ and
as ‘Negative’ if the value is ‘- ‘
Start [min] Retention Time – Window The result will be in minutes
End [min] Retention Time + Window The result will be in minutes

NCE CID Filter Will be exported as null if the filter is not found

Comment Name and Chemical Formula and Comment Will be exported in the format of:
N=<Name>;F=<Chemical Formula>;<Comment>.
Note that if the item is a Confirming I o n t h en we
will add a postfix “_CFn” to the name wh ere n is
the number of the current confirm ing i on in t his
component.

5.3.16.4 TSQ Quantiva and TSQ Endura

SRM Scan Mode

Scan Table Column CM component Mapping Comments

Compound Name

Retention Time (min) Retention Time

RT Window (min) Window * 2

Start Time Retention Time - Window

End Time Retention Time + Window

Polarity Polarity Filter If the filter is empty, export the value that was imported.

Precursor (m/z) Precursor

Product (m/z) XIC Mass

Collision Energy CID Filter If the filter is empty, export the value that was imported.

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SIM Scan Mode

Scan Table Column CM component Mapping Comments

Compound Name

Retention Time (min) Retention Time

RT Window (min) Window * 2

Start Time Retention Time - Window

End Time Retention Time + Window

Polarity Polarity Filter If the filter is empty, export the value that was imported.

Center Mass (m/z) XIC Mass

Full Scan Mode

Scan Table Column CM component Mapping Comments

Scan Range (Da) XIC Mass Range

Scan Rate Imported value

Polarity Polarity Filter If the filter is empty, export the value that was imported.

Q1 (or Q3) Resolutio n Imported value

(FWHM)

Source Fragmentation SID Filter If the filter is empty, export the value that was imported.
(V)

QED Scan Mode

Scan Table Column CM component Mapping Comments

Compound Name

Retention Time (min) Retention Time

RT Window (min) Window * 2

Start Time Retention Time - Window

End Time Retention Time + Window

Polarity Polarity Filter If the filter is empty, export the value that was imported.

Precursor (m/z) Precursor

Product (m/z) XIC Mass

Collision Energy CID Filter If the filter is empty, export the value that was imported.

Intensity Threshold Export the imported value

Precursor Ion Scan Mode

Scan Table Column CM component Mapping Comments

Product (m/z) Precursor

Polarity Polarity Filter If the filter is empty, export the value that was imported.

Scan Range (Da) XIC Mass Range

Product (m/z)
Collision Energy CID Filter If the filter is empty, export the value that was imported.

Product Ion Scan Mode

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Scan Table Column CM component Mapping Comments

Precursor (m/z) Precursor

Polarity Polarity Filter If the filter is empty, export the value that was imported.

Scan Range (Da) XIC Mass Range

Neutral Loss Scan Mode

Scan Table Column CM component Mapping Comments

Neutral Loss (m/z) Imported value

Polarity Polarity Filter If the filter is empty, export the value that was imported.

Scan Range (Da) XIC Mass Range

Collision Energy CID Filter If the filter is empty, export the value that was imported.

5.3.17Cobra Wizard
The Cobra Wizard helps to define the initial peak detection settings for a chromatogram. The follow ing parameters are
defined by the Wizard:

Parameter Description
Consider Void Peak Defines if the void volume should be considered when defining the peak detection.

Integration Area Definable by selecting the desired integration range.

Baseline Noise Range Defines the baseline noise range of the chromatogram.
Cobra Smoothing Width Definable by selecting the narrowest peak of interest o r b y ch oo si ng t h e A u to
setting.
Minimum Area Definable by selecting the smallest peak of interest or by choosing the Auto setting.

Injection Type Allows the settings to be restricted to a specific injection type.

Channel Allows the settings to be restricted to a specific injection type.

5.3.18SmartPeaks
SmartPeaks allow s for easy modification of the peak detection for unresolved peaks. When selected the user draw s a box
over the peaks of interest. SmartPeaks then show s various peak detection options (Figure 26). The user selects the one
they w ant to have and clicks OK. SmartPeaks then inserts the detection parameters required to reach this integration into
the detection parameter table. This ensures that the parameters are applied to all injections in the sequence.

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Figure 26: SmartPeaks Wizard - Select Alternative

The follow ing advanced options are available:

Parameter Sub Parameter Description

Effect starts with Peak Effect starts at the beginning of the first peak in the window.
Selection Effect starts at the start time for the window.

Chromatogram Effect starts at the beginning of the chromatogram.

Effect ends with Peak Effect ends at the end of the last peak in the window.
Selection Effect ends at the end time for the window.

Chromatogram Effect ends at the end of the chromatogram.

Restrict to current channel N/A Restricts the detection parameters to the current channel.

Restrict to current injection N/A Restricts the detection parameters to the current injection type.
type

5.3.19Component Table Wizard

The component table w izard helps to setup or update the component table. The follow ing settings can be made by the
w izard:

Parameter Sub Parameter Description

General Overwrite existing Overwrites the existing components (Only if co mpon en t t a ble al read y
components includes components).

Create and name Runs a spectral library search to identify components. When this o p t ion is
components according to selected, the name of the matching component in the sp e ctra l lib rary i s
spectral library screening applied to the identified component.
results
Time Range Use Auto Range Adds peaks detected in entire chromatogram to component table.

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Parameter Sub Parameter Description

From n to n [min] Adds peaks in the defined time range to component table.
Filter peaks N/A Defines which peaks to be added to component table

Apply to peaks with Area

Height
Relative Area
Relative Height
Greater than Defines comparison value.

Reference Spectrum Define Reference Spectrum Available options here are set in the processing method (see section
Using 5.3.6.1)

Enable peak tracking usin g Defines window type as “Spectrum and Time” or Spectrum only”
window type
Review N/A Allows reviewing of created component table. The following table co lumn s
can be updated:
Name (see section5.3.2.1)
Retention Time (see section5.3.2.2)
Window (see section5.3.2.3)
Comment (see section5.3.2.13)

5.3.20Layouts
It is possible to select a layout for the Processing Method. Each layout show s Processing Method tabs and panes, specific
to a task. The layouts consist of pre-defined subsets of processing method tabs as described in sections 5.3.1 through
5.3.12. Further each layout contains a Component Table variant consisting of a subset of columns described in section
5.3.1.2. Please refer to the respective sections for the general layout and component table variants for more information.
The follow ing layouts are available:

Name Description
Qualitative Layout with all setting for qualitative analysis
Quantitative Layout with all setting for quantitative analysis

3D Qualitative Layout with all setting for qualitative analysis for chromatograms containing 3D Fields

3D Quantitative Layout with all setting for quantitative analysis for chromatograms containing 3D Fields
MS Quantitative Layout with all setting for quantitative analysis for chromatograms containing Mass Spectral data

All Settings Layout with all available processing method settings

Chromeleon 6 Layout according to Chromeleon 6 QNT editor

Basic Quantitative One-page layout showing most used options; detection parameters, and a component table containing name,
retention time, window and amounts.
QD Quantitative Layout with all settings for quantitative analysis for chromatograms containing QD data

5.4 Data Processing Category

The pane buttons on the “Data Processing Home” ribbon allow show ing or hiding of panes. The follow ing panes are
available:
• Chromatogram (see section 5.4.1)
• Calibration Plot (see section 5.4.2)
• Interactive Results (see section 5.4.9)

• Processing Method (see section 5)

• Peak Properties (see section 5.4.3)
• Interactive Charts (see section 5.4.4)
• Contour/3D Plot (see section 5.4.5)
• UV-Vis Spectra (see section 5.4.6)

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• Fluorescence Spectra (see section 5.4.7)

• I-t Plot (see section 5.4.8)
• Injection Rack (see section 5.4.10)
• Fraction Tray (see section 5.4.11)
• Mass Spectra (see section 5.4.12)

• MS Components (see section 5.4.13)

• Tentatively Identified Peaks (see section 5.4.14)
• MS AutoFilters (see section 5.4.15)

5.4.1 Chromatogram Pane

The chromatogram view allow s the user to graphically define processing commands for either the chromatogram or for the
w hole sequence. Figure 27 show s a typical chromatogram view :

Figure 27: Chromatogram View in Chromatography Studio

5.4.1.1 Zooming and Navigating in the Chromatogram

The chromatogram view allow s zooming and navigating in the chromatogram as required w ith the follow ing options:

Function Description
Automatic Tool When active it is possible to zoom into the chromatogram by d rag ging a n a re a.
Additionally, other actions can be performed.
Zoom When active it is possible to zoom into the chromatogram by dragging an area.
Undo Zoom Reverts the recent zoom operation and returns to the previous view.

In addition, the follow ing zoom operations are available:

Function Description
Double Click on the signal axis Automatically resizes the chromatogram height to the highest peak currently visible.

Double Click on the retention axis Automatically resizes the chromatogram width to the co mp let e d ura tio n o f t he
chromatogram.

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Function Description
Signal axis zoom tools Shown when moving the cursor over the signal axis. The following f u nct ions a re
available:
+ zooms into the chromatogram vertically
Autoscale Signal resizes the chromatogram height to the highest p ea k cu rre nt ly
visible
- zooms out of the chromatogram vertically

Retention time axis zoom tools Shown when moving the cursor over the retention time axis. The following functions
are available:
+ zooms into the chromatogram horizontally
Autoscale Time resizes the chromatogram to the complete duration of the
chromatogram.
- zooms out of the chromatogram horizontally
Full size button Shown when moving the cursor to the bottom left corner of the chromatogram plot .
Click the full-size button to autoscale both axes simultaneously.

Undo Zoom Reverts the recent zoom operation and returns to the previous view.

The follow ing context menu operations are also available:

Function Description
Right Click select Full Size Automatically resizes the chromatogram height to the full size.

Right Click select Autoscale Automatically resizes the chromatogram height to the highest peak currently visible.
Right Click select Unzoom Reverts the recent zoom operation and returns to the previous view.

Holding down the right-hand mouse button and Zooms into the chromatogram area selected.
selecting an area of the chromatogram select Zoom

5.4.1.2 Graphical Entry of Integration Parameters

It is possible to graphically enter all detection parameters directly by right hand clicking on the chromatogram, selecting
“Insert Detection Parameter” and choosing the required parameter from the dialog presented. The retention time for the
commands is automatically entered as the retention time of the point on the chromatogram selected by the right hand click.
The most frequently used peak detection parameters are also available in the Processing ribbon from the “Insert” drop
button, see 5.4.1.8.
In addition, Chromeleon can automatically define detection parameter values based on the chromatogram. This is
performed by holding dow n the right-hand mouse button and selecting an area of the chromatogram. When this is done the
follow ing options are available depending on the peak detection algorithm:
For Chromeleon 6:

Function Description
Set Peak Slice & Sensitivity The peak slice and sensitivity are calculated based on the area selected.
Set Inhibit Integration Range The “Inhibit Integration” parameter is turned on at the retention time of the left si d e
of the window and turned off at the retention time of the right side of the window.
SmartPeaks Starts the SmartPeaks integration assistant (see 5.3.18).

For Cobra:

Function Description
Set Baseline Noise Range The left side of the selected area is entered into the Processing Method as the start
of the baseline noise range; the right side is entered as the end respectively.
Set Inhibit Integration Range The “Inhibit Integration” parameter is turned on at the retention time of the left si d e
of the window and turned off at the retention time of the right side of the window.
SmartPeaks Starts the SmartPeaks integration assistant (see 5.3.18).

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5.4.1.3 M anual Integration

The chromatogram view allow s integrating the chromatogram manually. The respective tools are selected either
automatically w hen the “Automatic” tool is active based on the cursor position or by explicitly selecting one of the follow ing
manual integration tools:

Function Description
Edit Baseline Tool Used to modify the baseline.
Edit Delimiter tool Used to move the peak start or peak end.

Insert Peak Tool Used to create a new peak.

Peak Type Changes the peak type into one of the following options:
- Main Peak
- Rider - Tangential at lower peak end
- Rider - Tangential at both peak ends
- Rider - Exponential
Shape shoulder Adds second peak below existing one.

Split peak Splits the peak at current mouse position.

Delete Peak Deletes the integration of the selected peak.

Delete All Peaks Deletes the integration of all peaks.

Remove Manual Integration Removes all manual integration from the chromatogram.

In order to retain manipulations made to a chromatogram, the changes must be saved. On saving the changes the
chromatogram view automatically show s that the chromatogram has been manually modified.

Note: any changes made to the detection parameters do not affect the modified chromatogram.

5.4.1.4 (M anual) Peak Identification

When a peak is selected it is possible to assign a component to the peak by creating a new component record or by starting
the Component Table Wizard. These options can be selected in the ‘Processing’ ribbon:

Figure 28: Processing Ribbon in the Chromatography Studio

Function Description
Add Component Adds a new component named “Component X ” t o t he co mp one nt t ab le a n d
automatically adds the peak retention time and window to the component table.
Component Table Wizard Start component table wizard (see section 5.3.19).

The Manual Peak Identfication page show s a list of all possible components for the currently selected channel.

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Figure 29: Component Assignment List

The component w hich is assigned to the currently selected peak is labeled w ith a bold font. The numbers in the second
column show the time distance in minutes betw een the retention time of the currently selected peak and the expected
retention time of the corresponding component. The number is formatted w ith enclosing brackets […] if the currently
selected peak is inside the retention w indow of the component. The follow ing assignment icons may appear in the list:

Icon Description

The component is automatically assigned to some peak in the chromatogram. The component which is assigned to the cu rren tly
selected peak is formatted with a bold font.
The component is not assigned to any peak in the chromatogram.

The component is manually assigned. The component(s) which is(are) manually assigned t o t he curre nt ly se l ec te d p e ak i s
formatted with a bold font.

The automatic component assignment can be changed manually.

Function Description
Assign Component Assigns the component(s) selected in the list to the currently selected peak i n t h e
chromatogram. Automatic assignment is automatically disabled for this p e ak a n d
the selected component(s).
If a new (component) name is entered in the edit field above the list you h ave t h e
choice to either create a new component record in t he P rocessi n g Me th od o r
assign a so-called arbitrary component name to the peak.
Remove Manual/Automatic Assignment Removes the manual/automatic component assignment of the currently se l e ct ed
peak.
Remove All Manual Assignments Removes all manual component assignments of any peak in the current
chromatogram.

Assigning multiple components to the currently selected peak is also possible. In this case all components w hich should be
assigned need to be selected in the list pressing via the Ctrl-key and clicking the left mouse button. Manually assigned
component are considered any more for the automatic assignment in the current chromatogram.

5.4.1.5 Overlay
It is possible to overlay chromatograms from samples in the same sequence or from different sequences. It is also possible
to overlay chromatograms acquired using different channels including virtual channels (e.g. overlay a chromatogram
acquired at 254 nm w ith a chromatogram acquired at 280 nm).

5.4.1.6 Properties
The follow ing chromatogram display options are available:

Plot Details

Parameter Sub Parameter Description

Axes Time Axis Displays a time axis on the chromatogram.

Signal Axis Displays a signal axis on the chromatogram.

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Font Allows the font type and size of the axes to be defined.

Axis to Plot Gap Defines the distance in mm between the axes and the
chromatogram plot.
Frame Frame that is drawn around the plot area.

Axes Descriptions Axes Titles Applies titles to the chromatogram axes.

Units Displays units on the axes of the chromatogram.

Font Allows the font type and size of the axes titles to be defined
Grid Signal axis grid lines Applies horizontal grid lines to the chromatogram.

Time axis grid lines Applies vertical grid lines to the chromatogram

Orientation Horizontal Displays the chromatogram in the landscape orientation.

Vertical Displays the chromatogram in the portrait orientation.

Signal details Raw data points Shows the raw data points.

Time Axis
This section allow s the user to define the scaling used for the time axis. The follow ing options are available.

Parameter Sub Parameter Description

Share time axes If your chromatogram plot includes overlaid ch rom at ogra ms
and you have selected a Stacked arrangement on the
Comparison page, you can select whether to use a co mmo n
(shared) time axis for the chromatogram stripes, or se p a ra t e
time axes. The unit on the time axis is always identica l f or a ll
chromatogram stripes.
Select the Share time axis check box to display a sin gle t ime
axis for all chromatograms (default). Clear the ch eck b o x t o
display separate time axes for each chromatogram.
If you have cleared the Share time axis check box, select t he
chromatogram from the Settings for chromatogram plot list f o r
which the settings under Range (see below) shall apply.
Range Autoscale or Fixed Determines the method for selecting the range. Can be set t o:
Autoscale or Fixed, Autoscale on Peak, or Fixed using
Autoscale on Peak Formula.
Fixed using Formula
Autoscale or Fixed From Defines the start time of the chromatogram. Eithe r A ut o o r a
specific time can be selected.
To Defines the end time of the chromatogram. Eit her A u to o r a
specific time can be selected.
Autoscale on Peak Selected Allows the user to select the peak by Name, Greatest He igh t,
Greatest Area, Number, or Component Table Number
Width Defines the width by which to pad the se l ecte d a ut osca le d
peak range. This can be defined or set to Autosize width.
Fixed using Formula From Defines the start time of the chromatogram using a formula
To Defines the end time of the chromatogram using a formula

Time mark intervals Fixed intervals of tick marks Defines whether tick marks should appear at selected intervals

Major tick mark Defines the interval for major tick marks
Minor tick mark Defines the interval for minor tick marks

Time axis units Minutes (min) The units for the time axis are minutes.
Seconds (s) The units for the time axis are seconds.

Signal Axis
This section allow s the user to define the scaling used for the signal axis. The follow ing options are available:

Parameter Sub Parameter Description

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Parameter Sub Parameter Description

Signal Axis Settings for chromatogram Determines the signal axis for which to define the setti ngs. T o b e
plot able to select between different signal axes, you h ave t o lo ad a t
least one Overlay. In addition, two signal axes must be displayed.
Range for selected plot Autoscale or Fixed Determines the method for selecting the ra ng e. Ca n b e se t t o:
Autoscale or Fixed, or Fixed using Formula.
Fixed using formula

Autoscale or Fixed To Defines the end value of the signal axis. Either Auto or a sp e cif ic
time can be selected.
From Defines the start value of the signal axis. Either Auto or a sp e c i fic
time can be selected.
Fixed using Formula From Defines the start value of the signal axis using a formula

To Defines the end value of the signal axis using a formula

Autoscale in time range or peak Autoscale in visible time Determines the signal autoscale options for the current
range chromatogram. Following options are enabled only fo r t he si gn al
scale mode ‘Autoscale or fixed’; Autoscale in visi ble t ime ra n ge,
Autoscale in fixed time range Autoscale in fixed time range, Autoscale on peak.
Autoscale on peak

Autoscale in visible time range N/A Calculates the signal minimum and / or maximum on th e b asi s o f
the current time range specified on the Time Axis properties page.
Autoscale in fixed time range From Custom start value to calculate signal minimum and / or maximum.
To Custom end value to calculate signal minimum and / or maximum.

Autoscale on peak Selected Calculates the signal minimum and / or maximum on th e b asi s o f
the range between peak start and end time. Following peak
selection modes are available; by name, by g rea te st h ei ght , b y
greatest area, by number, by component number.
Time mark intervals Fixed intervals of tick marks Defines whether tick marks should appear at selected intervals

Major tick mark Defines the interval for major tick marks
Minor tick mark Defines the interval for minor tick marks

Title
This section defines the caption that w ill be displayed in the chromatogram header. Left, middle and right captions can be
selected either based on simple text values or on user-defined formulas. Also defines the legend in the bottom left corner of
the chromatogram w hen several chromatograms are overlaid. The formula can be based on variables from the follow ing
sections:

• Global Functions (7.1)

• General (7.2)
• Sequence (7.3)
• Injection (0)
• Audit Trail (see section 7.5)

• Preconditions (see section 7.6)

• Chromatogram (7.8)
• Processing Method (7.21)
• Instrument Method (7.31)
• Custom Formulas (5.8.31)

Note: If a chromatogram is manually integrated the text “[manipulated]” is alw ays shown in the left caption.

In addition, the follow ing options are available:

Parameter Sub Parameter Description

Draw titles Displays chromatogram titles.

Font Allows the font type and size of the titles to be defined

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Parameter Sub Parameter Description

Left title Draw left title Displays the left part of the title.
When checked the left part of the title can be defined based on
formulas as described above.
Middle title Draw middle title Displays the middle part of the title.
When checked the middle part of t h e t i tle can b e d ef ine d
based on formulas as described above.
Right title Draw right title Displays the right part of the title.
When checked the right part of the title can be defined b a se d
on formulas as described above.
Legend Draw Legend Displays legend to the left of the chromatogram when seve ra l
chromatograms are overlaid.
When checked the legend can be defined based on fo rmula s
as described above.

Peak Characterization
This section defines how detailed peaks are characterized in the chromatogram plot. The follow ing options are available:

Parameter Sub Parameter Description

Peak delimiter Shows the peak delimiters.

Delimiter Allows defining color and line style for peak delimiters.
Separation Allows defining color and line style for the separation drop line.

Baseline Shows the baseline.

Main peak Allows defining color and line style for the base line un de r a
main peak.
Rider peak Allows defining color and line style for the base line un de r a
rider peak.
Peak tangents Shows the peak tangents.
Allows defining color and line style for peak tangents.

Draw peak width at Shows peak widths.

Peak widths
Allows defining color and line style for peak widths.

Draws a line at the given height. Default s h e ig ht s a re 5 % ,

10%, 50%, but are user definable
Peak Highlight Do not highlight any peaks The identified peak will not be shaded unless it has the focus

Highlight all identified peaks All identified peaks will be shaded in all plots

Highlight all detected peaks All detected peaks will be shaded in all plots

Peak Label
This section defines how peaks should be labeled. The follow ing options are available:

Parameter Sub Parameter Description

Identified peaks Label identified peaks Labels all identified peaks with details generated by the use r-
defined formula.
(Formula) The formula can be based on variables f ro m a ll t he a rea s
detailed in section 7.
Font Defines the font used for the identified peak labels.
Unidentified peaks Label unidentified peaks Labels all unidentified peaks with details g e n era te d b y t he
user-defined formula.
(Formula) The formula can be based on variables f ro m a ll t he a rea s
detailed in section 7.
Font Defines the font used for the unidentified peak labels.

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Parameter Sub Parameter Description

Undetected components Label undetected components Labels all not detected components i n t h e c h roma to gra m
generated by the user-defined formula. The labels are
positioned at the expected retention time of the not d et ect ed
component and tied to signal value of the chro mat og ram a t
this time.
(Formula) The formula can be based on variables f ro m a ll t he a rea s
detailed in section 7.
Font Defines the font used for the undetect ed co mp one nt p ea k
labels.
Label style Rotation Defines the angle the peak labels are shown at.

Peak Purity
This section defines plot options for peak purity and peak match.

Parameter Sub Parameter Description

Peak Purity Index Overlay peak purity index Shows the peak purity index in the chromatogram plot.

Line Style Allows defining line color, width and style for the peak p u ri ty
index.
Peak Match Overlay peak match factor Shows the peak match factor in the chromatogram plot.

Line Style Allows defining line color, width and style for the peak m a t c h
factor.

Peak Windows
Formulas used in this section can combine variables from the follow ing categories:

• Global (7.1)
• General (7.2)
• Sequence (7.3)
• Injection (0)

• Audit Trail (see section 7.5)

• Preconditions (see section 7.6)
• Chromatogram (7.8)
• Processing Method (7.21)
• Component (7.29)
• Unidentified Peak Group (7.30)
• Instrument Method (7.31)
• Custom Formulas (5.8.31)
The follow ing options are available:

Parameter Sub Parameter Description

Component table windows Show component table windows Displays peak windows for components from the co mpo ne nt
table (dotted lines indicating the width of the retention win dow
for the peak). Note: peak windows allow the retention time and
retention window of peaks to be adjusted graphically.
(Formula) Labels all peak calipers for identified peaks with details
generated by the user-defined formula.
Unidentified peak group windows Show unidentified peak group Displays peak windows for unidentified peak groups.
windows
(Formula) Labels all peak windows for unidentified p eaks wi t h d e t ails
generated by the user-defined formula.
Other options Show all peak window drop lines Displays dotted lines for all peaks, not only the currently
selected peak.

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Parameter Sub Parameter Description

Font Defines the font for peak windows.

Comparison
This section defines how chromatogram overlays are displayed. The follow ing options are available:

Parameter Sub Parameter Description

Arrangement Overlaid All overlaid chromatograms are shown in one window.
Stacked All overlaid chromatograms are shown in stacked windows.

Grouped by detector All overlaid chromatograms are grouped by detector.

Overlay order Sorted by injection list order All overlaid chromatograms are identical to the order of
injections and channels in the Navigation Pane.

Current chromatogram always o n Currently selected chromatogram is displayed in f ron t o f t he

top other chromatograms.
Offset Time Offset Offsets the overlaid chromatogram by the % time value
selected.
Signal Offset Offsets the overlaid chromatogram by the % signal value
selected.
Overlay Overlay with peak characterization If selected the peak characterization sett in gs su ch a s p e a k
names, peak delimiters or the baseline apply not o nly t o t h e
active chromatogram but also to all overlaid chromatograms.
Overlay with right signal axis. If selected the overlaid chromatogram is measured a g ainst a
right signal axis.
Mirror last overlaid injection Mirrors the chromatogram that was added to the overla y l ast
on the time axis.
Normalization Normalize signal Normalizes the signal against the reference peak.
Peak Allows specification of the reference peak

Retention time Allows specification of the retention time to be used for

normalization
Normalize time Allows to normalize the signal in x direction either by shifting or
stretching all chromatograms so that the retention time o f t h e
selected component matches for each overlaid chromatogram.
First peak Allows specification of the start peak for normalization
Second peak Allows specification of the end peak for normalization

Normalize signal Off No signal normalization

Peak Normalizes overlaid signal to height of specified peak

Retention time Normalizes overlaid signal to height of a specific data point

Full range Normalizes overlaid signal to maximum peak height

Normalize time Off No normalization by time

Shift to peak Shifts the overlaid chromatogram to overlay a specific peak

Stretch between start and peak Stretches the overlaid chromatogram between t h e st a rt a n d
specified peak
Stretch between two peaks Stretches the overlaid chromatogram between the two
selected peaks
Stretch between start and end Stretches the overlaid chromatogram between t h e st a rt a n d
end, in order that the run times match

Events
This section allow s defining w hich events that occurred during the data acquisition or data processing are display ed on the
chromatogram. The follow ing options are available:

Parameter Sub Parameter Description

Detection Parameters N/A Indicates the Detection Parameters.

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Parameter Sub Parameter Description

Gradients Show gradients Displays the corresponding gradient profile.
Line style Allows to define color, width and line styl e f o r t h e g rad ien t
profile.
Dwell time Defines the dwell time. This will draw a gradient profile that i s
in accordance with the retention time.
For this device only Allows to select the device for which the gradients sho u l d b e
shown. By default, gradients are displayed for all devices.
Signal parameters N/A Displays signal parameters in the chromatogram.
Triggers N/A Hide or show triggers from the instrument method in the
chromatogram.
Manual commands N/A Displays manual commands in the chromatogram.
Errors N/A Displays errors in the chromatogram.

Label Style Label events Displays event labels in the chromatogram.

Font Defines the event label font.

Fraction Tubes
This section defines how fraction tubes should be displayed. The follow ing options are available:

Parameter Sub Parameter Description

Tubes Show tubes Displays the tubes collected

Label tubes Displays a label for the tube based on a formula using
Chromeleon Report Variables
Fractions Show fractions Displays the fractions collected

Hide tubes inside fractions Removes distinctions between tubes collected as part o f t he
same fraction
Label fractions Displays a label for the fraction base d o n a f orm ula u si n g
Chromeleon Report Variables
Label Style Font Allows the font type and size of the labels to be determined
Rotation Allows the orientation of the label to be determined

Alignment Allows the location of the label to be determined

MS Quantitation Channel
This section defines special plot and display options to be applied w hen the MS Quantitation trace is displayed.

Parameter Sub Parameter Description

Trace visualization Trace offset If selected, each XIC is plot with a vertical offset compared t o
the previous XIC; otherwise, all XICs are plotted on a common
using their true y-axis values

Show only display range of If selected, the XIC plot range is limited to the display range as
extracted ion trace defined in the component table of the processing method.
If not selected, the full-time range of the XIC is plotted.
Use alternating colors If selected, the XICs are drawn using a rotating color p a let te
as defined in the Line and Fill Styles tab.
If not selected, the XICs are drawn usi ng t h e p rim ary p lot
color, as defined in the Line and Fill Styles tab.
Show peak characterization If selected, the MS Quantitation plot is annotat ed wi t h p ea k
characterizations (peak delimiters, peak tangen ts, b a se lin e
and width.)
Label traces Label quantitation peaks Shows or hides the XIC peak labels
(Formula) The formula can be based on variables f ro m a ll t he a rea s
detailed in section 7.

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Label style Alignment Defines if the peak labels should be placed abo ve t h e p ea k
apex or at the lower right of each peak trace.
Draw Frames If selected, a box is drawn around the peak labels

Font Defines the font for peak labels.

Rotation Defines the angle the peak label is shown at.

Spectral Thumbnails
This section defines how spectral thumbnails should be displayed. The follow ing options are available:

Parameter Sub Parameter Description

Show Thumbnails Automatic Displays the thumbnails only when the UV-Vis Spectra Plot is
also displayed.
UV Always displays the thumbnails if UV spectral data are
available.
Fluorescence Always displays the thumbnails if fluorescence spectral d at a
are available.
Amperometry Displays the thumbnails of any existing I-t plots in all channels.
MS Displays the thumbnails of any existing MS plots in all
channels.
None Don’t display any UV spectra thumbnails in the
chromatogram.
Thumbnails Size Width Defines the width of the thumbnail in mm.
Height Defines the height of the thumbnail in mm.

Range Bars Draw average range bars Marks and labels the ranges from which bunched spectra
were taken in the chromatogram. The number of spectra
averaged within a range is displayed in parenthesis.

Line & Fill Styles

This section allow s a consistent color scheme for the objects in the chromatogram plot to be defined. The follow ing items
can have their line color defined:
• Chromatograms 1-8 • Peak tangents • Manual Commands
• Temporary scan extract • Peak w idth • Errors

• Peak delimiter • Raw data points • Peak purity index

• Peak separation • Detection parameters • Peak match index
• Baseline • Gradients • Tubes
• Rider baseline • Signal Parameters • Fractions
• Free baseline • Triggers • Selected peak
The follow ing items can have their fill color defined:
• Background • Peak label • Event label
• Detection parameter label • Tube label • Tubes
• Fractions • Selected peak • Selected peak label

Interactive Settings
This section defines the interactive settings in the chromatogram. The follow ing options are available:

Function Description
Maximum hit test distance Specify the distance when the shape of the mouse point er ch an ge s wh e n yo u
approach an object in the chromatogram plot.
Show overview plot When this check box is selected, the miniature overview of the chromatogram plot
is displayed when zooming into the chromatogram.

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Function Description
Show popup controller When this check box is selected, the full-size button, vertical and horizontal z o om
toolbars on the chromatogram axes are visible.
Visualize selections When this check box is selected, visualization of selected objects, such as a
selected peak, is enabled.
Highlight selected chromatogram Enables or disables the highlighting of the selected chromatogram.

Manual Peak Identification

This section allow s manual peak identification (also see 5.4.1.4). The “Currently selected peak” section contains read only
fields, w hich show properties of the currently selected peak. The “Assign component or add arbitrary name for selected
peak” section contains the follow ing options:

Function Description
Component List of peaks in the component table. This filed also gives the possibility to enter an
arbitrary name.
Assign Component Manually Forces the peak to be identified with the selected component from the compon ent
table.
Assign Arbitrary Name Assigns arbitrary name (entered in the Component box) to the peak.

Remove manual assignment Removes the manual component assignment of a peak.

Remove all manual assignments Removes all manual component assignments of any peaks in the current
chromatogram.

5.4.1.7 Hotkeys
It is possible to navigate around the chromatogram using hotkeys. The follow ing hotkeys are supported by Chromeleon:

Key Function
Left Cursor / 4 on Number Pad Scroll time axis left by 5%.

Right Cursor / 6 on Number Pad Scroll time axis right by 5%.

Up Cursor / 8 on Number Pad Scroll signal axis up by 10%.

Down Cursor / 2 on Number Pad Scroll signal axis down by 10%.

Home Scroll to the chromatogram start. No scale changes.

End Scroll to the chromatogram end. No scale changes.

/ (Divide) Zoom time axis out by 25 %.

* (Multiply) Zoom time axis in by 20 %.

- (Minus) Zooms signal axis out by 25 %.

+ (Plus) Zooms signal axis in by 20 %.

5 (5 on number pad) Returns the chromatogram to full scale on the time and signal axes.
Ctrl together with Left Cursor Selects the previous peak.

Ctrl together with Right Cursor Selects the next peak.

Space Changes to next mouse tool (Automatic → Delimiter → B a se line → De t ect ion
Parameter → Insert Peak → Spectra Tool).
Delete Delete selected peak.
Ctrl together with Y Redo the last peak manipulation

Ctrl together with Z Undo the last peak manipulation.

Alt together with Backspace Undo the last peak manipulation.

F4 Replaces active chromatogram with next chromatogram.

Shift together with F4 Replaces active chromatogram with previous chromatogram.

F1 Shows context sensitive help.

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5.4.1.8 Detection Parameters

The “Insert” button on the “Processing” ribbon allow s the follow ing detection parameters to be created at the retention time
position of the cursor:
• Inhibit Peak Detection • Fixed Baseline Point • Minimum Width
• Baseline Type Valley to Valley (On) • Minimum Area • Baseline Noise Range
• Detect Negative Peaks (On) • Minimum Height • Cobra Smoothing Width
In addition, “Other Parameter” show s a dialog to choose from a complete list of all available detection parameters.

5.4.1.9 Export Chromatogram

The chromatogram can be exported to a text file using the context menu command “Export Chromatogram (Text format)”.
The command launches a dialog w ith further options (Figure 30).

Figure 30: Chromatogram Export Option Dialog Box

The follow ing options are available:

Parameter Sub Parameter Description

Destination Clipboard Exports a textual description of the chromatogram data or raw
data into the clipboard.
File Exports a textual description of the chromatogram data or raw
data into a file.
Options Chromatogram data Exports only the chromatogram data.

Raw data Exports chromatogram data including raw data.

Additionally, the chromatogram plot can be copied into the clipboard as an image using the Ctrl + C hotkey.

5.4.1.10 Arithmetic Combination

The Arithmetic Combination combines tw o existing channels, from the same or different injections (including an injection in
another Data Vault), using the arithmetic operations: add, subtract, multiply, and divide.
The command launches a dialog w ith further options (Figure 31).

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Chromeleon 7

Figure 31: Channel Processing Arithmetic Combination Dialog Box

The follow ing options are available:

Parameter Sub Parameter Description

Channel A Original channel The original channel (read-only) that will be used as Chan ne l
A in the arithmetic operation.
Factor A User defined factor with which Channel A is multiplied.

Channel B Current channel A selectable channel from the current sequence th at will b e
used as Channel B in the arithmetic operation.
Fixed channel A channel from another data vault that will be used as
Channel B in the arithmetic operation.
Factor B The factor with which Channel B is multiplied.

Output Operation The arithmetic operation that will be used to combine the data
points in Channel A and Channel B: A+B, A-B, A*B, A/B, B/A.
Result channel Name for the new channel.

Apply to the following i nje ctio ns Processing action options: current, selected/pinned, all, type.
within the current sequence
Overwrite existing channels Option to overwrite a channel if it already exists in the curre nt
sequence.

5.4.1.11 Copy Channel

The chromatogram channel can be copied using the context menu command “Copy Channel”. This command is available
on the Navigation Pane; Under Channels, right-click the channel that you w ant to copy, or on the chromatogram plot, right-
click in the chromatogram, and then click Copy Channel.
The command launches a dialog w ith further options (Figure 32).

Figure 32: Chromatogram Copy Channel Dialog Box

The follow ing options are available:

Function Description

Original channel The name of the original channel (read-only) to be copied.

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Function Description

Result channel Name for the new channel.

Apply to the following injections wi t hin t he c u rren t Processing action options: current, selected/pinned, all, type as eithe r Un kn own ,
sequence Blank, Check Standard, Calibration Standard, Matrix, Spiked and Unspiked.
Overwrite existing channels Option to overwrite a channel if it already exists in the current sequence.

Note: If the chromatogram w as manually modified before the channel w as copied, any modifications w ill be copied too.

5.4.1.12 Derivatives
The derivative processing action outputs the first or second derivative of an existing channel to a new channel.
The command launches a dialog w ith further options (Figure 33).

Figure 33: Channel Processing Derivatives Dialog Box

The follow ing options are available:

Function Description

Original channel The original channel (read-only) that will be used to calculate the first o r se co n d
derivative.
Derivative First and second derivative options.

Result channel Name for the new channel.

Apply to the following injections wi t hin t he c u rren t Processing action options: current, selected/pinned, all, or specify injection type a s
sequence either Unknown, Blank, Check Standard, Calibration Standard, Matrix, Spiked and
Unspiked.
Overwrite existing channels Option to overwrite a channel if it already exists in the current sequence.

5.4.1.13 Power Law

Applies a pow er factor to an existing channel such that the data points are raised by a pow er of betw een 1.0 and 2.0, w ith
the results being output to a new channel (the original channel remains unchanged).
The command launches a dialog w ith further options (Figure 34).

Figure 34: Channel Processing Power Law Dialog Box

The follow ing options are available:

Function Description

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Chromeleon 7

Function Description

Original channel The original channel (read-only) to which the power factor will be applied.
Power factor Power factor between values of 1.0 and 2.0.

Result channel Name for the new channel.

Apply to the following injections wi t hin t he c u rren t Processing action options: current, selected/pinned, all, or specify injection type a s
sequence either Unknown, Blank, Check Standard, Calibration Standard, Matrix, Spiked and
Unspiked.
Overwrite existing channels Option to overwrite a channel if it already exists in the current sequence.

5.4.1.14 Smooth Channel

Smoothes the data in an existing channel. The smoothing process applies a digital filter (smoothing algorithm) to the
channel data to reduce signal noise.
The command launches a dialog w ith further options (Figure 35).

Figure 35: Channel Processing Smooth Channel Dialog Box

The follow ing options are available:

Function Description

Original channel The original channel (read-only) to which the smoothing process will be applied.

Filter type Smoothing process filters: Moving Average, Olympic, Savitzky-Golay, Gaussian.
Filter size The number of input data points used to generate each output data point.

Result channel Name for the new channel.

Apply to the following injections wi t hin t he c u rren t Processing action options: current, selected/pinned, all, or specify injection type a s
sequence either Unknown, Blank, Check Standard, Calibration Standard, Matrix, Spiked and
Unspiked.
Overwrite existing channels Option to overwrite a channel if it already exists in the current sequence.

5.4.2 Calibration Plot Pane

The calibration view can be modified to display calibration curves in various different w ays. In addition, zooming into the
calibration curve is possible.
Double clicking a calibration point show s the associated chromatogram in the chromatogram pane (if show n) and also
selects the respective line in the interactive result tables.
Figure 36 show s a typical calibration curve view .

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Figure 36: Calibration Plot View

The follow ing calibration curve display options are available.

5.4.2.1 Scale

Parameter Sub Parameter Description

Proportional n.a. If selected, changes are applied to all calibration plots.
Amount Axis From Defines the start value of the amount axis.

To Defines the end value of the amount axis.

Autoscale If selected the full range is shown and the values are not
considered.
Logarithmic Scale Applies the logarithmic scale to the amount axis.
Fixed intervals of tick marks Customizes the interval of tick marks via typing or selecting a
number in the Major tick mark and/or Minor tick mark boxes.
Response Axis From Defines the start value of the response axis.

To Defines the end value of the response axis.

Autoscale If selected the full range is shown and the values are not
considered.
Logarithmic Scale Applies the logarithmic scale to the response axis.
Fixed intervals of tick marks Customizes the interval of tick marks via typing or selecting a
number in the Major tick mark and/or Minor tick mark boxes.
Apply log-log linear transformation n.a. Applies a log-log linear transformation to the current plot.

5.4.2.2 Frame & Axes

Parameter Sub Parameter Description

Axes Amount Axis Displays an amount axis on the calibration plot.
Response Axis Displays a response axis on the calibration plot.

Fonts Allows the font type and size of the axes to be defined.

Axis to Plot Gap Defines the distance in mm between the axes and the
chromatogram plot.
Frame Allows the calibration curve frame to be removed.
Axis Titles Axis Titles Applies titles to the calibration plot axes.

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Parameter Sub Parameter Description

Units Displays units on the axes of the calibration plot.
Fonts Allows the font type and size of the axis titles to be defined.

Grid Horizontal grid lines Applies horizontal grid lines to the calibration plot.

Vertical grid lines Applies vertical grid lines to the calibration plot.

5.4.2.3 Title
This section defines if titles are displayed and how titles should be displayed:

Parameter Sub Parameter Description

Draw titles Shows a title for the calibration plot.

Font Allows the font for the calibration plot title to be defined.

Left title Draw left title Displays the left part of the title.
Use default When checked left part of the title is shown as in Chrome leon
7.2.
When not checked the left part of t he t i tle can b e d e fin ed
based on formulas in the edit field.
Center title Draw center title Displays the middle part of the title.

Use default When checked middle part of the title is shown as in

Chromeleon 7.2.
When not checked the middle part of the title can b e d ef ine d
based on formulas in the edit field.
Right title Draw right title Displays the right part of the title.
Use default When checked right part of the title is shown as in Chromeleon
7.2.
When not checked the right part of the t i tle can b e d ef ine d
based on formulas in the edit field.

5.4.2.4 Options
The follow ing options are available:

Parameter Sub Parameter Description

Check Standard & Draw check standard Draws points for check standard injection points on the calibration plot.
Current Injection injection points
Draw level tolerance lines Displays concentration level tolerance lines on the calibration plot.

Draw response/amount Draws a horizontal line from the from the response axis (response va lu e o f t he
quantification lines of current injection). Where the line hits the calibration curve, a vertical line is dra wn
current injection to the amount axis.
Confidence Interval Draw upper and lower Draws the upper and lower confidence limits of the calibration curve.
confidence limits

Upper probability, Lower The confidence probability to be used when calculating the confidence limits. Th e
probability following values can be selected:
• 95 %
• 97.5 %
• 99 %
• 99.5 %
• 99.9 %
• 99.95
%
• 99.995
%
Draw Hubaux-Vos Draws the Hubaux-Vos detection limits for the calibration curve.
detection limit

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5.4.2.5 Line & Fill Styles

This section allow s a consistent color scheme for the objects in the calibration plot to be defined. The follow ing items can
have their line color defined:
• Grid • Markers • Original markers
• Axes • Selected marker • Hubaux-Vos lines
• Calibration curve • Disabled markers • Quantification lines
• Confidence interval curves • Check standard markers
• Prediction limit curves • Check Standard outlier markers

The follow ing items can have their fill color defined:
• Background

5.4.2.6 SmartLink
The follow ing options are available:

Group Sub Parameter Description

Link to Chromatogram N/A Links the object to the chromatogram.
Multiple Peak Selection When selected, the peaks that are selected in the chromato gra m
plot define which peaks are displayed in the calibration plot.
Zoom Area When selected, the zoom area of the chromatogram plot d ef ines
which peaks are shown in the calibration plot.

5.4.2.7 Interactive Settings

This section defines w hat optional zoom/unzoom tools are displayed on the calibration plot.

Function Description
Always display the selected plot first Displays the calibration plot of the selected peak in the chromatogram first.
Show overview plot When this check box is selected, the miniature overview of the calibra tio n p lo t i s
displayed when zooming into the calibration plot.
Show popup controller When this check box is selected, the full-size button, vertical and horizontal z o om
toolbars on the chromatogram axes are visible.

5.4.3 Peak Properties Pane

The peak properties pane offers 3 property pages to view the results and/or edit properties of the currently selected peak or
component. The 3 property pages are
Peak: Lists configurable results of the currently selected peak
Components: Lists the properties of the currently selected component
MS Detection: Lists and allow s to edit the MS detection settings for so-called Extracted Ion Chromatograms (XIC, see
5.3.2.21 for details)

5.4.3.1 Peak
In the upper part of the property page “Peak” a configurable number of results is show n for the currently selected peak in the
chromatogram (see Figure 37 below ).

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Chromeleon 7

Figure 37: Peak Properties Pane – Page “Peak”

The list of Property Name / Value pairs can be configured. The corresponding settings are stored in the currently active View
Settings. The follow ing options are available:

Function Description

Edit Opens the result formula dialog to edit the current result formula, its format and the label (Propert y Na m e co lumn ). T he
corresponding peak result is shown in the currently selected row of the Property Name / Value list.
Insert Opens the result formula dialog to select a new formula, its format and the label (Property Name column). A new result ro w
is inserted at the currently selected row into the Property Name / Value list.
Delete Removes the currently selected result row from the Property Name / Value list.
Append Opens the result formula dialog to select a new formula, its format and the label (Property Name column). A new result ro w
is appended to the Property Name / Value list.
Move Up Moves the currently selected row one position up in the Property Name / Value list.
Move Down Moves the currently selected row one position down in the Property Name / Value list.

The low er part of this page allow s to manually modify the automatic component assignment of the currently selected peak.
The corresponding user interface and options are identical to the corresponding options in the Manual Peak Identification
Page in the properties dialog of the Chromatogram Pane (see 5.4.1.4 for details).

5.4.3.2 Component
The property page “Component” lists the properties for the currently selected component. This is especially useful if the
component table of the Processing Method Editor is not open. It is possible to edit the properties. The changes w ill be
transferred to the component table. The follow ing properties are listed (see section 5.3.1.2 for descriptions):

• Name • Ret.Index • Mol.Mass

• Channel • Conc.Unit • CAS
• Comment • Peak Type • Chem.Formula
• Factor • Up.Conf.Prob. • Ref.Mass.Spec.Settings

• Eval.Type • Low .Conf.Prob. • Extr.Ion.Chm

• Cal.Type • Ref.UV.Spec. • Charge
• Stand.Meth. • Match Crit • Requires Reference Peak
• Ret.Time • Threshold • RTS Ratio Tolerance
• Window • WL-Range • Peak Group(s)

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• Prev.Retention • Spec.Deriv. • Peptide Group

• Left Limit • Rel.Max.Dev.
• Right Limit • Check Extr.

5.4.3.3 M S Detection
The MS Detection page is only present for Extracted Ion Chromatograms (XIC, see 5.3.2.21 for details). It show s the MS
Detection settings for the currently selected XIC and allow s also to edit them in the section below the Detection Settings
label (see Figure 38 below ).

Figure 38: Peak Properties Pane – Page “MS Detection”

Function Sub Function Description

Component Show the name of the currently selected component and allows the select t h e n ext o r
previous one of the component table.
XIC Shows the currently selected XIC of the component and allows the sel ect t he n ext o r
previous one, i.e. MS Quantitation Peak or MS Confirmation Peak(s).

Use Processing Method Shows the MS Detection settings of currently selected XIC in the De te ct ion S et ti ngs
(applied for all injections) below if the MS Detection settings are used from the Processing Method.
Selects to use the MS Detections settings from the Processing Method instead injection
specific ones.

Use MS default Shows or selects to use the MS default detection settings which are stored in the
detection settings Processing Method and applied for all injections wh i ch h ave a ssi g ned t he curre nt
Processing Method.
Apply… Opens up a dialog to (bulk) apply the MS default det ect ion se t ti ngs t o so m e o r a ll
components and XICs.
Use XIC specifi c Shows or selects to use XIC specific detection settings which are stored in the
detection settings Processing Method and applied for all injections wh i ch h ave a ssi g ned t he curre nt
Processing Method.
Copy and apply... Opens up a dialog to (bulk) copy and apply the currently selected XIC specific detection
settings to some or all components and XICs.

Use Injection Specific Shows the MS Detection settings of currently selected XIC in the De te ct ion S et ti ngs
detection settings below if the MS Detection settings are only valid for the currently selected injection.
Selects to use the MS Detections settings for the currently selected injection only instead
of the MS Detection settings stored in the Processing Method.

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Chromeleon 7

Function Sub Function Description

Set Detection Reference Opens up a dialog to select the XIC-type (Quantitation, 1st Confirming, 2nd Confirming ,
XIC … etc…) and the components / peptides for which this XIC-type should become the
reference detection XC. For peptides there is also the choice to select either the Mast er
Peptide or any Charge State component record. All other X I Cs o f t h e comp on ent /
peptide will be integrated based on the integra tio n o f t he com pon ent p ea k (p e ak
start/end, baseline) in the reference XIC.

Remove Detection Opens up a dialog to select the components for which th e re f ere nc e d e te ct ion X IC
Reference XIC … should be removed.

5.4.4 Interactive Charts Pane

The Interactive Charts pane allow s the user to instantly display charts of chromatography results, making the results easy to
interpret at a glance. Interactive Charts can be used to display the values of any appropriate variable across a range of
injections, or across the peaks w ithin an individual injection.
Selecting any data point in an Interactive Chart updates the selections in all the other panes, so the underlying data of a
point of interest can be immediately accessed. The Interactive Chart can be modified to display Chromeleon report formulas
in various different w ays. In addition, zooming into the calibration curve is possible. Figure 39 show s an Interactive Chart
Pane.

Figure 39: Interactive Charts view in the Chromatography Studio

There are tw o types of Interactive Charts:
• Peak Charts: charts displaying chromatography results of the peaks w ithin a chromatogram.

• Injection Charts: charts displaying chromatography results of the injections in a (virtual) sequence.
When inserting a new chart, the follow ing templates are available:

Function Description
Retention Time Injection chart: displays retention time trend of a selected peak.
Column Performance Injection chart: displays theoretical plates, resolution and asymmetry of a selecte d
peak.
Component Area Injection chart: displays area of a selected peak.

Rel. Peak Area Peak chart: displays relative peak area of peaks in chromatogram.

Check Standard Injection chart: displays check standard amount of a selected peak.
Amount Deviation Injection chart: displays deviation for the selected peak of the calculated amount in
calibration and check standards against the amount entered in the amount
columns of the processing method.
Electrolytic Devices Injection chart: displays status of electrolytic devices.

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Function Description
Isotopic Distribution Injection chart: displays peak area distribution of each isotope across all injections.
If a summed peptide is selected, peak area ratios are displayed against t h e m ost
abundant observed isotope peak area. If a peptide charge state is selected, p ea k
area ratios are displayed against a theoretical isotopic distribution.
Isotopic Ratios Injection chart: displays relative intensities of isotopes normalized to a sum total o f
100% across all injections. When the summed peptide is selected, the plotted data
is for observed data only. When a peptide charge state is sele ct ed , t h e p lo tt ed
data consists of both theoretical distribution as well as observed distribution.

The follow ing Interactive Chart display options are available.

5.4.4.1 Data Settings

Parameter Sub Parameter Description

Horizontal Axis Variable n.a. Displays horizontal axis variable that can be user defined
based on all report formulas from all t he are as d e t ai led i n
section 7.
Note: This option is only available for scatter charts.
Variables Chart Type Defines chart type. All chart types from se ct io n 5 . 4. 4. 2 a re
available.
Chart Variable Defines chart variable that can be based on all report formulas
from all the areas detailed in section 7.
Style Defines color, line style and symbol type for the chart.

Notes:
For the bubble chart type an additional Circle Diameter parameter is displayed to define the bubble diameter.
For the High Low chart type tw o additional lines are displayed, to define formulas used for start and end values.
For each selected Control Chart option (5.8.22.13) a line is displayed to define the formula.

5.4.4.2 Chart Type

The follow ing chart types are available:

Scatter

• Scatter w ith only points • Scatter w ith points & lines • Scatter w ith points & splines
• Scatter w ith Lines • Scatter w ith Splines

Line
• Line • Line w ith points • Spline w ith points
• Spline

Column
• Column • Stacked column (100%) • Stacked column 3D

• Stacked column • Column 3D • Stacked column (100%) 3D

Area
• Area • Stacked area (100%) • Stacked area 3D
• Stacked area • Area 3D • Stacked area (100%) 3D

Pie & Doughnut

• Pie • Pie 3D • Doughnut 3D

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Chromeleon 7

• Doughnut

Miscellaneous
• Bubble • Range Area • Column range 3D
• High Low • High Low 3D • Range area (100%) 3D

• Column Range

5.4.4.3 Filter Options – Injection Charts

Parameter Sub Parameter Description

Include Injection Types Unknown Displays values from unknown injections.
Calibration Standard Displays values from calibration standard injections.

Check Standard Displays values from check standard injections.

Matrix Displays values from matrix blank injections.

Blank Displays values from blank run injections.

Spiked Displays values from spiked injections.

Unspiked Displays values from unspiked injections.

Custom Conditions And (Any field from the injectio n Restrict the data points shown based on comparing the selected
list – including user defined variable with a user-defined value and using the following logical
columns) arguments:
Is equal to (=)
Is not equal to (<>)
Is larger than (>)
Is smaller than (<)
Is larger than or equal to (=>)
Is smaller than or equal to (=<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
Is during previous
Is not during previous
And [Any field from the inject ion As for the previous parameter.
list – including user defined
columns]

5.4.4.4 Filter Options –Peak Charts

Parameter Sub Parameter Description

Include Peaks Identified Peaks Shows all peaks that have been identified.
Unidentified Peaks Shows all peaks that have not been identified.

Undetected Components Includes rows for those components of the Compone nt t ab le

(in the Processing Method) that have not been detected in t h e
current injection.

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Parameter Sub Parameter Description

Custom Conditions And (Any field from the i nje ctio n Restrict the data points shown based on comparing the
list – including user defined selected variable with a user-defin ed va lu e a nd u sin g t h e
columns) following logical arguments:
Is equal to (=)
Is not equal to (<>)
Is larger than (>)
Is smaller than (<)
Is larger than or equal to (=>)
Is smaller than or equal to (=<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
Is during previous
Is not during previous

And [Any field from the in ject ion As for the previous parameter.
list – including user defined
columns]

5.4.4.5 Grouping Options – Injection Charts

Parameter Sub Parameter Description

Sort the injections according to Injection Number Sorts the injections according to injection number.

Evaluation of this formula Injections are grouped by the user-defined formula base d o n
all report formulas from all the areas detailed in section 7..
Ignore case comparing text results Ignore case when comparing text results.

Use Chromeleon 6 Sort Order Uses the sort order used in Chromeleon 6.
Group Labels Displays group labels in interactive charts.

5.4.4.6 Grouping Options – Peak Charts

Parameter Sub Parameter Description

Sort the peaks according to Peak Number Sorts the peaks according to peak number.
Evaluation of this formula Injections are grouped by the user-defined formula base d o n
all report formulas from all the areas detailed in section 7.
Ignore case comparing text results Ignore case when comparing text results.

Use Chromeleon 6 Sort Order Uses the sort order used in Chromeleon 6.

Group Labels Displays group labels in interactive charts.

5.4.4.7 Title

Parameter Sub Parameter Description

Draw titles Displays interactive chart titles.
Font Allows the font type and size of the titles to be defined.

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Chromeleon 7

Parameter Sub Parameter Description

Left title Draw left title Displays the left part of the title.
When checked the middle part of t h e t i tle can b e d ef ine d
based on all report formulas from all t he are as d e t ai led i n
section 7.
Middle title Draw middle title Displays the middle part of the title.
When checked the middle part of t h e t i tle can b e d ef ine d
based on all report formulas from all t he are as d e t ai led i n
section 7.
Right title Draw right title Displays the right part of the title.
When checked the middle part of t h e t i tle can b e d ef ine d
based on all report formulas from all t he are as d e t ai led i n
section 7.

5.4.4.8 Frame & Axes

Formulas used in this section can combine variables from the follow ing categories:
• Global Functions (7.1) • Peak Calibration (7.12)

• General (7.2) • Peak Purity and Identification (7.13)

• Sequence (7.3) • Processing Method (7.21)
• Injection (0) • Component (7.29)
• Audit Trail (7.5) • Unidentified Peak Group (7.30)
• Preconditions (7.6) • Instrument Method (7.31)
• Chromatogram (7.8) • Custom Formulas (5.8.31)
• Peak results (7.11)

Parameter Sub Parameter Description

Axes Horizontal Axis Displays a horizontal axis on the interactive chart.
Vertical Axis Displays a vertical axis on the interactive chart.

Axes Description Draw Axes Title Applies titles to the interactive chart axes.
Units Displays units on the axes of the interactive chart.

Group labels Displays the group labels.

Horizontal Axis Label Formula Labels horizontal axis with details g e n erat ed b y t he use r-
defined formula based on all report formulas from all the areas
detailed in section 7.
Font Allows the font type and size of the axes to be defined.

Grid Horizontal grid lines Applies horizontal grid lines to the interactive chart.

Vertical grid lines Applies vertical grid lines to the interactive chart.

5.4.4.9 Horizontal Axis

Parameter Sub Parameter Description

Range From Defines the start value of the horizontal axis. Either Auto or a
specific value can be selected.
To Defines the end value of the horizontal axis. Either Auto or a
specific value can be selected.

5.4.4.10 Vertical Axis

Parameter Sub Parameter Description

Settings for axis Determines the vertical axis for which to define the settings. T o b e
able to select between different vertical axes, you have to h ave at
least two chart variables.

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Parameter Sub Parameter Description

Range From Defines the start value of the vertical axis. Either Auto or a specific
time can be selected.
To Defines the end value of the vertical axis. Either Auto or a sp e cif ic
time can be selected.

5.4.4.11 Data Labels

This section defines how peaks should be labeled. The follow ing options are available:

Parameter Sub Parameter Description

Data Point Labels Draw Data Point Labels Labels all data points with details g e ne rat ed b y t h e u se r-
defined formula.
Font Defines the font for data point labels.

Chart variable name Displays the (short) name of chart variable in the label.

X value Displays x value of the data point (for scatter charts only).
Y value Displays y value of the data point.

Report Formula The formula can be based on variables f ro m a ll t he a rea s

detailed in section 7.
Legend Show Legend Displays legend in the upper right corner of the chart. Options:
Inside plot area
Outside plot area

5.4.4.12 Statistics

Function Description
Mean Displays a horizontal line at the average value of the data set.
Linear trend line Displays a linear trend line of the data set.
Show trend line formula includes the linear formula for the trend line in its data label
1s (Mean +/- 1 Std. Deviation) Displays two horizontal lines at the 1s level of significance value of the data set.

2s (Mean +/- 2 Std. Deviation) Displays two horizontal lines at the 2s level of significance value of the data set.

3s (Mean +/- 3 Std. Deviation) Displays two horizontal lines at the 3s level of significance value of the data set.
Font Defines the font for the labels.

5.4.4.13 Control Chart

Function Description
Upper Limit Displays the line of the defined upper limit value or report formula.

Target Displays the line of the defined target value or report formula.

Lower Limit Displays the line of the defined lower limit value or report formula.
Font Defines the font for control chart labels.

Note: The Upper Limit, Target, and Low er Limit values or report formulas have to be defined on the Data Setting
properties page (5.4.4.1).

5.4.4.14 Appearance
This section allow s a consistent color scheme for the objects in the interactive chart to be defined. The follow ing items can
have their line color defined:

• Mean • 3s • Gridlines
• Linear trend line • Upper Limit • Minor Gridlines
• 1s • Target
• 2s • Low er Limit

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Chromeleon 7

The follow ing items can have their fill color defined:
• Back Interior • Chart Interior

Parameter Sub Parameter Description

Border Style n.a. Defines the border style for the interactive chart:
None
Emboss
Arrangement Overlaid All charts are shown overlaid.
Stacked All charts are shown stacked (above each other).

3D Mode n.a. Shows chart as 3-dimensional chart.

5.4.4.15 SmartLink
The follow ing options are available:

Group Sub Parameter Description

Link to Chromatogram N/A Links the object to the chromatogram.

Chromatogram overlays When selected, the injections that are overlaid in the
chromatogram plot for comparison define wh ich i nje ct ion s a re
displayed in the linked objects.
Multiple Peak Selection When selected, the peaks that are selected in the chromato gra m
plot define which peaks are displayed in the interactive chart.
Zoom Area When selected, the zoom area of the chromatogram plot d ef ines
which peaks are shown in the interactive chart.

5.4.5 Contour/3D Plot

The Contour/3D Plot displays the 3D Field of a sample and associated data. When accessed from the layout presets the
view consists of a combination of four panes: - Peak Properties pane, Chromatogram plot, Spectra plot (or I-t plot for 3D
Amperometry) and the Contour/3D plot. The Peak Properties information pane cannot be modified by the display options
w hich are available for the other panes.
Figure 40 show s a typical Contour Plot layout corresponding to a preset pane configuration.

Figure 40: Contour Plot Panes Preset

The follow ing Contour/3D plot options are available.

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5.4.5.1 Scale

Parameter Sub Parameter Description

Time Axis From: Defines the start value of the time axis.

To: Defines the end value of the time axis.

Autoscale When selected the contour plot and th e ch roma to gra m p lot a re
scaled to show the whole chromatogram. This option is also
available in the layout ribbon.
Units Minutes [min] or Seconds [s]

Scan Axis From: Defines the start value of the scan axis.
To: Defines the end value of the scan axis.

Autoscale When selected the contour plot and the spectra plot a re sca l ed t o
show the whole scan range. This option is a l so a vaila ble in t he
layout ribbon.
Signal Axis From: Defines the start value of the signal axis.
To: Defines the end value of the signal axis.

Autoscale When selected the contour plot and th e ch roma to gra m p lot a re
scaled to show the whole signal range.
Gradient Linear scale Signal values are colored using a linear scale.

Logarithmic scale Signal values are colored using a logarithmic scale. Thi s o p tio n i s
also available in the layout ribbon.

5.4.5.2 General

Parameter Sub Parameter Description

View 3D View Displays a three-dimensional view of the 3D d a ta f ield f rom a ny
angle of view.
Data 3D data field If more than one type of 3D data field is available, the required field
can be selected from the list.
Axes Axis to Plot Gap Defines the distance in mm between the axes and the
chromatogram plot.
Font N/A Defines the font to be used for axes and labels in the Contour Plot.
Options Use black for zero Black represents a signal value of zero on t he p lot . T his o p t ion
generates the fewest possible color repeats. A p o int ’s co lo r ca n
change when the scale changes.
Draw optimum integration path Draws the optimum integration path over the plot.

Spectra Retrieval Use raw spectra When selected raw spectra are shown and the UV settings from the
processing method are ignored. This option is also available i n t h e
layout ribbon.

Apply baseline correction settings from When selected the settings selected on the UV Spectra tab page o f
current processing method the processing method are applied to the raw data and include peak
spectrum bunching and baseline correction options. This o p t ion is
also available in the layout ribbon.

5.4.5.3 3D View Settings

Parameter Sub Parameter Description

Show Grid 3D View Shows a grid on the 3D plot.

Rotation X Type or select the angle of rotation around X axis of the 3D plot.
Y Type or select the angle of rotation around Y axis of the 3D plot.

Z Type or select the angle of rotation around Z axis of the 3D plot.

Reset Returns the axes to their default angles of rotation.

Performance N/A Best Quality using the same number of spectra used by the contour
plot. Best Performance using the fewest number of spectra.

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5.4.5.4 Title
This section defines if titles are displayed and how titles should be displayed:

Parameter Sub Parameter Description

Draw titles Shows a title for the contour/3D plot.
Font Allows the font for the contour/3D plot title to be defined.

Left title Draw left title Displays the left part of the title.

Use default When checked left part of the title is shown as in Chrome leon
7.2.
When not checked the left part of t he t i tle c an b e d e fin ed
based on formulas in the edit field.
Center title Draw center title Displays the middle part of the title.

Use default When checked middle part of the title is shown as in

Chromeleon 7.2.
When not checked the middle part of the title can b e d ef ine d
based on formulas in the edit field.
Right title Draw right title Displays the right part of the title.

Use default When checked right part of the title is shown as in Chromeleon
7.2.
When not checked the right part of the t i tle can b e d ef ine d
based on formulas in the edit field.

5.4.5.5 Interactive Settings

Function Description
Show popup controller When this check box is selected, the full-size button, vertical and horizontal z o om
toolbars on the plot axes are visible.

5.4.5.6 Contour/3D Plot Layout Ribbon

In addition, the follow ing options are available in the layout ribbon.

Group Sub Parameter Description

Autoscale Full Size Resizes contour plot, chromatogram plot and spectra p lot so t h a t
the complete chromatogram and wavelength range are shown.
Time Resizes contour plot and chromatogram plot to show the f u ll-tim e
scale.
Scan Resizes the contour plot and spectra plot to show the full scan
scale.
Color Gallery N/A Allows choosing from different color schemes for signa l val ues i n
the contour plot.
Overlays Stop Overlaying Scans Stops multiple scans being overlaid.

Optimum Integration Path Displays optimum integration path on the contour plot.

5.4.5.7 Chromatogram Plot

This Chromatogram plot pane of the Contour Plot layout preset offers the same functionality as the stand-alone
Chromatogram plot.

5.4.5.8 Spectra Plot Properties

This section defines the properties for the spectra plot pane of the Contour Plot layout preset. The follow ing options are
available:

Frame & Axes

Parameter Sub Parameter Description

Axes Wavelength Axis Shows the wavelength axis.

Absorbance Axis Shows the absorbance axis.

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Parameter Sub Parameter Description

Font Allows defining the font to be used for the axes.
Axis to Plot Gap Defines the distance in mm between the axes and the
chromatogram plot.
Axis Titles Axis Titles Shows axis titles.
Units Shows units of the axis.

Font Allows defining the font to be used for the axis titles and units.
Grid Horizontal grid lines Applies horizontal grid lines to the spectra plot.

Vertical grid lines Applies vertical grid lines to the spectra plot.

Normalization None No normalization is performed. Signal response is reported in mAU.

Absolute maximum Performs spectra normalization relative to the absolute maximum of
the spectra.
Relative maximum Performs spectra normalization relative to the relative maximum of
the spectra.
Fixed Wavelength at Performs spectra normalization relative to t he f ixed wa ve leng th
selected.

Label

Parameter Sub Parameter Description

Label Maxima Rotation Defines the angle the spectrum label is shown at.

Maxima count Defines how many maxima should be labeled.

Font Defines the font for the spectrum label.

Options Show match Displays the match of each spectrum with the corresponding m a in
spectrum. The main spectrum is either the p ea k sp e ct ru m, o r a
reference spectrum (spectra comparison), or the top spectrum i n a
spectra library selection.
Show baseline correction info Displays information about the baseline correction in the header.

Interactive Settings

Function Description

Show overview plot When this check box is selected, the miniature overview of the calibra tio n p lo t i s
displayed when zooming into the calibration plot.
Show popup controller When this check box is selected, the full-size button, vertical and horizontal z o om
toolbars on the chromatogram axes are visible.

5.4.5.9 Export
The 3D field can be exported to a text file using the context menu command “Export 3DFIELD (text format)”. The command
launches a dialog w ith further options (Figure 41).

Figure 41: 3D Field Export Dialog Box

The follow ing options are available:

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Chromeleon 7

Parameter Sub Parameter Description

Destination Clipboard Exports a textual description of the 3D data into the clipboard.
File Exports a textual description of the 3D data into a text file.

Additionally, the contour plot can be copied into the clipboard as an image using the Ctrl + C hotkey.

5.4.5.10 Extract
The extract command available from the context menu in the contour plot allow s the user to extract information from the 3D
data.
The follow ing options are available:

Signals
This option allow s a chromatogram measured at any w avelength to be extracted from the 3D data as a new chromatogram
file. The command launches a new dialog w ith further options (Figure 42).

Figure 42: Extract Signal Dialog Box with further options

The follow ing options are available:

Parameter Description
Source 3D field Shows the 3D data field (read-only) from which the signals will be extracted.
Wavelength Wavelength of the chromatogram to be extracted

Use scan interpolation The resolution of a 3D field is, for example, 1.9 nm. Therefore, the data p o int s a re
usually not located at integer wavelengths. Select the Use scan interpolation ch eck
box to calculate the chromatogram at the desired wavelength, via interpolation. If this
check is cleared, Chromeleon uses the chromatogram of the nearest wavelength.
Bandwidth Bandwidth to be used when extracting the chromatogram.

Result channel Channel name of the extracted file.

Apply to the following injections within t he c u rren t Processing action options: current, selected/pinned, all, or specify injection t ype a s
sequence either Unknown, Blank, Check Standard, Calibration Standard, Matrix, Spike d a nd
Unspiked.
Overwrite existing channels Option to overwrite a channel if it already exists in the current sequence.

Optimum Integration Path

A chromatogram that has been recorded at a fixed w avelength usually does not have an optimum Signal-to-Noise Ratio for
all included peaks. The selected w avelength is often a compromise that allow s you to "see" all substances.
It w ould be ideal to detect peak 1 at 230 nm, peak 2 at 254 nm, peak 3 at 320 nm, etc.
This option extracts a chromatogram from the 3D field by selecting the w avelength for each peak that gives the optimum
signal-noise-ratio (Figure 43). Therefore, the w avelength changes throughout the chromatogram.

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Figure 43: Optimum Integration Path Dialog Box

The follow ing options are available:

Parameter Description
Source 3D field Shows the 3D data field (read-only) from which the signals will be extracted.
Original channel Shows the name of the current (original) channel containin g t h e 3 D a bso rb an ce
data.
Bandwidth The bandwidth to be used when extracting the chromatogram.
Result channel Channel name of extracted file.

Apply to the following injections within t he cu rren t Processing action options: current, selected/pinned, all, or specify injection t ype a s
sequence either Unknown, Blank, Check Standard, Calibration Standard, Matrix, Spike d a nd
Unspiked.
Overwrite existing channels Option to overwrite a channel if it already exists in the current sequence.

Extract Amperometry Signals

This option allow s a chromatogram at any w aveform time to be extracted from the 3D Amp data set as a new chromatogram
file. The command launches a new dialog w ith further options.
The follow ing options are available:

Parameter Description

Channel Name Channel name for the extracted file.

Extract Raw Data @ waveform time Extracts raw amperometric data corresponding to a single point along the waveform
axis
Extract integrated data Generates a chromatogram by integrating (summing) the si g nal p o int s o ve r t he
specified integration interval (segment of the wave fo rm). B y d e fa ult , o nl y o n e
integration interval is listed; additional integration intervals can be defined by clicking
on the last row of the table and entering a retention time at which each new interval
should be applied, and the desired start times and end t imes o f t h e in te grat ion
intervals (relative to the waveform cycle).
Use scan interpolation A 3D Amp data set may not have data points at the exact waveform t ime d esi red .
The Use scan interpolation check box calculates the chromatogram at th e d e si red
waveform time, via interpolation. If this check box is cleared, Chromeleon u se s t h e
chromatogram of the nearest waveform time.
Extract to all injections Extracts a chromatogram for each injection in the current sequence.

5.4.6 UV-Vis Spectra Pane

The spectra view can be modified to display peak spectra in various different w ays. Figure 44 show s a typical UV-Vis
spectra view .

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Chromeleon 7

Figure 44: UV-Vis Spectrum View

The follow ing peak spectra display options are available.

5.4.6.1 Scale

Parameter Sub Parameter Description

Apply scaling to all plots N/A When linking is enabled and multiple spectral are disp la yed,
this option determines whether or not the scaling se t t ing s o f
the currently selected plot apply to all linked plots.
Wavelength From Defines the start value of the wavelength axis.
To Defines the end value of the wavelength axis.

Autoscale When this is selected the plot is scaled to show the full
wavelength range of the spectrum.
Fixed intervals of tick marks Chromeleon automatically determines t h e i nt erv a l o f t ic k
marks (the small lines that mark values) on the time axis. T o
customize the intervals, select the Fixed intervals of tick marks
check box and then type or select a number in the Majo r t ick
mark and/or Minor tick mark box. A tick mark inte rva l o f 0 . 0
removes the tick marks.
Absorbance From Defines the start value of the absorbance axis.

To Defines the end value of the absorbance axis.

Autoscale When this is selected the plot is scaled to show the full
absorbance range of the spectrum.
Fixed intervals of tick marks Chromeleon automatically determines t h e i nt erva l o f t ick
marks (the small lines that mark values) on the time axis. T o
customize the intervals, select the Fixed intervals of tick marks
check box and then type or select a number in the Majo r t ic k
mark and/or Minor tick mark box. A tick mark inte rva l o f 0 . 0
removes the tick marks.

5.4.6.2 Frame & Axes

This section allow s defining axes, grid and normalization of the spectral plot.

Parameter Sub Parameter Description

Axes Wavelength axis Displays a wavelength axis on the spectra plot.
Absorbance axis Displays an absorbance axis on the spectra plot.

Font Allows the font type and size of the axes to be defined.

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Parameter Sub Parameter Description

Axis to Plot Gap Defines the distance in mm between the axes and the
chromatogram plot.
Frame Displays a frame around the plot.

Axis Titles Axis Titles Applies titles to the spectra plot axes.
Units Displays units on the axes of the spectra plot.

Font Allows the font type and size of the axis titles to be defined
Grid Horizontal grid lines Applies horizontal grid lines to the spectra plot.

Vertical grid lines Applies vertical grid lines to the spectra plot.

Orientation Horizontal Displays the plot in the landscape orientation.

Vertical Displays the plot in the portrait orientation.

Normalization None No normalization is performed. Signal response is reported in

mAU.
Absolute maximum Performs spectra normalization relative to the absolute
maximum of the spectra.
Relative maximum Performs spectra normalization relative to the relative
maximum of the spectra.
Fixed Wavelength at Performs spectra normalization relative to the fixed
wavelength selected.

5.4.6.3 Title
This section defines if titles are displayed and how titles should be displayed:

Parameter Sub Parameter Description

Draw titles Shows a title for the UV-Vis spectra plot.
Font Allows the font for the UV-Vis spectra plot title to be defined.

Left title Draw left title Displays the left part of the title.
Use default When checked left part of the title is shown as in Chrome leon
7.2.
When not checked the left part of t he t i tle can b e d e fin ed
based on formulas in the edit field.
Center title Draw center title Displays the middle part of the title.

Use default When checked middle part of the title is shown as in

Chromeleon 7.2.
When not checked the middle part of the title can b e d ef ine d
based on formulas in the edit field.
Right title Draw right title Displays the right part of the title.
Use default When checked right part of the title is shown as in Chromeleon
7.2.
When not checked the right part of the t i tle can b e d ef ine d
based on formulas in the edit field.

5.4.6.4 Peak Spectra

This section allow s selecting w hich spectra should be show n.

Parameter Sub Parameter Description

Spectra Sampling Points Apex Spectrum Displays the spectrum at the peak apex.

Front 1 (%) Displays the spectrum at the selected % he igh t o f t he p eak

ascending flank.
Front 2 (%) Displays the spectrum at the selected % he igh t o f t he p eak
ascending flank.
Tail 1 (%) Displays the spectrum at the selected % he igh t o f t he p eak
tailing flank.

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Chromeleon 7

Parameter Sub Parameter Description

Tail 2 (%) Displays the spectrum at the selected % he igh t o f t he p eak
tailing flank.
Reference Spectrum None No reference overly is displayed.

Apex spectrum of recent The spectrum of the currently displayed peak is overl aid wi th
calibration standard the spectrum of the peak with the same name f ro m t h e l ast
calibration standard injection of the sequence.
Apex spectrum of a fixed injection The spectrum of the currently displayed peak is overl aid wi th
the spectrum of the peak with the same name from the
selected injection.

Reference spectrum in The spectrum of the currently displayed peak is overl aid wi th
corresponding component table the reference spectrum from the component table of the
processing method.
Spectral library screening results The spectrum of the currently displayed peak is overl aid wi th
the spectra of the results of the spectral library screening (t h e
number of hits to be shown can be selected).

5.4.6.5 Label
This section allow s defining how labels are show n in the spectral plot.

Parameter Sub Parameter Description

Label Maxima Rotation Defines the angle the spectrum label is shown at.

Maxima count Defines how many maxima should be labeled.

Font Defines the font for the spectrum label.

Options Show match factor Displays the match of each spectrum with the corresp o nd ing
main spectrum. The main spectrum is either the peak
spectrum, or a reference spectrum (spectra compa riso n), o r
the top spectrum in a spectra library selection.
Show baseline correction info Displays information about the baseline correction in the
header.

5.4.6.6 Analysis
This section controls how spectra analysis is performed.

Parameter Sub Parameter Description

Spectra Analysis None No analysis is performed.
Difference Forms the difference between the main sp e ct ru m a nd t h e
remaining individual spectra of the pane. Depending on
whether normalization is performed (see Frame & Axes),
representation of the difference spectra is in percent or in t he
corresponding dimension; for example, mAU.
First derivative Calculates and displays the first derivative of each sp e ct rum
displayed.
Second derivative Calculates and displays the second derivative of each
spectrum displayed.

Background spectra used for Displays the subtracted background spectrum in a se p ara te
baseline correction spectra plot.
Overlay Overlay background spectra used Overlays the spectrum with the spectrum used f o r b ase l ine
for baseline correction correction.

Overlay spectra without base line Overlays each spectrum with the corresp on ding sp e ctru m
correction without baseline correction.

5.4.6.7 Comparison
This section defines comparing multiple spectral. The follow ing options are available:

Parameter Sub Parameter Description

Arrangement Overlaid All overlaid plots are shown in one window.

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Parameter Sub Parameter Description

Stacked All overlaid plots are shown in stacked windows.
Offset Scan Offset Offsets the overlaid plots by the % scan value selected.

Intensity Offset Offsets the overlaid plots by the % intensity value selected.

Overlay Overlay with right signal axis. If selected the overlaid plot is measured against a right si g na l
axis.
Mirror Mirror signal Inverts the intensity axis of the overlaid or stacked plots.

5.4.6.8 Line & Fill Styles

This section allow s the color of each item in the peak spectra plot to be defined. The follow ing items can have their color
defined:
• Grid lines • Uncorrected spectrum • First front spectrum
• Axes • Spectrum 1-8 • Second front spectrum

• Reference Spectrum • Library Spectrum 1-7 • First tail spectrum

• Background spectrum • Apex Spectrum • Second tail spectrum
The follow ing items can have their fill color defined:

• Background

5.4.6.9 SmartLink
The follow ing options are available:

Link to Chromatogram

Group Sub Parameter Description

Link to Chromatogram N/A Links the object to the chromatogram.

Multiple Peak Selection When selected, the peaks that are selected in the chromato gra m
plot define which peaks are displayed in the calibration plot.
Zoom Area When selected, the zoom area of the chromatogram plot d ef ines
which peaks are shown in the calibration plot.

Link to Injection

Parameter Sub Parameter Description

Link to Injections Allows multiple injections to be included in the array of SmartLink objects

Include Current Selections/Pins In addition to those injections specified by type or by custom c on dit ion
(below), the currently selected and pinned injections will be includ ed in
the list of SmartLink injections
Include Injection Types Unknown Displays values from unknown injections.
Calibration Standard Displays values from calibration standard injections.

Check Standard Displays values from check standard injections.

Matrix Displays values from matrix blank injections.

Blank Displays values from blank run injections.

Spiked Displays values from spiked injections.

Unspiked Displays values from unspiked injections.

Custom Conditions Only include injections that match Displays only injections that fulfill certain conditio ns, b a se d o n re port
the following conditions variables.

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Parameter Sub Parameter Description

Link to Injections Allows multiple injections to be included in the array of SmartLink objects
Include Current Selections/Pins In addition to those injections specified by type or by custom con dit ion
(below), the currently selected and pinned injections will be includ ed in
the list of SmartLink injections

ALL (Any field from the inje c tio n Restrict the data points shown based on comparing the selected variable
list – including user defined with a user-defined value and using the following logical arguments:
columns) Is equal to (=)
Is not equal to (<>)
Is larger than (>)
Is smaller than (<)
Is larger than or equal to (=>)
Is smaller than or equal to (=<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty

AND [Any field from the injection As for the previous parameter.
list – including user defined
columns]
or Allows for matching based on only one comparison in the rule
and Forces matching based on every rule in the list. The or sub p a ra met er
overrides the requirement to match every comparison in the specific rule
list.

Display By
Defines how the SmartLink objects w ill be ordered.

Parameter Description
Peaks per injection When a single injection is selected, the peak objects for that injection are plotted in horizontal order.
When multiple injections are selected, each injection has its own row and each peak has its own column.
Injections per peak When a single peak is selected, the peak objects for each injection are plotted in horizontal order.
When multiple peaks are selected, each peak has its own row and each injection has its own column.

5.4.6.10 Interactive Settings

This section defines w hat optional zoom/unzoom tools are displayed on the calibration plot.

Function Description

Show overview plot When this check box is selected, the miniature overview of the plot i s d isp l ay ed
when zooming into the plot.
Show popup controller When this check box is selected, the full-size button, vertical and horizontal z o om
toolbars on the plots axes are visible.

5.4.6.11 Spectra Plot Tools Contextual Ribbon

In addition, the follow ing options are available in the Spectra Plot Tools Contextual ribbon:

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Group Sub Parameter Description

Autoscale Full Size Resizes spectra plot so that the full response and wavelength range
are shown.
Wavelength Resizes spectra plot so that the full wavelength range is shown.

Absorbance Resizes spectra plot so that the full response range is shown.
Library Find in Library Performs a library search in any spectra library available in the
sequence and shows the results in the “Ad Hoc Library Search”
window.
Add Spectrum Adds the currently visible spectrum to the libra ry se l e ct ed in t he
library selection drop list.
Add All Spectra Adds all retention spectra in this chromatogram to the library
selected in the library selection drop list.

N/A (list of spectral libraries in the Selects the library where spectra should be added.
sequence)
Previous peak Selects the previous peak.

Next peak Selects the next peak.

5.4.6.12 Ad Hoc Library Search Window

The figure below show s the results of a library search initiated from the layout ribbon of the spectra plot.
On the upper left criteria for the library search can be defined; on the upper right the currently selected spectrum overlaid
w ith any selected library spectrum is show n.
On the low er half a list of all library matches according to the defined criteria is show n. Spectra can be selected by clicking in
the list holding dow n Shift or Ctrl keys.

Figure 45: Ad Hoc Library Search Window

The follow ing search criteria are available in the Ad Hoc Library Search w indow :

Parameter Sub Parameter Description

Spectral Libraries to be N/A (list of all libraries in the sequence) Each library with a set check mark is included in the search.
searched in It is also possible to specify that all libraries in a given folder wi ll b e
searched.

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Chromeleon 7

Parameter Sub Parameter Description

Spectral Match Conditions Match Criterion Determines the mathematical method that is use d f o r c o mpa ring
spectra.
Least Square: Forms the sum of the squared signal d e via tio ns a t
each wavelength and determines the avera ge sq u a re de viat ion
between two spectra (standard method).
Weighted Least Square: The squared deviations are weighted by the
signal height (for spectra extracted close to the detection limit).
Correlation: Usual match criterion in statistics if a linear co rre lat ion
between two curves is presumed (similar to Least Square ; u su a lly
provides the same result).
Hit Threshold Hits below the specified Match Factor are not returned.

Spectrum Derivative Specifies if library screening is to be performed based on a derivative

of the peak spectrum.
None: Disables library screening based on a derivative of t h e p e ak
spectrum.
1st Derivative: Calculates and displays the first derivat ive o f e ach
spectrum plot displayed. This type of representation increases
absorption or current maxima and thus enables a better evaluation of
whether two spectra plots are from the same substance or not.
2nd Derivative: Calculates and displays the se co nd d eriva tive o f
each spectrum plot displayed. The "exaggeration" of local maxima is
further increased.
Restrict Wavelength Range from Restricts the wavelength range for spectra screening.

5.4.6.13 Export
The spectrum can be exported to a text file using the context menu command “Export Spectrum (text format)”. The
command launches a dialog w ith further options (Figure 46).

Figure 46: Spectrum Export Dialog Box

The follow ing options are available:

Parameter Sub Parameter Description

Destination Clipboard Exports a textual description of the spectru m d at a i nt o t h e
clipboard.
File Exports a textual description of the spectrum data into a t e xt
file.
Options Format Export format: CM-ASCII or STIP-ASCII.

Parameters Options to use baseline correction settings from P ro cessi n g

Method or use fixed scan step.

Additionally, the spectrum plot can be copied into the clipboard as an image using the Ctrl + C hotkey.

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5.4.7 Fluorescence Spectra Pane

The fluorescence spectra pane can be modified to display excitation and emission spectra in various w ays. Figure 47 shows
a typical fluorescence spectra view.

Figure 47: Fluorescence Spectra Pane

The follow ing peak spectra display options are available.

5.4.7.1 Scale

Parameter Sub Parameter Description

Apply scaling to all plots N/A When linking is enabled and multiple spectral are disp la yed,
this option determines whether or not the scaling se t t ing s o f
the currently selected plot apply to all linked plots.
Wavelength From Defines the start value of the wavelength axis.

To Defines the end value of the wavelength axis.

Autoscale When this is selected the plot is scaled to show the full
wavelength range of the spectrum.
Fixed intervals of tick marks Chromeleon automatically determines t h e i nt erva l o f t ick
marks (the small lines that mark values) on the time axis. T o
customize the intervals, select the Fixed intervals of tick marks
check box and then type or select a number in the Majo r t ick
mark and/or Minor tick mark box. A tick mark inte rva l o f 0 . 0
removes the tick marks.
Intensity From Defines the start value of the intensity axis.

To Defines the end value of the intensity axis.

Autoscale When this is selected the plot is scaled to show the full
intensity range of the spectrum.
Fixed intervals of tick marks Chromeleon automatically determines t h e i nt erva l o f t ick
marks (the small lines that mark values) on the time axis. T o
customize the intervals, select the Fixed intervals of tick marks
check box and then type or select a number in the Majo r t ick
mark and/or Minor tick mark box. A tick mark inte rva l o f 0 . 0
removes the tick marks.

5.4.7.2 Frame & Axes

This section allow s defining axes, grid and normalization of the fluorescence spectral plot.

Parameter Sub Parameter Description

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Chromeleon 7

Parameter Sub Parameter Description

Axes Wavelength axis Displays a wavelength axis on the spectra plot.
Intensity axis Displays an intensity axis on the spectra plot.

Font Allows the font type and size of the axes to be defined.

Axis to Plot Gap Defines the distance in mm between the axes and the
chromatogram plot.
Axis Titles Axis Titles Applies titles to the spectra plot axes.
Units Displays units on the axes of the spectra plot.

Font Allows the font type and size of the axis titles to be defined

Grid Horizontal grid lines Applies horizontal grid lines to the spectra plot.
Vertical grid lines Applies vertical grid lines to the spectra plot.

Orientation Horizontal Displays the plot in the landscape orientation.

Vertical Displays the plot in the portrait orientation.

Normalization None No normalization is performed. Signal response is reported in
mAU.
Absolute Maximum Performs spectra normalization relative to the absolute
maximum of the spectra.
Relative Maximum Performs spectra normalization relative to the relative
maximum of the spectra.
Fixed Wavelength at Performs spectra normalization relative to the fixed
wavelength selected.

5.4.7.3 Title
This section defines if titles are displayed and how titles should be displayed:

Parameter Sub Parameter Description

Draw titles Shows a title for the fluorescence spectra plot.
Font Allows the font for the fluorescence sp e c tra p lot t it le t o b e
defined.
Left title Draw left title Displays the left part of the title.
Use default When checked left part of the title is shown as in Chrome leon
7.2.
When not checked the left part of t he t i tle can b e d e fin ed
based on formulas in the edit field.
Center title Draw center title Displays the middle part of the title.

Use default When checked middle part of the title is shown as in

Chromeleon 7.2.
When not checked the middle part of the title can b e d ef ine d
based on formulas in the edit field.
Right title Draw right title Displays the right part of the title.
Use default When checked right part of the title is shown as in Chromeleon
7.2.
When not checked the right part of the t i tle can b e d ef ine d
based on formulas in the edit field.

5.4.7.4 Spectra Filter

This section allow s defining w hich fluorescence spectra are show n.

Parameter Sub Parameter Description

Scan type Any Displays any spectrum found, regardless of the scan type.

Emission Displays emission scans only.

Excitation Displays excitation scans only.

Synchronous Displays synchronous scans only.

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Parameter Sub Parameter Description

Photomultiplier Any Displays any spectrum found, regardless of which
photomultiplier tube (PMT) measured the spectrum.
Photomultiplier 1 Displays spectra measured by the primary PMT only.

Photomultiplier 2 Displays spectra measured by the secondary PMT only.

More Options N/A Adds additional filter criteria.

5.4.7.5 Overlay
This section allow s reference spectra overlays.

Parameter Sub Parameter Description

Reference Overlay None Displays only the fluorescence spectra of the selected peak.

Peak Spectra of recent calibration Overlays the fluorescence spectra from a matching peak fro m
standard the most recent available standard (backwards in time).
Peak Spectra of a fixed injection Overlays the fluorescence spectra from a matching peak fro m
a manually selected injection.

5.4.7.6 Label
This section allow s defining how labels are show n in the spectral plot.

Parameter Sub Parameter Description

Label Maxima Rotation Defines the angle the spectrum label is shown at.

Maxima Count Defines how many maxima should be labeled.

Font Defines the font for the spectrum label.

Options Show match Displays the match of each spectrum with the corresp o nd ing
main spectrum. The main spectrum is either the peak
spectrum, or a reference spectrum (spectra compa riso n), o r
the top spectrum in a spectra library selection.
Show baseline correction info Displays information about the baseline correction in the
header.

5.4.7.7 Analysis
This section controls how spectra analysis is performed.

Parameter Sub Parameter Description

Spectra Analysis None No analysis is performed.

Difference Forms plots representing the difference b et ween t he ma in

spectrum and the remaining individual spectra o f t h e p an e.
Depending on whether normalization is performed (see Frame
& Axes), representation of the difference spectra is in percen t
or in the corresponding dimension.
First derivative Calculates and displays the first derivative of each sp e ct rum
displayed.
Second derivative Calculates and displays the second derivative of each
spectrum displayed.

5.4.7.8 Comparison
This section defines comparing multiple spectral. The follow ing options are available:

Parameter Sub Parameter Description

Arrangement Overlaid All overlaid plots are shown in one window.

Stacked All overlaid plots are shown in stacked windows.

Offset Scan Offset Offsets the overlaid plots by the % scan value selected.

Intensity Offset Offsets the overlaid plots by the % intensity value selected.

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Parameter Sub Parameter Description

Overlay Overlay with right signal axis. If selected the overlaid plot is measured against a right si g na l
axis.
Mirror Mirror signal Inverts the intensity axis of the overlaid or stacked plots.

5.4.7.9 Line & Fill Styles

This section allow s the color of each item in the peak spectra plot to be defined. The follow ing items can have their color
defined:
• Grid lines • Uncorrected spectrum • Second front spectrum

• Axes • Spectrum 1-8 • First tail spectrum

• Reference spectrum • Apex Spectrum • Second tail spectrum
• Background spectrum • First front spectrum
The follow ing items can have their fill color defined:
• Background

5.4.7.10 SmartLink
The follow ing options are available:

Link to Chromatogram

Group Sub Parameter Description

Link to Chromatogram N/A Links the object to the chromatogram.

Multiple Peak Selection When selected, the peaks that are selected in the chromato gra m
plot define which peaks are displayed in the calibration plot.
Zoom Area When selected, the zoom area of the chromatogram plot d ef ines
which peaks are shown in the calibration plot.

Link to Injection

Parameter Sub Parameter Description

Link to Injections Allows multiple injections to be included in the array of SmartLink objects

Include Current Selections/Pins In addition to those injections specified by type or by custom con dit ion
(below), the currently selected and pinned injections will be inc lud ed in
the list of SmartLink injections
Include Injection Types Unknown Displays values from unknown injections.
Calibration Standard Displays values from calibration standard injections.

Check Standard Displays values from check standard injections.

Matrix Displays values from matrix blank injections.

Blank Displays values from blank run injections.

Spiked Displays values from spiked injections.

Unspiked Displays values from unspiked injections.

Custom Conditions Only include injections that match Displays only injections that fulfill certain conditio ns, b a se d o n re port
the following conditions variables.

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Parameter Sub Parameter Description

Link to Injections Allows multiple injections to be included in the array of SmartLink objects
Include Current Selections/Pins In addition to those injections specified by type or by custom c on dit ion
(below), the currently selected and pinned injections will be includ ed in
the list of SmartLink injections

ALL (Any field from the inje ctio n Restrict the data points shown based on comparing the selected variable
list – including user defined with a user-defined value and using the following logical arguments:
columns) Is equal to (=)
Is not equal to (<>)
Is larger than (>)
Is smaller than (<)
Is larger than or equal to (=>)
Is smaller than or equal to (=<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty

AND [Any field from the injection As for the previous parameter.
list – including user defined
columns]
or Allows for matching based on only one comparison in the rule
and Forces matching based on every rule in the list. The or sub p a ra met er
overrides the requirement to match every comparison in the specific rule
list.

Display By
Defines how the SmartLink objects w ill be ordered.

Parameter Description
Peaks per injection When a single injection is selected, the peak objects for that injection are plotted in horizontal order.
When multiple injections are selected, each injection has its own row and each peak has its own column.
Injections per peak When a single peak is selected, the peak objects for each injection are plotted in horizontal order.
When multiple peaks are selected, each peak has its own row and each injection has its own column.

5.4.7.11 Interactive Settings

This section defines w hat optional zoom/unzoom tools are displayed on the calibration plot.

Function Description

Show overview plot When this check box is selected, the miniature overview of the plot i s d isp l ay ed
when zooming into the plot.
Show popup controller When this check box is selected, the full-size button, vertical and horizontal z o om
toolbars on the plots axes are visible.

5.4.7.12 Spectra Plot Tools Layout Ribbon

In addition, the follow ing options are available in the layout ribbon:

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Group Sub Parameter Description

Autoscale Full Size Resizes spectra plot so that the full response and wavelength range
are shown.
Wavelength Resizes spectra plot so that the full wavelength range is shown.

Intensity Resizes spectra plot so that the full intensity range is shown.

5.4.8 I-t Plot Pane

The I-t Plot pane displays plots of current versus w aveform time w hen a selected injection has 3D amperometric data.
These I-t plots may be “Peak I-t Plots”, w hich are retrieved from the chromatographic peak currently selected in the
Chromatogram pane at up to 5 pre-defined points of the peak, and/or “Time I-t Plots” that correspond to manually selected
points along the chromatogram.
Figure 48 show s a typical I-t plot pane display.

Figure 48: I-t Plot Pane

The follow ing display options are available for Peak I-t Plots.

5.4.8.1 Scale

Parameter Sub Parameter Description

Apply scaling to all plots N/A When linking is enabled and multiple spectral are disp la yed,
this option determines whether or not the scaling se t t ing s o f
the currently selected plot apply to all linked plots.
Waveform Time From Defines the start value of the waveform axis.

To Defines the end value of the waveform axis.

Autoscale When this is selected, the plot is scaled to show the full
waveform range of the I-t plot.

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Parameter Sub Parameter Description

Fixed intervals of tick marks Chromeleon automatically determines t h e i nt erva l o f t ick

marks (the small lines that mark values) on the time axis. T o
customize the intervals, select the Fixed intervals of tick marks
check box and then type or select a number in the Majo r t ick
mark and/or Minor tick mark box. A tick mark inte rva l o f 0 . 0
removes the tick marks.
Current From Defines the start value of the response axis.

To Defines the end value of the response axis.

Autoscale When this is selected, the plot is scaled to show the full
response range of the I-t plot.
Fixed intervals of tick marks Chromeleon automatically determines t h e i nt erv a l o f t ic k
marks (the small lines that mark values) on the time axis. T o
customize the intervals, select the Fixed intervals of tick marks
check box and then type or select a number in the Majo r t ick
mark and/or Minor tick mark box. A tick mark inte rva l o f 0 . 0
removes the tick marks.

5.4.8.2 Frame & Axes

This section defines settings for the axes, grid and normalization of the I-t plot.

Parameter Sub Parameter Description

Axes Waveform time axis Displays a waveform time axis on the I-t plot.
Current axis Displays a current axis on the I-t plot.

Font Allows the font type and size of the axes to be defined.
Axis to Plot Gap Defines the distance in mm between the axes and the
chromatogram plot.
Axis Titles Axis Titles Applies titles to the I-t plot axes.
Units Displays units on the axes of the I-t plot.

Font Allows the font type and size of the axis titles to be defined
Grid Horizontal grid lines Applies horizontal grid lines to the I-t plot.

Vertical grid lines Applies vertical grid lines to the I-t plot.

Orientation Horizontal Displays the plot in the landscape orientation.

Vertical Displays the plot in the portrait orientation.

Normalization None No normalization is performed. Signal response is reported in

mAU.
Absolute Maximum Performs I-t plot normalization relative to the absolute
maximum of the I-t plots.
Relative Maximum Performs I-t plot normalization relative to the relative
maximum of the I-t plots.
Fixed Waveform Time at Performs I-t plot normalization relative to the fixed wa v ef orm
time point selected.

5.4.8.3 Title
This section defines if titles are displayed and how titles should be displayed:

Parameter Sub Parameter Description

Draw titles Shows a title for the I-t plot.
Font Allows the font for the I-t plot title to be defined.

Left title Draw left title Displays the left part of the title.
Use default When checked left part of the title is shown as in Chrome leon
7.2.
When not checked the left part of t he t i tle can b e d e fin ed
based on formulas in the edit field.
Center title Draw center title Displays the middle part of the title.

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Chromeleon 7

Parameter Sub Parameter Description

Use default When checked middle part of the title is shown as in
Chromeleon 7.2.
When not checked the middle part of the title can b e d ef ine d
based on formulas in the edit field.
Right title Draw right title Displays the right part of the title.
Use default When checked right part of the title is shown as in Chromeleon
7.2.
When not checked the right part of the t i tle can b e d ef ine d
based on formulas in the edit field.

5.4.8.4 Peak I-t Plots

This section defines w hich I-t plots are show n.

Parameter Sub Parameter Description

I-t plot Sampling Points Apex I-t plot Displays the I-t plot at the peak apex.

Front 1 (%) Displays the I-t plot at the selected % height of the peak
ascending flank.
Front 2 (%) Displays the I-t plot at the selected % height of the peak
ascending flank.
Tail 1 (%) Displays the I-t plot at the selected % height of the peak tailing
flank.
Tail 2 (%) Displays the I-t plot at the selected % height of the peak tailing
flank.
Reference Overlay None No reference overlay is displayed.

Apex I-t plot of recent calibrat ion The I-t plot of the currently displayed peak is overlaid with the I-
standard t plot of the peak with the same name from the last calibrat ion
standard injection of the sequence.
Apex I-t plot of a fixed injection The I-t plot of the currently displayed peak is overlaid with the I-
t plot of the peak with the same name from the selected
injection.

5.4.8.5 Label
This section defines how labels are show n in the I-t plot.

Parameter Sub Parameter Description

Label Maxima Rotation Defines the angle at which the I-t plot label is shown.

Maxima Count Defines how many maxima should be labeled.

Font Defines the font for the I-t plot label.

Options Show match factor Displays, in the caption for each I-t plot, the match f act or f o r
that I-t plot relative to the corresponding main I-t plot. The main
I-t plot is either the peak I-t plot, or a reference I-t plot (I -t p lo t
comparison).
Show baseline correction info Displays information about baseline correction in the caption of
each I-t plot.

5.4.8.6 Analysis
This section controls how I-t plot analysis is performed.

Parameter Sub Parameter Description

I-t plot Analysis None No analysis is performed.

Difference Forms the difference between the main I-t plot and the
remaining individual I-t plot s o f t he p an e. De p en ding o n
whether normalization is performed (see Frame & Axes),
representation of the difference I-t plots is in percent or in t h e
corresponding dimension (nA).

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Parameter Sub Parameter Description

First derivative Calculates and displays the first derivat ive o f ea ch I -t p lot
displayed.
Second derivative Calculates and displays the second derivative of each I-t p lot
displayed.

5.4.8.7 Comparison
This section defines comparing multiple spectral. The follow ing options are available:

Parameter Sub Parameter Description

Arrangement Overlaid All overlaid plots are shown in one window.

Stacked All overlaid plots are shown in stacked windows.

Offset Scan Offset Offsets the overlaid plots by the % scan value selected.

Intensity Offset Offsets the overlaid plots by the % intensity value selected.

Overlay Overlay with right signal axis. If selected the overlaid plot is measured against a right si g na l
axis.
Mirror Mirror signal Inverts the intensity axis of the overlaid or stacked plots.

5.4.8.8 Line & Fill Styles

This section defines the color of each item in the peak I-t plot. The follow ing items can have their color defined:
• Grid Lines • Uncorrected I-t plot • Second Front I-t plot

• Axes • I-t plot 1-8 • First Tail I-t plot

• Reference I-t plot • Apex I-t plot • Second Tail I-t plot
• Background I-t plot • First Front I-t plot
The follow ing items can have their fill color defined:

• Background

5.4.8.9 SmartLink
The follow ing options are available:

Group Sub Parameter Description

Link to Chromatogram N/A Links the object to the chromatogram.

Multiple Peak Selection When selected, the peaks that are selected in the chromato gra m
plot define which peaks are displayed in the calibration plot.
Zoom Area When selected, the zoom area of the chromatogram plot d ef ines
which peaks are shown in the calibration plot.

5.4.8.10 Interactive Settings

This section defines w hat optional zoom/unzoom tools are displayed on the calibration plot.

Function Description

Show overview plot When this check box is selected, the miniature overview of the plot i s d isp l ayed
when zooming into the plot.
Show popup controller When this check box is selected, the full-size button, vertical and horizontal z o om
toolbars on the plot’s axes are visible.

5.4.8.11 I-t plot Layout Ribbon

In addition to the above settings, w hich are all available via the Properties dialog of the I-t Plot Pane, the follow ing options
are available in the layout ribbon:

Parameter Sub Parameter Description

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Chromeleon 7

Parameter Sub Parameter Description

Autoscale Full Size Resizes I-t plot so that the full response and wavef orm ra n ge a re
shown.
Waveform Time Resizes I-t plot so that the full waveform range is shown.

Current Resizes I-t plot so that the full current range is shown.

5.4.8.12 Export
The I-t plot can be exported to a text file using the context menu command “Export Spectrum (Text format)”. The command
launches a dialog w ith further options (Figure 49).

Figure 49: Spectrum Export Dialog Box

The follow ing options are available:

Parameter Sub Parameter Description

Destination Clipboard Exports a textual description of the spectru m d at a i nt o t h e
clipboard.
File Exports a textual description of the spectrum data into a t e xt
file.
Options Format Export format: CM-ASCII or STIP-ASCII.

Parameters Options to use baseline correction settings from P ro cessi n g

Method or use fixed scan step.

Additionally, the I-t plot can be copied into the clipboard as an image using the Ctrl + C hotkey.

5.4.9 Interactive Results Pane

The interactive results tables contain a set of report tables that provide a screen view of the chromatographic data. Each
specific report table has its ow n specific data and can be customized as required.
The report tables that can be included are the same as the report tables in the Report Template (except the Fraction and
Tube Report tables):
• Results Table: Integration (see section 5.8.15.2)
• Results Table: Peak Summary (see section 5.8.15.3)
• Results Table: Consolidated Table (see section 5.8.15.4)

• Results Table: Test Case (see section 5.8.15.5)

• Results Table: MS Raw Spectra (see section 5.8.15.6)
• Results Table: Frame Table (see section 5.8.15.7)
• Results Table: Tentative Identification (see section 5.8.15.8)
• Processing Method Table: Component Table (see section 5.8.15.10)

• Processing Method Table: Peak Group Table (see section 5.8.15.13)

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 Chromeleon 7

• Processing Method Table: Detection Settings (see section 5.8.15.14)

• Processing Method Table: Calibration History (see section 5.8.15.15)
• Processing Method Table: System Suitability IRC (see section 5.8.15.16)
• Processing Method Table: MS Detection Settings (see section 5.8.15.17)
• Processing Method Table: Peptide Table (see section 5.8.15.18)

• Instrument Method Table: Overview (see section 5.8.15.19)

• Instrument Method Table: Script (see section 5.8.15.20)
• Instrument Method Table: MS Instrument Method (XRAW) (see section 5.8.15.21)
• Instrument Method Table: MS Tune (see section 5.8.15.22)
• Instrument Method Table: Smart Startup/Shutdow n/Standby Settings (see section 5.8.15.23)
• Instrument Method Table: Extended (see section 5.8.15.24)
• Status and Audit Table: Audit Trail (see section 5.8.15.25)
• Status and Audit Table: Data Audit Trail (see section 5.8.15.26)
• Status and Audit Table: Chromeleon 6 History (see section 5.8.15.26)
• Status and Audit Table: MS Device Information (see section 5.8.15.28)
• Status and Audit Table: MS Status Log (see section 5.8.15.31)
• Fractionation Table: Fraction Report (see section 5.8.15.32)
• Fractionation Table: Tube Report (see section 5.8.15.33)
Additionally, for the tables that support this, the grouping options apply (see section 5.8.15.1).

5.4.10Injection Rack Pane

The injection rack pane provides a graphical display of the injection vial positions for the current sequence in the assigned
instruments autosampler. The follow ing options are available:

Function Description

Copy to Clipboard Copies the current rack image to the clipboard.

Full Size Scale the rack view to full size.

Zoom in (+) Zoom into the rack view.

Zoom out (-) Zoom out of the rack view.

In the Injection Rack pane properties dialog, there are several options:

5.4.10.1 General

Parameter Sub Parameter Description

Show Overview Displays the rack overview in the top right corner of t he ra ck
view.
Positions Displays the vial positions in the rack view. (Only visible when
zoom allows.)

Tray name Displays the tray names on the rack view.

Visible Trays Show all trays Shows all configured trays for the select ed a ut osa mp ler i f
supported.

Hide inactive tray Hides trays that are configured but do not contain any
injections (i.e. are not used) in the current sequence.

5.4.10.2 Title

Parameter Sub Parameter Description

Draw Title N/A Displays the title in the top center of the plot.

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Chromeleon 7

Parameter Sub Parameter Description

Font N/A Allows defining the font to be used for the title of the plot.

5.4.10.3 Tooltip

Function Description

Enable tooltip Displays information about a vial/tube.

Tooltip formula The content of the tooltip can be adapted depending on the context the Rack V i e w
control is used, based on variables contained in the Injection category section 7. X.

5.4.10.4 Interactive Settings

Parameter Sub Parameter Description

Scaling Enable scaling Disables zooming of the rack view.

Rotation Enable rotation Disables rotation of the rack view.

5.4.11Fraction Tray Pane

The fraction tray pane provides a graphical display of the fraction tube positions for the current sequence in the assigned
instruments autosampler. The follow ing options are available:

Function Description
Copy to Clipboard Copies the current rack image to the clipboard.

Full Size Scale the rack view to full size.

Zoom in (+) Zoom into the rack view.

Zoom out (-) Zoom out of the rack view.

In the Fraction Tray pane properties dialog, there are several options:

5.4.11.1 General

Parameter Sub Parameter Description

Show Overview Displays the rack overview in the top right corner of t he ra c k
view.

Positions Displays the vial positions in the rack view. (Only visible when
zoom allows.)

Tray name Displays the tray names on the rack view.

5.4.11.2 Title

Parameter Sub Parameter Description

Draw Title N/A Displays the title in the top center of the plot.

Font N/A Allows defining the font to be used for the title of the plot.

5.4.11.3 Fill styles

In the fraction tray, the fill colors of various objects can be defined. The follow ing options are available:

Parameter Sub Parameter Description

Tubes collected during sequence run N/A Defines the color for all tubes collected during the current sequence

Tubes collected from current injection N/A Defines the color for all tubes from the currently selected injection

Currently selected tube/fraction N/A Defines the color of the currently selected tube or fraction

5.4.11.4 Tooltip

Function Description

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Function Description
Enable tooltip Displays information about a vial/tube.

Tooltip formula The content of the tooltip can be adapted depending on the context the Tray V ie w
control is used, based on variables contained in the Injection category section 7. X.

5.4.11.5 Interactive Settings

Parameter Sub Parameter Description

Scaling Enable scaling Disables zooming of the rack view.

Rotation Enable rotation Disables rotation of the rack view.

5.4.12Mass Spectrum Pane

The Mass Spectrum view allow s the user to graphically view and interact w ith the mass spectrum plot(s) extracted fr om the
sample data. Figure 50 show s a typical mass spectrum view :

Figure 50: Mass Spectrum View in Chromatography Studio

5.4.12.1 Zooming and Navigating in the Mass Spectrum

The mass spectrum view allow s zooming and navigating as required w ith the follow ing options:

Function Description
Zoom When active it is possible to zoom into the chromatogram by dragging an area.

Undo Zoom Reverts the recent zoom operation and returns to the previous view. Accesse d b y
right-clicking on the plot and selecting Unzoom
Full Scale Reverts the recent all zooming and re-plots the data full scale. Accessed b y ri gh t-
clicking on the plot and selecting Full Scale

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Chromeleon 7

Function Description
Y axis zoom tools Shown when moving the cursor over the Y axis. The following functions are
available:
+ zooms into the plot vertically
Autoscale Signal resizes the plot height to the highest mass abundance cu rre nt ly
visible
- zooms out of the plot vertically

X axis zoom tools Shown when moving the cursor over the X axis. The following functions are
available:
+ zooms into the plot horizontally
Autoscale Time resizes the plot to the complete mass range of the acquired data.
- zooms out of the plot horizontally
Full size button Shown when moving the cursor to the bottom left corner of the plot. Click t h e f u ll-
size button to autoscale both axes simultaneously.

In addition, the follow ing zoom operations are available:

Function Description
Double Click on the abundance axis Automatically resizes the plot height to the highest m a ss a b u nd an ce cu rren tly
visible.
Double Click on the m/z axis Automatically resizes the plot width to the complete mass pane of the acquired data

Undo Zoom Reverts the recent zoom operation and returns to the previous view.
Drag the abundance axis Scrolls the y axis limits

Drag the m/z axis Scrolls the x axis limits

The follow ing context menu operations are also available:

5.4.12.2 Copy
Copies the mass spectrum plot to the clipboard as an image. This is also possible by using the Ctrl + C hotkey.

5.4.12.3 Zero M ass Offset

The zero-mass offset feature lets you set any mass on the mass spectral plot as the zero mass point. The masses of all
mass peaks on the plot are then show n relative to the new zero point. To use, point to the mass on the mass spectral plot
that you w ant to set as the new zero point, and select this context menu item.

5.4.12.4 Remove Zero M ass Offset

Removes any previously set zero mass offset for the plot.

5.4.12.5 Extract Ion Chromatogram

The function allow s the user to extract ion chromatograms from the data set. Selecting this context menu item displays the
follow ing dialog:

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Figure 51: Extract Mass Spectrum Channel

Parameter Description
Trace Specify the chromatogram trace type to be extracted
TIC (Total Ion Current)—all ions matching the filter entered in the Filter list will be extracted from the
raw data.
Base Peak—base peak ions that match the filter entered in the Filter list will be extracted f ro m t he
raw data.
Mass Range—ions that match the filter entered in the Filter list and with a mass that m atch es t h e
mass or mass range entered in the Mass range(s) box will be extracted from the raw data.
Filter Specifies the acquisition filter from which the chromatogram will be extracted

Mass ranges Defines the mass, mass range, or a set of mass ranges to be extracted

Smoothing Specifies the type of smoothing to be performed on the chromatogram data when it is extracted.
Channel Name Defines the label that will be used to identify this extracted ion chromatogram in the channels list

Make channel permanent Creates a permanent channel when selected or if check bo x i s cl ea r a t emp ora ry cha nn el i s
created.

5.4.12.6 Clear Temporary Extract Ion Chromatograms

Removes any temporary ion chromatograms previously extracted from the data

5.4.12.7 Export Spectrum

Exports the mass spectrum to a text file. The follow ing options are available:

Parameter Sub Parameter Description

Destination Clipboard Exports a textual description of the mass spectrum dat a i nt o
the clipboard.
File Exports a textual description of the mass spectrum data into a
text file.
Format CM-ASCII The exported mass spectrum contains complete information
STIP-ASCII The exported mass spectrum plot contains condensed
information
Parameters Use baseline correction settings Uses the baseline correction settings from MS settings tab o f
from Processing method the processing method
Use fixed scan step Changes the resolution for the exported mass spectrum

5.4.12.8 Remove Time Spectra

Removes any time spectra plots sharing the pane w ith the peak spectrum

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Chromeleon 7

5.4.12.9 Find in Library

This menu item performs an ad hoc library search on the displayed mass spectrum using the parameters specified on the
MS Library Search tab of the processing method.
The follow ing search window is displayed:

Figure 52: Ad Hoc Library Search Window

In the top section, criteria for the library search can be defined. In the middle section, search results are displayed. In the
bottom section, the reference and library spectra are displayed.
The follow ing search criteria are available in the Ad Hoc Library Search w indow :

Parameter Sub Parameter Description

MS Libraries to be N/A (list of all libraries in the sequence) Each library with a set check mark is included in the search.
searched in
Search Type Identity Three options are available:
Normal: Uses a standard pre-screen search filter. This is the default
search type.
Quick: Uses a fast pre-screen search filter.
Penalize Rare Compounds: Limits the impact of rare compounds b y
reducing their match factors. This option is effective only wh en you
have selected a NIST Mass Spectral Library (such as, m a inlib ). I t
has no effect on spectra in internal NIST libraries or other
commercial libraries.
Each reference spectrum in a NIST Mass Spectral Library contains a
record of other commercial libraries containing information about the
compound. A compound is considered 'rare' if it is present in a
limited number of these libraries.

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Parameter Sub Parameter Description

Similarity Simple: Finds a large set of spectra to compare with the su b m itt ed
spectrum. This search option is generally slower t h an a n i den tit y
search.
Hybrid: Uses a combination of the Simple and Neutral Loss se a rch
types. When Hybrid is selected, the Search with Mol. Weight edit box
under Search Options is enabled. Enter an estimate of the submitted
spectrum's molecular weight.
Neutral Loss: Compares neutral losses of the submitte d sp e ct rum
with spectra in the library data. The neutral losses in a spectrum a re
the mass differences between the molecular ion a n d o th er m ajo r
ions in the spectrum. For certain classes o f co m p o und s, n eu tra l
losses can be a very characteristic spectral feature. In a Neutral Loss
search, Chromeleon identifies the molecular ion o f t h e su b mit te d
spectrum and includes the molecular ion in the search, a long wit h
the spectrum. Significant neutral losses of the submitte d sp e ct rum
are calculated and compared with the library data. Hits are return ed
according to matches of the molecular ion and i ts n e u tra l l osse s.
When Neutral Loss is selected, the Search with Mol. Weight edit box
under Search Options is enabled. Enter an estimate of the submitted
spectrum's molecular
Search with Molecular Wt When a value is supplied, searches will be restricted to library entries
with the indicated molecular weight.
Reverse Search When checked, this parameter indicates that a reverse search will be
performed instead of a standard search
Thresholds Match Factor Defines the minimum match factor below which matches will no t b e
reported
Reverse Match Factor Defines the minimum reverse match factor below which matches will
not be reported
Probability Defines the minimum probably below which m at ch es wi l l n ot b e
reported

5.4.12.10 Elemental Composition…

This menu item displays a pop up w indow for investigating various possible chemical formulas w hich are consistent w ith the
selected mass.
The defaults setting for this w indow are taken from the Elemental Composition property page, but may be changed in the
dialog. The function is only available for HRAM mass spectra.

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Chromeleon 7

.
Figure 53: Ad Hoc Elemental Composition Window

Section Parameter Description

Selected Mass Specifies the exact mass (more precisely, the mass-to-
charge ratio, m/z) to be analyzed for elemental composition.
This field is read-only. To select a new mass to analyze, click
inside the ad-hoc MS plot that is displayed on the right.
Max. # Candidates Specifies the number of the highest-ranking candidate
chemical formulas to display in the results table below . The
default value is 10.
Prediction Settings and Elements These sections have fields identical to those displayed in
in Use: the Elemental Composition page of the Mass Spectra
Ad-hoc Properties.
Elemental Composition Initially, the fields are also populated w ith the same values,
Settings but the settings here can be updated w ithout affecting the
Mass Spectra pane plot.
Clicking Update Results only applies the settings to the ad-
hoc MS plot on the right and refreshes the results in the table
below . When this dialog is closed, the settings in the
Properties dialog are the same as they w ere before any ad-
hoc elemental composition analysis.
Update Results Clicking Update Results applies the settings to the ad-hoc
MS plot on the right and refreshes the results in the table
below .

The MS Plot w indow is a simplified version of the mass spectra plots displayed in the Mass Spectra pane. The plot
supports:
• Quick selection of mass to be analysed. Click inside the plot to select the mass to be analyzed for mass composition.
The selected value is displayed in the Selected Mass in the settings area to the left. To select precisely the mass of
a peak, click the formula above the peak.

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• Zooming in and out: This w orks the same as normal zoominng and unzooming. The Unzoom and Full Size options
can also be found in the right-click menu.
• Copying: The plot also enables copying and pasting into other applications. To copy the plot into the clipboard, right-
click the plot and select Copy

The Results table lists the highest-ranking results of elemental composition analysis for the selected mass, using analysis
settings as specified in the settings area above. To update the table for new settings, click the Update Results button.
Note: The table supports re-sizing of columns, custom re-ordering of column order and sorting of result row s by any of the
columns (in the case of Delta Mass, by its absolute value). These custom settings for the dialog layout are saved to the user
profile.
The follow ing columns are displayed in the results table:

Column Description

Rank The order of scoring of the candidate formula, w here 1 is the best.
Formula The candidate chemical formula that w as considered and scored.
Score A composite value summarizing how w ell the candidate formula fits the measured data. Value 100
means a perfect match, value 0 means completely different results.
Theo. Mass Theoretical mass (more precisely, the mass-to-charge ratio, m/z) of the candidate formula.
Delta Mass (ppm) The absolute difference betw een the theoretical m/z value of the considered formula and the
measured m/z value that is targeted.

Matched Peaks Number of peaks in measured data that match the theoretical isotope pattern calculated around the
candidate formula.
Spectral Distance The total distance, w here each fragment is searched in a range from the expected mass based on
the chemical formula and the expected mass plus the delta mass between the precursor ion and its d i sp la ye d
formula.

RDB Displays the number of ring and double-bond equivalents that w as calculated for the candidate formula

The follow ing sections describe the tabs of the Properties dialog accessed from the context menu.

5.4.12.11 Scale

Parameter Sub Parameter Description

Apply scaling to all plots N/A Allows the user to apply the same scaling to all plots
simultaneously when checked.
Mass From Defines the start value of the mass axis.

To Defines the end value of the mass axis.

Autoscale When this is selected the plot is scaled to show the ful l ma ss
range of the data
Fixed intervals of tick marks Chromeleon automatically determines t h e i nt erva l o f t ick
marks (the small lines that mark values) on the time axis. T o
customize the intervals, select the Fixed intervals of tick marks
check box and then type or select a number in the Majo r t ick
mark and/or Minor tick mark box. A tick mark inte rva l o f 0 . 0
removes the tick marks.
Intensity From Defines the start value of the intensity axis.
To Defines the end value of the intensity axis.

Autoscale When this is selected the plot is scaled to show the full
intensity range of the mass spectrum.
Fixed intervals of tick marks Chromeleon automatically determines t h e i nt erva l o f t ick
marks (the small lines that mark values) on the time axis. T o
customize the intervals, select the Fixed intervals of tick marks
check box and then type or select a number in the Majo r t ic k
mark and/or Minor tick mark box. A tick mark inte rva l o f 0 . 0
removes the tick marks.

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5.4.12.12 Frame & Axes

This section allow s defining axes, grid and normalization of the mass spec plot.

Parameter Sub Parameter Description

Axes Mass axis Displays a mass axis on the mass spec plot.
Intensity axis Displays an abundance axis on the mass spec plot.

Font Allows the font type and size of the axes to be defined.

Axis to Plot Gap Defines the distance in mm between the axes and the plot.
Frame Displays a frame around the plot

Axis Titles Axis Titles Applies titles to the mass spec plot axes.
Units Displays units on the axes of the mass spec plot.

Font Allows the font type and size of the axis titles to be defined

Grid Horizontal grid lines Applies horizontal grid lines to the mass spec plot.
Vertical grid lines Applies vertical grid lines to the mass spec plot.

Orientation Horizontal Scan type is the horizontal axis, and signal is the vertical axis

Vertical Scan type is the vertical axis, and signal is the horizontal axis.
Normalization None No normalization is performed.

Absolute maximum Performs spectra normalization relative to the absolute

maximum of the spectra.

5.4.12.13 Title
This section defines if titles are displayed and how titles should be displayed:

Parameter Sub Parameter Description

Draw titles Shows a title for the fluorescence spectra plot.

Font Allows the font for the fluorescence sp e ctra p lot t it le t o b e

defined.
Left title Draw left title Displays the left part of the title.
Use default When checked left part of the title is shown as in Chrome leon
7.2.
When not checked the left part of t he t i tle can b e d e fin ed
based on formulas in the edit field.
Center title Draw center title Displays the middle part of the title.

Use default When checked middle part of the title is shown as in

Chromeleon 7.2.
When not checked the middle part of the title can b e d ef ine d
based on formulas in the edit field.
Right title Draw right title Displays the right part of the title.
Use default When checked right part of the title is shown as in Chromeleon
7.2.
When not checked the right part of the t i tle can b e d ef ine d
based on formulas in the edit field.

5.4.12.14 Peak Spectra

This section allow s selecting w hich auxiliary mass spectra should be show n.

Parameter Sub Parameter Description

Spectra Sampling Points Apex Spectrum Displays the mass spectrum at the peak apex as a thumbnail

Front 1 (%) Displays the mass spectrum at the selected % h e ight o f t he

peak ascending flank as a thumbnail.
Front 2 (%) Displays the mass spectrum at the selected % h e ight o f t he
peak ascending flank as a thumbnail.

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Parameter Sub Parameter Description

Tail 1 (%) Displays the mass spectrum at the selected % h e ight o f t he

peak tailing flank as a thumbnail.
Tail 2 (%) Displays the mass spectrum at the selected % h e ight o f t he
peak tailing flank as a thumbnail.
Reference Spectrum None No reference overly is displayed.

Apex spectrum of recent The mass spectrum of the currently displayed peak is overlaid
calibration standard with the mass spectrum of the peak with the same name f rom
the last calibration standard injection of the sequence.
Apex spectrum of a fixed injection The mass spectrum of the currently displayed peak is overlaid
with the mass spectrum of the peak with the same name f rom
the selected injection.
Spectral library screening results The mass spectrum of the currently displayed peak is overlaid
with the mass spectra of the results of the spectral library
screening (the number of hits to be shown can be selected).

5.4.12.15 Label
This section allow s defining how labels are show n in the mass spectral plot.

Parameter Sub Parameter Description

Peak Label Rotation Defines the angle the mass spectrum label is shown at.
Maximum threshold The threshold intensity (in %) at which ma ss p e a ks wi l l b e
labeled
Font Defines the font for the mass spectrum label.

Options Show baseline correction info Displays information about the baseline correction in the
header.

Show detected mass info for peak Checking this box will cause the detected mass f o r t h e p e ak
spectra spectrum to be displayed horizontally on top of the mass peak.
If the monitored mass is not detected, no information is
displayed.

Show detected mass info for time Checking this box will cause the detected mass f o r t h e t i me
spectra spectrum to be displayed horizontally on top of the mass peak.
If the monitored mass is not detected, no information is
displayed.

5.4.12.16 Analysis
This section controls how mass spectra analysis is performed.

Parameter Sub Parameter Description

Spectra Analysis None No analysis is performed.

Difference Forms the difference between the main mass spect ru m a n d
the remaining individual mass spectra of the pane. Depending
on whether normalization is performed (see Frame & A xes),
representation of the difference mass spectra is in percen t o r
in the corresponding dimension;

Background spectra used for Displays the subtracted background spectrum in a se p ara te
baseline correction spectra plot.
Overlay Overlay background spectra used Overlays the mass spectrum with the mass spectrum used for
for baseline correction baseline correction.

Overlay spectra without base line Overlays each mass spectrum with the correspond ing ma ss
correction spectrum without baseline correction.

5.4.12.17 Elemental Composition

This section contains the parameters used for performing Elemental Composition analysis, w hich is a prediction of the most
likely chemical formula for the m/z values in the mass spectrum, These formulas may be displayed directly on the mass
spectrum plot.
Note: Elemental Composition is only performed on HRAM spectra, and may not return any results if the entered parameters
do not yield any potential formulas

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Chromeleon 7

Parameter Description

Mass Tolerance Specifies a mass tolerance that restricts the elemental compositions that a re co nsi de red . T he a lg orit hm
returns a result only if the theoretical mass matches the submitted mass within the specified tolerance.
Available units are:
PPM: parts-per-million (default)
AMU: atomic mass units
MMU: millimass units
Note: If the tolerance is specified in PPM, the absolute tolerances are mass-dep en den t a n d g et l arg er a t
higher masses and smaller at lower masses.
Charge Specifies the charge state that is used to calculate the candidate molecular formulas.
Min/Max RDBE These fields specify a range of values for the ring and double bond e quiva lent s (RDB E ) t h a t l imit s t h e
considered formulas to those that make sense chemically.
Nitrogen Rule Specifies whether or how to use the nitrogen rule in the formula calculation:
Even Electron Ions (default): Select this option if the targeted ion is an even-electron ion, such as prot ona te d
molecular ions arising from chemical ionization.
Odd Electron Ions: Select this option if the targeted ions is an odd-electron, such as radical-cation mo lec ula r
ions arising from electron ionization.
Note: Nitrogen rule is often used to narrow down the ion parity based on knowing t h e n umb er o f n itro ge n
atoms. This case is the reverse, to narrow down the number of nitrogen atoms to odd o r e ven va lu es, i on
parity must be provided.
Centroid Algorithm Specifies the centroiding algorithm for profile data. The selection should be based on the MS instrument use d
for measuring the data.
Normalization Mode Specifies one of the following normalization modes for the spectral peak intensities:
Base peak (default): The most common normalization mode. Normalizes the isotope peaks to the base p ea k
height of 100%. Its disadvantage is the propagation of the intensity error o f t h e b ase p e ak t o a l l iso t o pe
intensities.
Linear: Normalizes the theoretical and measured patterns so that the sum of all isotopic pattern inten sit ies i s
the same.
Quadratic: Normalizes the theoretical and measured patterns so that the error squares (intensity differe nces)
are minimized.

Use Representative Specifies which isotope abundance table is used by the elemental composition analysis algorithm.
Elements When this check box is selected (default), the elemental analysis algorithm uses the Representative Elements
table, where the abundance of 12C is 0.9893 and the abundance of 13C is 0.0107.
Clear the check box to use the Protein Elements table, where the abundance of 12C is 0.989136445 and t h e
abundance of 13C is 0.010863555.
Intensity Threshold % Specifies the isotope intensity threshold (relative to the base peak of the theoretical isotope pattern) t h at t he
algorithm considers in scoring candidate chemical formulas. If the expected intensity of an isotopic pe ak i n a
simulated pattern is below the threshold, the algorithm does not lo ok f o r t h e p eak i n t h e e xpe rimen ta l
spectrum, and the peak is not part of the score calculation.
Elements in Use This table defines which isotopes of elements and how many atoms of a given isotope are considered wh en
the algorithm calculates candidate elemental compositions for the submitted mass value.
Isotope: Lists the isotopes that the algorithm will consider wh en i t calcu lat es t h e ca ndid at e e lem ent al
compositions for a monoisotopic ion with a given mass.
Mass: Displays the exact isotopic mass for each isotope. These values are read-only and cannot be edited.
Min: Specifies the smallest considered number of atoms of the given isotope in the molecular formula. Range:
0 to 10000.
Max: Specifies the largest considered number of atoms of the given isotope in the molecular formula. Range :
0 to 10000.

5.4.12.18 Comparison
This section allow s defining how multiple mass spectra are arranged

Group Sub Parameter Description

Arrangement Stacked Plots are stacked on a single plot and share the sa m e sca n a xis;
each stacked plot has a separate intensity axis.
Overlaid Plots are overlaid on a single plot and share t h e sa m e sca n a n d
intensity axes

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Group Sub Parameter Description

Offset Scan Offset To offset overlaid plots on the scan axis, select the check b o x a nd
enter the offset percentage in the box.
Intensity Offset To offset overlaid plots on the intensity axis, select t he che ck b o x
and enter the offset percentage in the box
Overlay Overlay with right signal axis When plots are overlaid, select this check box to include a se co n d
signal axis on the right side of the plot
Mirror Mirror Signal Select this check box to invert the intensity axis of t h e o verla id o r
stacked plots. The plots "mirror" the main spectrum or I-t plot.

5.4.12.19 Line & Fill Styles

This section allow s the color of each item in the mass spec plot to be defined. The follow ing items can have their color
defined:
• Grid lines • Uncorrected spectrum • Second front spectrum
• Axes • Spectrum 1-8 • First Tail spectrum

• Reference • Apex Spectrum • Second tail spectrum

• Background spectrum • First front spectrum •
The follow ing items can have their fill color defined:
• Background • •

5.4.12.20 M S Settings

Group Sub Parameter Description

TIC Spectrum Filter Filter This option works in combination with t he Time S pe ct ra T oo l t o
select a mass spectrum from a specific acquisition filter.
Select the acquisition filter in the Filter list (or type a filter definit ion),
and then use the Time Spectra Tool to select a retention time on the
chromatogram. The spectrum from the selected filter at the selected
retention time is shown on the plot.
If the selected filter was not in use at the selected retention time, the
spectrum at the retention time nearest to when the selected filter was
in effect is shown.
Noise Reduction Use setting of processing method Use the parameters from the MS Settings page of t h e p ro cessi n g
method.
Do not reduce Noise No noise reduction calculations will be performed

Relative Threshold Allows masses below a specified percentage of the base peak to b e
ignored
Fixed Threshold Limits spectra to only N largest mass intensities for a peak

5.4.12.21 Data Presentation

Group Sub Parameter Description

Plot Mode Automatic Select this option to display the mass spectral data in the f orm at in
which it was acquired. For centroid format data, the plot d isp la ys a
discrete vertical line for each mass peak. For profile format data, th e
plot is a continuous curve, with each mass peak consisting of
multiple data points.
Centroid Select this option to always display the data in centroid format, even
if profile data was acquired.
Mass precision N/A Select whether to use the mass precision defined on the MS
Settings tab page of the processing method, or to define a cu st o m
number of significant figures to include in the mass peak l a b els o n
the plot.
Mass tolerance N/A Select whether to use the default mass tolerance range defin ed o n
the MS Settings page of the processing method, or to define a
custom range.

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Chromeleon 7

5.4.12.22 SmartLink
This section defines how the SmartLink functionality applies to the mass spec plot

Link to Chromatogram

Group Sub Parameter Description

Link to Chromatogram N/A When this option is selected, the plot will adapt to sho w o nly t h e
spectra for peaks visible in the chromatogram plot. When the p lot
is linked, the plot pane splits into several panes to show plots from
multiple peaks
Multiple Peak Selection When selected, the peaks that are selected in the chromato gra m
plot define which peaks are displayed in the mass spec plot
Zoom Area When selected, the zoom area of the chromatogram plot d ef ines
which peaks are shown in the mass spec plot

Link to Injection

Parameter Sub Parameter Description

Link to Injections Allows multiple injections to be included in the array of SmartLink objects

Include Current Selections/Pins In addition to those injections specified by type or by custom con dit ion
(below), the currently selected and pinned injections will be includ ed in
the list of SmartLink injections
Include Injection Types Unknown Displays values from unknown injections.

Calibration Standard Displays values from calibration standard injections.

Check Standard Displays values from check standard injections.

Matrix Displays values from matrix blank injections.

Blank Displays values from blank run injections.

Spiked Displays values from spiked injections.

Unspiked Displays values from unspiked injections.

Custom Conditions Only include injections that match Displays only injections that fulfill certain conditio ns, b a se d o n re port
the following conditions variables.
ALL (Any field from the inje ctio n Restrict the data points shown based on comparing the selected variable
list – including user defined with a user-defined value and using the following logical arguments:
columns) Is equal to (=)
Is not equal to (<>)
Is larger than (>)
Is smaller than (<)
Is larger than or equal to (=>)
Is smaller than or equal to (=<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty

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Parameter Sub Parameter Description

Link to Injections Allows multiple injections to be included in the array of SmartLink objects
Include Current Selections/Pins In addition to those injections specified by type or by custom con dit ion
(below), the currently selected and pinned injections will be includ ed in
the list of SmartLink injections

AND [Any field from the injection As for the previous parameter.
list – including user defined
columns]
or Allows for matching based on only one comparison in the rule
and Forces matching based on every rule in the list. The or sub p a ra met er
overrides the requirement to match every comparison in the specific rule
list.

Display By
Defines how the SmartLink objects w ill be ordered.

Parameter Description

Peaks per injection When a single injection is selected, the peak objects for that injection are plotted in horizontal order.
When multiple injections are selected, each injection has its own row and each peak has its own column.
Injections per peak When a single peak is selected, the peak objects for each injection are plotted in horizontal order.
When multiple peaks are selected, each peak has its own row and each injection has its own column.

5.4.12.23 Interactive Settings

This section defines w hat optional zoom/unzoom tools are displayed on the mass spec plot

Function Description

Show overview plot When this check box is selected, the miniature overview of the mass spectrum plot
is displayed when zooming into the chromatogram.
Show popup controller When this check box is selected, the full-size button, vertical and horizontal z o om
toolbars on the chromatogram axes are visible.

5.4.13MS Components Pane

The MS Components pane allow s the user to visualize and interact w ith MS component quantitation and confirmation (if
applicable) XICs.

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Chromeleon 7

Figure 54: MS Components View in Chromatography Studio

5.4.13.1 Zooming and Navigating in the MS Components View

The MS Components view allow s zooming and navigating as required w ith the follow ing options:

Function Description
Zoom When active it is possible to zoom into the chromatogram by dragging an area.

Undo Zoom Reverts the recent zoom operation and returns to the previous view. Accesse d b y
right-clicking on the plot and selecting Unzoom
Full Scale Reverts the recent all zooming and re-plots the data full scale. Accessed b y ri gh t-
clicking on the plot and selecting Full Scale
Y axis zoom tools Shown when moving the cursor over the Y axis. The following functions are
available:
+ zooms into the plot vertically
Autoscale Signal resizes the plot height to the data point with the highest int en sit y
currently visible
- zooms out of the plot vertically

X axis zoom tools Shown when moving the cursor over the X axis. The following functions are
available:
+ zooms into the plot horizontally
Autoscale Time resizes the plot to the complete time range of the XIC as defined by
the processing method.
- zooms out of the plot horizontally
Full size button Shown when moving the cursor to the bottom left corner of the plot. Click t h e f u ll-
size button to autoscale both axes simultaneously.

In addition, the follow ing zoom operations are available:

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Function Description

Double Click on the intensity axis Automatically resizes the plot height to the highest intensity da ta p o int cu rren tly
visible.
Double Click on the time axis Automatically resizes the plot width to the comp let e t ime ra ng e o f t he X I C a s
defined by the processing method.
Undo Zoom Reverts the recent zoom operation and returns to the previous view.

Drag the abundance axis Scrolls the y axis limits

Drag the m/z axis Scrolls the x axis limits

5.4.13.2 Copy
Copies the MS Components plot to the clipboard as an image. This is also possible using the Ctrl + C hotkey.

5.4.13.3 Export Chromatogram

Exports the MS Components plot to a text file. When 1 or more confirmation XICs are displayed, the exported data is for the
plot w here the context menu w as activated. The follow ing options are available:

Parameter Sub Parameter Description

Destination Clipboard Exports a textual description of the MS component trace i nt o
the clipboard.
File Exports a textual description of the MS component trace into a
user defined text file.
Options Chromatogram data The exported MS component trace includes any corre ct ion s
such as a delay time or chromatogram subtraction.
Raw data The exported MS component trace is the raw data as
acquired without corrections

5.4.13.4 Tools
Function Description

Automatic Tool The tools in this section are selected either automatically when the “Automatic” tool
is active based on the cursor position
Delimiter Tool Used to move the peak start or peak end.
Baseline Tool Used to modify the baseline.
Peak Window Tool Used to modify peak detection window

Detection Parameter Tool User to move or edit detection parameters

Insert Peak Tool Used to create a new peak.

Spectra Plot Tool Used to display mass spectrum of selected data point.
Zoom Tool Used to zoom into MS component plot

5.4.13.5 Insert Detection Parameter…

When Chromeleon 6 or Cobra algorithms are selected in the MS Detection tab in the processing method, Insert Detection
Param eters… becomes enabled. This allow s the user to insert additional detection parameters at the retention time of the
cursor

5.4.13.6 Edit Detection Parameter…

If detection parameters are available in the MS component trace w indow , right clicking on a parameter and selecting Edit
Detection Param eter… allow s the user to modify the selected Chromeleon 6 or Cobra detection parameter

5.4.13.7 Delete Detection Parameter(s)

If detection parameters are available in the MS component trace w indow, right clicking on a parameter and selecting Delete
Detection Param eter(s) allow s the user to delete the selected Chromeleon 6 or Cobra detection parameter.

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Chromeleon 7

5.4.13.8 Set Detection Reference XIC…

This command opens up a dialog to select the XIC-type (Quantitation, 1st Confirming, 2nd Confirming, etc…) and the
components / peptides for w hich this XIC-type should become the reference detection XC. For peptides there is also the
choice to select either the Master Peptide or any Charge State component record. All other XICs of the component / peptide
w ill be integrated based on the integration of the component peak (peak start/end, baseline) in the reference XIC.

5.4.13.9 Remove Detection Reference XIC…

If the currently selected XIC is a se as a detection reference XIC this command w ill open up a dialog to select the
components / peptides for w hich the reference detection XIC should be removed.

5.4.13.10 Show Spectrum

Similar to the Tim e Spectra Tool in the Chromatogram pane Layout ribbon, this allow s the user to display the mass
spectrum of the data point nearest the mouse cursor.

5.4.13.11 Overlay Spectrum

This allow s the user to add additional spectra to the MS Spectra pane. If the MS Spectrum layout is set to Overlaid, the new
spectrum w ill be overlaid. Otherw ise, the new spectrum w ill be displayed stacked.

5.4.13.12 Remove Time Spectra

This removes all mass spectra that w ere displayed using the Show Spectrum and Overlay Spectrum functions

5.4.13.13 M S Spectra Baseline Correction

Function Description

No Baseline Correction Mass spectra display functions are forced to display uncorrected spectra
Peak Dependent Correction Mass spectra display functions are forced to display spectra adjusted for bunch ing
regions before and after the end of the selected peak as defined by the processi n g
method
Fixed Correction Mass spectra display functions are forced to display spectra adjusted for an explicit
baseline region defined by a start and end time in the processing method.

5.4.13.14 Properties
The follow ing MS Component display options are available:

Plot Details
This section defines w hich parts of the plot framew ork are show n. The parameters available are:

Parameter Sub Parameter Description

Axes Time Axis Displays a time axis on the chromatogram.

Signal Axis Displays a signal axis on the chromatogram.

Font Allows the font type and size of the axes to be defined.

Axis to Plot Gap Defines the distance in mm between the axes and the
chromatogram plot.
Frame Frame that is drawn around the plot area.
Axes Descriptions Axes Titles Applies titles to the chromatogram axes.

Units Displays units on the axes of the chromatogram.

Font Allows the font type and size of the axes titles to be defined
Grid Signal axis grid lines Applies horizontal grid lines to the chromatogram.

Time axis grid lines Applies vertical grid lines to the chromatogram
Orientation Horizontal Displays the chromatogram in the landscape orientation.

Vertical Displays the chromatogram in the portrait orientation.

Signal details Raw data points Shows the raw data points.

Time Axis

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The time w indow for MS Component plots is defined in the component table of the processing method and cannot be
changed on this page. Separate time axes and tick mark intervals are not supported for MS Components. Please refer to
section 5.3.2.20 for more details.

Signal Axis
This section allow s the user to define the scaling used for the signal axis. The follow ing options are available:

Parameter Sub Parameter Description

Range for component XICs Autoscale or Fixed Determines the method for selecting the ra ng e. Ca n b e se t t o:
Autoscale or Fixed, Autoscale using reference injectio n o r Fi xed
Autoscale using reference using Formula.
injection
Fixed using formula

Autoscale or Fixed To Defines the end value of the signal axis. Either Auto or a sp e cif ic
time can be selected.
From Defines the start value of the signal axis. Either Auto or a sp e c i fic
time can be selected.
Fixed using Formula From Defines the start value of the signal axis using a re p ort v a riab le
formula
To Defines the end value of the signal axis usi n g a re p ort vari able
formula

Title
This section defines the caption that w ill be displayed in the chromatogram header. Left, middle and right captions can be
selected either based on simple text values or on user-defined formulas. The formula can be based on variables from the
follow ing sections:
• Global Functions (7.1)
• General (7.2)
• Sequence (7.3)

• Injection (0)
• Audit Trail (see section 7.5)
• Preconditions (see section 7.6)
• Chromatogram (7.8)
• Processing Method (7.21)

• Instrument Method (7.31)

• Custom Formulas (5.8.31)
In addition, the follow ing options are available:

Parameter Sub Parameter Description

Draw titles Displays chromatogram titles.

Font Allows the font type and size of the titles to be defined

Left title Draw left title Displays the left part of the title.
When checked the left part of the title can be defined based on
formulas as described above.
Middle title Draw middle title Displays the middle part of the title.
When checked the middle part of t h e t i tle can b e d ef ine d
based on formulas as described above.
Right title Draw right title Displays the right part of the title.
When checked the right part of the title can be defined b a se d
on formulas as described above.
Legend Draw legend Displays the user-defined legend string in a legend box on t he
MS Component plot.

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Peak Characterization
This section defines how detailed peaks are characterized in the MS Components plot. The follow ing options are available:

Parameter Sub Parameter Description

Peak delimiter Shows the peak delimiters.

Delimiter Allows defining color and line style for peak delimiters.

Separation Allows defining color and line style for the separation drop line.

Baseline Shows the baseline.

Main peak Allows defining color and line style for the base line un de r a
main peak.
Rider peak Allows defining color and line style for the base line un de r a
rider peak.
Peak tangents Shows the peak tangents.

Allows defining color and line style for peak tangents.

Peak widths Shows peak widths.

Allows defining color and line style for peak widths.

Draw peak width at Draws a line at the given height. Default s h e ig ht s a re 5 % ,

10%, 50%, but are user definable
Peak Highlight Do not highlight peaks The identified peak will not be shaded in any pa ne u n less i t
has the focus

Highlight identified peaks in all The identified peak will be shaded in all sub-panes
plots

Peak Label
This section defines how peaks should be labeled. The follow ing options are available:

Parameter Sub Parameter Description

Identified peaks Label identified peaks Labels all identified peaks with details generated by the use r-
defined formula.
(Formula) The formula can be based on variables f ro m a ll t he a rea s
detailed in section 7.
Unidentified peaks Label unidentified peaks Labels all unidentified peaks with details g e n era te d b y t he
user-defined formula.
(Formula) The formula can be based on variables f ro m a ll t he a rea s
detailed in section 7.
Label style Font Defines the font for peak labels.

Rotation Defines the angle the peak label is shown at.

Peak Windows
This section defines the caption that w ill be displayed in the MS Components plot peak w indow indicator. Caption can be
selected either based on simple text values or on user-defined formulas. The formula can be based on variables from the
follow ing sections:
• Global Functions (7.1)
• General (7.2)
• Sequence (7.3)

• Injection (0)
• Audit Trail (see section 7.5)
• Preconditions (see section 7.6)
• Chromatogram (7.8)
• Processing Method (7.21)

• Component (7.29)

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• Instrument Method (7.31)

• Custom Formulas (5.8.31)
In addition, the follow ing options are available:

Parameter Sub Parameter Description

Component table windows Show component table windows Shows the component retention time window
Other options Show all peak window drop lines Shows the peak window start and stop times as dashed lin es
on the MS Component plot
Font Defines the font for component table window indicator

Comparison
This section defines how MS Components plot overlays are displayed. The follow ing options are available:

Parameter Sub Parameter Description

Arrangement Overlaid All overlaid MS Component plots are shown in one window.

Stacked All overlaid MS Component plots are shown in stacked

windows.
Overlay order Sorted by injection list order Not applicable for MS Component Plots

Current chromatogram always o n Not applicable for MS Component Plots

top
Offset Time Offset Offsets the overlaid chromatogram by the % time value
selected.
Signal Offset Offsets the overlaid chromatogram by the % signal value
selected.
Overlay Overlay with peak characterization If selected the peak characterization sett in gs su ch a s p e a k
names, peak delimiters or the baseline apply not o nly t o t h e
active chromatogram but also to all overlaid chromatograms.
Overlay with right signal axis. If selected the overlaid chromatogram is measured a g ainst a
right signal axis.
Mirror last overlaid chromatogram Plots the last confirmation peak mirrored against quanti tat ion
and all other confirmation peak(s) (if applicable).
Normalization Normalize signal Normalizes the signal against the reference peak.
XIC Display Options Show these XIC types Allows display of all XIC plots, only the quantitation ion or on ly
the confirming ions

Show the XICs of the ISTD When checked, the quantitation and confirming i on p lo ts f o r
associated with the component. the ISTD of a component are also plotted.

Reference Injection
This section defines an optional reference injection w hich can be used for scaling and overlays.:

Parameter Sub Parameter Description

Specify dynamic or fixed injection Use injection in current sequence If selected, one can specify a series of ru le s t o ch oose t h e
that matches this rule injection of interest. If multiple injections match the ru le, t he n
one can further specify the first, most recent or last m a tchin g
injection be used.

Use fixed injection from arb it rary If selected, the browse button may be used to navigat e t o a n
sequence injection in a sequence from elsewhere in a data vault.
Options Show as an overlay in every If selected, then the data from the specified reference injection
component tile is plotted as an overlay on each data tile.

Show as a separate component If selected, then the data from the specified reference injection
tile in the first position of the v ie w is plotted in a separate tile in the upper left p osi t ion o f e a ch
pane or plot group of tiles.

Events
This section allow s defining w hich events that occurred during the data acquisition or data processing are display ed on the
MS Components plot. The follow ing options are available:

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Chromeleon 7

Parameter Sub Parameter Description

Detection Parameters Show detection parameters Indicates the Detection Parameters.
Label Style Label events Displays event labels in the chromatogram.

Font Defines the event label font.

Spectral Thumbnails
This section defines how spectral thumbnails should be displayed. The follow ing options are available:

Parameter Sub Parameter Description

Show Thumbnails Automatic Displays the thumbnails only when the UV-Vis Spectra Plot is
also displayed.
UV Always displays the thumbnails if UV spectral data are
available.
Fluorescence Always displays the thumbnails if fluorescence spectral d at a
are available.
Amperometry Displays the thumbnails of any existing I-t plots in all channels.

MS Always displays the thumbnails if mass spectrum data is

available.
None Don’t display any UV spectra thumbnails in the
chromatogram.
Thumbnails Size Width Defines the width of the thumbnail in mm.

Height Defines the height of the thumbnail in mm.

Range Bars Draw average range bars Marks and labels the ranges from which bunched spectra
were taken in the chromatogram. The number of spectra
averaged within a range is displayed in parenthesis.

Line & Fill Styles

This section allow s a consistent color scheme for the objects in the MS Components plot to be defined. The follow ing items
can have their line color defined:

• Chromatograms 1-8 • Peak delimiter • Peak separation

• Peak tangents • Peak w idth • Baseline
• Rider baseline • Free baseline • Raw data points
• Detection parameters • Selected peak
The follow ing items can have their fill color defined:
• Background • Peak label • Detection parameter label
• Selected peak • Selected peak label

SmartLink
This section defines how the SmartLink functionality applies to the MS Components plot

Link to Chromatogram
Group Sub Parameter Description
Link to Chromatogram N/A When this option is selected, the plot will adapt to sho w o nly t h e
MS component traces within the chromatogram plot t i me ra n ge.
When the plot is linked, the plot pane splits into several p ane s t o
show plots from multiple peaks
Chromatogram Overlays When this option is selected, the MS Components plot will adapt to
show the component traces for injections that are overlaid in t he
chromatogram plot.
Multiple Peak Selection When selected, the components that are selected in the
chromatogram plot or pinned in the Components se ct i o n o f t he
navigation pane define which peaks a re d i sp l ayed in t he MS
Components plot

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Group Sub Parameter Description

Zoom Area When selected, the zoom area of the chromatogram plot d ef ines
which peaks are shown in the mass spec plot

Link to Injection
Parameter Sub Parameter Description

Link to Injections Allows multiple injections to be included in the array of SmartLink objects
Include Current Selections/Pins In addition to those injections specified by type or by custom c on dit ion
(below), the currently selected and pinned injections will be includ ed in
the list of SmartLink injections
Include Injection Types Unknown Displays values from unknown injections.

Calibration Standard Displays values from calibration standard injections.

Check Standard Displays values from check standard injections.

Matrix Displays values from matrix blank injections.

Blank Displays values from blank run injections.

Spiked Displays values from spiked injections.

Unspiked Displays values from unspiked injections.

Custom Conditions Only include injections that match Displays only injections that fulfill certain conditio ns, b a se d o n re port
the following conditions variables.
ALL (Any field from the inje ctio n Restrict the data points shown based on comparing the selected variable
list – including user defined with a user-defined value and using the following logical arguments:
columns) Is equal to (=)
Is not equal to (<>)
Is larger than (>)
Is smaller than (<)
Is larger than or equal to (=>)
Is smaller than or equal to (=<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
AND [Any field from the injection As for the previous parameter.
list – including user defined
columns]
or Allows for matching based on only one comparison in the rule

and Forces matching based on every rule in the list. The or sub p a ra met er
overrides the requirement to match every comparison in the specific rule
list.

Display By
Defines how the SmartLink objects w ill be ordered.

Parameter Description

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Chromeleon 7

Parameter Description

Peaks per injection When a single injection is selected, the peak objects for that injection are plotted in horizontal order.
When multiple injections are selected, each injection has its own row and each peak has its own column.
Injections per peak When a single peak is selected, the peak objects for each injection are plotted in horizontal order.
When multiple peaks are selected, each peak has its own row and each injection has its own column.

Interactive Settings
This section defines w hat optional zoom/unzoom tools are displayed on the mass spec plot

Function Description
Maximum hit test distance Specifies the distance when the shape of the mouse pointer changes wh e n t oo ls
become available

The illustration shows the areas around the left and right peak delimiters of a p e ak
where the shape of the pointer changes to the shape of a tool. The smaller the h it
test distance a is, the smaller the area where the tool pointers appear.

Show overview plot When this check box is selected, the miniature overview of the mass spectrum plot
is displayed when zooming into the chromatogram.
Show popup controller When this check box is selected, the full-size button, vertical and horizontal z o om
toolbars on the chromatogram axes are visible.
Visualize selections Disables or enables visualization of selected objects (such as a se l e ct e d p ea k),
(Not available for MS AutoFilters plots)
Highlight selected chromatogram Enables or disables the highlighting (bold) of the selected chromatogram.

5.4.14Tentatively Identified Peaks Pane

Chromatograms of unknow n injections in mass spectrometry (MS) data often contain peaks that are not identified by the
entries in the component table. Chromeleon can tentatively identify these peaks and estimate the amount value of each
peak using the nearest internal standard peak as a reference.
To tentatively identify the peaks, Chromeleon performs MS library screening on the apex spectrum of each unidentified peak
and determines the top tw elve matches (hits) for each peak. The component name of the top match (hit #1) is assigned to
each peak.
The Tentatively Identified Peaks pane can be used to view or change the tentative identities. The columns in the pane
provide the follow ing information for each tentatively identified peak: Retention Time, the name tentatively assigned to the
unidentified peak, the CAS number of the tentative component name, the estimated amount of the unidentified peak, Match
Factor (SI), Reverse Match Factor (RSI), Probability (%) (available for the Identity search type only), Library, and the internal
standard nearest to the unidentified peak.
You can change the tentative assignment of a peak by selecting another hit from the screening list, or by manually naming
the peak.
Right-clicking on a row w ill provide an option to move the peak and its component name from the Tentatively Identified
Peaks table to the processing method component table (thereby confirming the tentative assignment).

5.4.15MS AutoFilters Pane

The MS AutoFilters pane allow s a user to visualize all MS acquisition filters across single or multiple injections w ithout
manually creating a channel from an XIC or an MS component in the component table. If a filter is of interest, a user is also
able to make a permanent channel from the filter.

5.4.15.1 Zooming and Navigating in the MS AutoFilters pane

The MS AutoFilters view allow s zooming and navigating as required w ith the follow ing options:

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Function Description
Zoom When active it is possible to zoom into the chromatogram by dragging an area.
Undo Zoom Reverts the recent zoom operation and returns to the previous view. Accesse d b y
right-clicking on the plot and selecting Unzoom
Full Scale Reverts the recent all zooming and re-plots the data full scale. Accessed b y ri gh t-
clicking on the plot and selecting Full Scale
Y axis zoom tools Shown when moving the cursor over the Y axis. The following functions are
available:
+ zooms into the plot vertically
Autoscale Signal resizes the plot height to the data point with the highest int en sit y
currently visible
- zooms out of the plot vertically

X axis zoom tools Shown when moving the cursor over the X axis. The following functions are
available:
+ zooms into the plot horizontally
Autoscale Time resizes the plot to the complete time range of the XIC as defined by
the processing method.
- zooms out of the plot horizontally
Full size button Shown when moving the cursor to the bottom left corner of the plot. Click t h e f u ll-
size button to autoscale both axes simultaneously.

In addition, the follow ing zoom operations are available:

Function Description
Double Click on the intensity axis Automatically resizes the plot height to the highest intensity da ta p o int cu rren tly
visible.
Double Click on the time axis Automatically resizes the plot width to the comp let e t ime ra ng e o f t he X I C a s
defined by the processing method.
Undo Zoom Reverts the recent zoom operation and returns to the previous view.

Drag the abundance axis Scrolls the y axis limits

Drag the m/z axis Scrolls the x axis limits

5.4.15.2 Copy
Copies a single selected MS acquisition filter chromatogram to the clipboard as an image This is also possible using the Ctrl
+ C hotkey.

5.4.15.3 Export Chromatogram

Exports a single selected MS acquisition filter chromatogram to a text file. The follow ing options are available:

Parameter Sub Parameter Description

Destination Clipboard Exports a textual description of the MS component trace i nt o
the clipboard.
File Exports a textual description of the MS component trace into a
user defined text file.
Options Chromatogram data The exported MS component trace includes any corre ct ion s
such as a delay time or chromatogram subtraction.
Raw data The exported MS component trace is the raw data as
acquired without corrections

5.4.15.4 Create M S Channel

The function allow s the user to create a permanent channel from the MS acquisition filter chromatogram. Selecting this
context menu item displays the follow ing dialog w ith appropriate fields prefilled:

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Chromeleon 7

Figure 55: Extract MS Channel

Parameter Description
Trace Specify the chromatogram trace type to be extracted
TIC (Total Ion Current)—all ions matching the filter entered in the Filter list will be extracted from the
raw data.
Base Peak—base peak ions that match the filter entered in the Filter list will be extracted f ro m t he
raw data.
Mass Range—ions that match the filter entered in the Filter list and with a mass that m atc h es t h e
mass or mass range entered in the Mass range(s) box will be extracted from the raw data.
Filter Specifies the acquisition filter from which the chromatogram will be extracted
Mass ranges Defines the mass, mass range, or a set of mass ranges to be extracted

Smoothing Specifies the type of smoothing to be performed on the chromatogram data when it is extracted.

Channel Name Defines the label that will be used to identify this extracted ion chromatogram in the channels list
Make channel permanent Creates a permanent channel when selected or if check bo x i s cl ea r a t emp ora ry cha nn el i s
created.

5.4.15.5 Properties
The follow ing MS AutoFilters display options are available:

Plot Details
This section defines w hich parts of the plot framew ork are show n. The parameters available are:

Parameter Sub Parameter Description

Axes Time Axis Displays a time axis on the chromatogram.
Signal Axis Displays a signal axis on the chromatogram.

Font Allows the font type and size of the axes to be defined.

Axis to Plot Gap Defines the distance in mm between the axes and the
chromatogram plot.
Frame Frame that is drawn around the plot area.
Axes Descriptions Axes Titles Applies titles to the chromatogram axes.

Units Displays units on the axes of the chromatogram.

Font Allows the font type and size of the axes titles to be defined
Grid Signal axis grid lines Applies horizontal grid lines to the chromatogram.

Time axis grid lines Applies vertical grid lines to the chromatogram

Orientation Horizontal Displays the chromatogram in the landscape orientation.

Vertical Displays the chromatogram in the portrait orientation.

Signal details Raw data points Shows the raw data points.

Scale
This section defines the scaling behavior of the time axes for the MS AutoFilters plots.

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Parameter Sub Parameter Description

Time axis scale mode Full time range Displays the plot from t = 0min to the end of the a cq uisi t ion
regardless of whether data was acquired d urin g t h e e nt ire
duration of the injection. Zooming functions are subsequently
synchronized between all plot time axes.
Extracted time range Displays the plot from the first point where data was acquired
to the last point where data was acquired. As MS fi lte rs a re
often acquired during different retention time ranges,
subsequent zooming actions apply only to the selected plot.

Peak Characterization
This section defines how detailed peaks are characterized in the MS AutoFilters plots. Peak characterization is show n only if
a valid processing method is available. The follow ing options are available:

Parameter Sub Parameter Description

Peak delimiter Shows the peak delimiters.

Delimiter Allows defining color and line style for peak delimiters.
Separation Allows defining color and line style for the separation drop line.

Baseline Shows the baseline.

Main peak Allows defining color and line style for the base line un de r a
main peak.
Rider peak Allows defining color and line style for the base line un de r a
rider peak.
Peak tangents Shows the peak tangents.
Allows defining color and line style for peak tangents.
Draw peak width at Shows peak widths.
Peak widths
Allows defining color and line style for peak widths.

Draws a line at the given height. Default s h e ig ht s a re 5 % ,

10%, 50%, but are user definable

Peak Label
This section defines how peaks should be labeled. The follow ing options are available:

Parameter Sub Parameter Description

Identified peaks Label identified peaks Labels all identified peaks with details generated by the use r-
defined formula.
(Formula) The formula can be based on variables f ro m a ll t he a rea s
detailed in section 7.
Unidentified peaks Label unidentified peaks Labels all unidentified peaks with details g e n era te d b y t he
user-defined formula.
(Formula) The formula can be based on variables f ro m a ll t he a rea s
detailed in section 7.
Label style Font Defines the font for peak labels.

Rotation Defines the angle the peak label is shown at.

Line & Fill Styles

This section allow s a color scheme for the objects in the MS AutoFilters plot to be defined. The follow ing items can have
their line color defined:

• Chromatograms 1-8 • Peak delimiter • Peak separation

• Baseline • Rider baseline • Free baseline
• Peak tangents • Peak w idth • Raw data points

Functional Specifications, 7.3.1, Rev. 1.0 Page 171

Chromeleon 7

• Detection parameters • Raw data points • Selected Peaks

The follow ing items can have their fill color defined:

• Background • Peak label • Detection parameter label

• Selected peak • Selected peak label •

SmartLink
This section defines how the SmartLink functionality applies to the MS Components plot

Group Sub Parameter Description

Link to Chromatogram N/A When this option is selected, the plot will adapt to sho w o nly t h e
MS acquisition filters within the chromatogram plot time range.
Chromatogram Overlays When this option is selected, the MS AutoFilters plot will ada pt t o
show the MS acquisition filters for injections that are overlaid in the
chromatogram plot.
Multiple Peak Selection This option has no effect on the MS AutoFilters plot.

Zoom Area When selected, the zoom area of the chromatogram plot d ef ines
which filters are shown in the MS AutoFilters plot.

Interactive Settings
This section defines w hat optional zoom/unzoom tools are displayed on the MS AutoFilters plot

Function Description
Show overview plot When this check box is selected, the miniature overview of the mass spectrum plot
is displayed when zooming into the chromatogram.
Show popup controller When this check box is selected, the full-size button, vertical and horizontal z o om
toolbars on the chromatogram axes are visible.

AutoFilter Filtering
This section defines the refined MS acquisition filter list to be displayed

Function Description
Precursor Mass Defines the precursor mass of MS2 based acquisition filters to be displayed on the
MS AutoFilters plot
XIC Mass(es) or Range(s) Defines the product mass of MS2 or target mass of MS1 based acquisition filters to
be displayed on the MS AutoFilters plot.
Filters to be displayed (Read Only) Displays the refined or full list of filters that is currently being displayed
on the MS AutoFilters plot.

5.4.16SmartLink
In the Data Processing Category, it is possible to link the follow ing panes interactively to the chromatogram and/or the
injection list:

• Interactive Results (section 5.4.9)

• Interactive charts (section 5.4.4)
• MS components (section 5.4.13)
• Calibration plot (section 5.4.2)

• Spectral plots (UV-VIS (section 5.4.6), Fluorescence (section 5.4.7), I-t (section 5.4.8), MS (section 5.4.12)
The specific available options depend on the respective pane. Please refer to the corresponding section for details.

5.4.16.1 Chromatogram Linking

If the chromatogram plot is modified to show only certain peaks or injections, the linked panes w ill interactively adapt to
show only these peaks or injections. When the calibration plot, spectral plot, or I-t plot is linked, the plot pane splits into
several panes to show plots from multiple peaks.

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The follow ing SmartLink options are available:

Parameter Description
Link to Chromatogram Allows multiple peaks to be included in the array of SmartLink objects

Chromatogram Overlays Injections that are overlaid in the chromatogram plot for comparison define which injections are disp la yed i n
the linked objects.
Multiple Peak Selection Peaks that are selected in the chromatogram plot or in the Components group on the Navigation Pane define
which peaks are displayed in the linked objects.
Zoom Area Zoom area of the chromatogram plot defines which peaks are shown in the linked objects.

5.4.16.2 Injection Linking

When injection-based linking is enabled, the linked panes w ill interactively adapt to show data from all of the injections
specified in the SmartLink settings (below )

Parameter Sub Parameter Description

Link to Injections Allows multiple injections to be included in the array of SmartLink objects

Include Current Selections/Pins In addition to those injections specified by type or by custom c on dit ion
(below), the currently selected and pinned injections will be inc lud ed in
the list of SmartLink injections
Include Injection Types Unknown Displays values from unknown injections.

Calibration Standard Displays values from calibration standard injections.

Check Standard Displays values from check standard injections.

Matrix Displays values from matrix blank injections.

Blank Displays values from blank run injections.

Spiked Displays values from spiked injections.

Unspiked Displays values from unspiked injections.

Custom Conditions Only include injections that match Displays only injections that fulfill certain conditio ns, b a se d o n re port
the following conditions variables.

ALL (Any field from the inje ctio n Restrict the data points shown based on comparing the selected variable
list – including user defined with a user-defined value and using the following logical arguments:
columns) Is equal to (=)
Is not equal to (<>)
Is larger than (>)
Is smaller than (<)
Is larger than or equal to (=>)
Is smaller than or equal to (=<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
AND [Any field from the injection As for the previous parameter.
list – including user defined
columns]
or Allows for matching based on only one comparison in the rule

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Chromeleon 7

Parameter Sub Parameter Description

Link to Injections Allows multiple injections to be included in the array of SmartLink objects
Include Current Selections/Pins In addition to those injections specified by type or by custom con dit ion
(below), the currently selected and pinned injections will be includ ed in
the list of SmartLink injections
and Forces matching based on every rule in the list. The or sub p a ra met er
overrides the requirement to match every comparison in the specific rule
list.

5.4.16.3 Display By
Defines how the SmartLink objects w ill be ordered.

Parameter Description

Peaks per injection When a single injection is selected, the peak objects for that injection are plotted in horizontal order.
When multiple injections are selected, each injection has its own row and each peak has its own column.
Injections per peak When a single peak is selected, the peak objects for each injection are plotted in horizontal order.
When multiple peaks are selected, each peak has its own row and each injection has its own column.

5.4.17On-Demand View Updating

In order to improve softw are responsiveness w hen w orking w ith large MS sequences containing many XICs, a new
sequence property (see 4.3.2) is now available to defer real-time updating of data and results in calculation intensive panes
of the Chromatography Studio. The option applies to both the Data Processing and Report Designer categories of the
Studio.
When the Sequence property “Update View s for MS Data” is set to “On-demand”, the follow ing changes in Studio behavior
w ill occur:

5.4.17.1 Views
Calculation-intensive panes of the Studio w ill have a “View Out Of Date” w atermark w hen the sequence is opened in the
Studio, as w ell as w hen changes have been made to the processing method or injection information. The panes w ill be
refreshed w ith current results when the user triggers an update (see next tw o sections)

5.4.17.2 M essage Bar

When one or more visible panes has a “View Out Of Date” w atermark, the Studio Message Bar w ill be displayed, notifying
the user of this situation. The Studio Message Bar w ill also include a hyperlink to initiate reprocessing of the data and
updating of the view panes.

5.4.17.3 Ribbon Bar

When one or more visible panes has a “View Out Of Date” w atermark, the ‘Data Processing Home’ Ribbon of the Ribbon
Bar w ill include controls to initiate reprocessing of the data and updating of the view panes.

5.5 Non-Targeted MS Processing Category (SIEVE)

The Non-Targeted MS Processing Category has tw o similar but different user interfaces, depending on the choice of new
peak detection algorithm. This section describes the functionality w hen the SIEVE Algorithm is used. For a description of the
functionality w hen the BioPharma Finder Algorithm is used, see 5.6)

5.5.1 Ribbon Bar

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In the Non-Targeted MS Processing category, the buttons on the “Panes” section of the ribbon allow show ing or hiding of
panes. The follow ing panes are available:
• Processing (see section 5.5.2)
• Frame Plot (see section 5.5.3)
• Frame Report (see section 5.5.4)
• Chromatogram Plot (see section 5.5.5)
• Mass Spectra (see section 5.5.6)

5.5.2 Processing Pane

Note: This pane is only available via the Non-Targeted MS Processing category (see section 5, 1.d.).

The Processing pane serves as the central point to control and monitor data processing of the Non-Targeted MS
Processing category. This is divided into 4 tabs: Setup, Preparation, Alignment, and Detection. The Non-Targeted MS
processing w orkflow is such that a user w ould typically setup processing parameters on the Setup tab, then either Start
processing the entire w orkflow or execute each of the steps (Preparation, Alignment, and Detection) manually. The tabs are
described below .

5.5.2.1 Setup
Setup is used to define processing parameters for Non-Targeted MS Processing. The parameters are stored as part of the
Chromeleon Processing Method.

Parameter Sub Parameter Description

Relative Integer Defines the injection number to use as a reference for Non-
Fixed Targeted MS Processing. Use of this option will allow the
processing method to be used with other sequences and maintain a
reference injection at the user defined position within the sequence.
Selection of this parameter and/or sub parameter will result in
generation of suggested default frame parameters.
Path Defines a static reference injection inside or outside of the sequence
to be used for Non-Targeted MS Processing. Use defines an
explicit injection that will always be referenced independen t o f t h e
sequence the processing method is associated with.
Selection of this parameter and/or sub parameter will result in
generation of suggested default frame parameters.
m/z Min Defines the start of the m/z range in which the algorithm is permitted
to create a frame.
m/z Max Defines the end of the m/z range in which the algorithm is permitted
to create a frame.
m/z Width [ppm] Defines the m/z width, in ppm, of a frame that is created to evaluate
whether signal meets or exceeds the peak intensity threshold.
This combined with Frame Time Width defines the rectangular si ze
of the frame.
Retention Time Start [min] Defines the start time of the range in which the algorithm is
permitted to create a frame.
Retention Time Stop [min] Defines the end time of the range in which the algorithm is permitted
to create a frame.
Frame Time Width [min] Defines the retention time width, in min, of a frame that is created to
evaluate whether signal meets or exceeds the peak intensity
threshold. This combined with m/z Width defines the re ct an gula r
size of the frame.
Max. Number of Frames Defines the maximum number of frames the algorithm wi ll d et ect
before stopping. The software maximum is 16000.
Peak Intensity Threshold Fixed Defines the minimum signal intensity in a frame in order to
designate a frame as valid.

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Chromeleon 7

Parameter Sub Parameter Description

Auto-compute Calculates the minimum signal inten sit y in a f ram e i n o rde r t o
designate a frame as valid based on a selected value
TIC – percent of total ion intensities of the injection
BPC – percent of the base peak of the injection
Reference TIC – percent of total ion intensitie s o f t h e re f ere nce
injection
Reference BPC – percent of the base peak of the reference
injection
Scan Filter(s) List of Full Scan MS Filters Selection defines which MS filter TICs the algorithm is a l lo wed t o
evaluate and create frames for.
Advanced Opens advanced parameters for Non-Targeted MS Processing.

Reset Resets the frame parameters to suggested defaults.

Start Starts processing the injection workflow from Preparation t hro ugh
Detection.

Options in the dialog displayed w hen the Advanced button is clicked are described below

Parameter Description
Description User defined description of the experiment – meta data which has no effect on results.

Max Threads Maximum number of logical CPU cores the algorithm will use for computation.

Alignment Bypass Defines whether the alignment step of the Preparation, Alignment, and Detection workflow will be executed o r
skipped.
Alignment Min Intensity Minimum intensity threshold for alignment.

CorrelationBinWidth Comparison width at the mass spectra level between reference and unknown injection u se d f or d a t a p oin t
correlation for TIC alignment.
Max RT Shift Maximum allowable retention time shift of a datapoint when aligning an unknown against a reference TIC.

Tile Size The initial size of a correlation tile in number of scans for base peak alignment. Increased comput ing p o wer
and memory are required for larger tile size values.

5.5.2.2 Preparation
Preparation is used to manually cache injections for Non-Targeted MS Processing and/or monitor the progress of caching.
This tab displays information only for the selected injection.

5.5.2.3 Alignment
Alignment is used to manually start alignment of an unknow n TIC against a reference TIC as defined by the processing
method independent of the overall w orkflow and/or monitor the progress of alignment. This tab displays information only for
the selected injection.

5.5.2.4 Detection
Detection is used to manually start valid frame detection in the unknow n or reference TIC and/or monitor the progress of
detection. This tab displays information only for the selected injection.

5.5.3 Frame Plot Pane

Note: This pane is only available via the Non-Targeted MS Processing category (see section 5, 1.d.).

The Frame Plot displays the reference, unknow n aligned, and unknow n unaligned XICs. At any given time, only 1 frame
can be displayed. This is defined by the frame selected in the navigation pane or in the Frame Report pane. The datapoints
are indicated w ith a small vertical dash. Left clicking on the plots w ill display the mass spectrum for the selected data point.
Ctrl + left clicking w ill display multiple mass spectra simultaneously. The plot controls for zooming and panning are identical
to the Chromatogram plot object.
The Frame Plot ribbon controls w hich are new are defined below . Please see section 5.4.1 for details on other controls.
Entries shared w ith the Frame Plot context menu are noted as such

Group Sub Parameter Description

Data Reference Toggles display of reference XIC on the frame plot

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Group Sub Parameter Description

Unaligned Toggles display of the unaligned unknown XIC on the frame plot
Remove Spectra Toggles display of the aligned unkn o wn X I C o n t h e f ra me p lo t
(available in Frame Plot pane context menu).

5.5.3.1 Scale
This section allow s the user to define the scaling used for the time (X) and signal count (Y) axes of the frame plot. The
follow ing options are available:

Parameter Sub Parameter Description

Time axis From Defines the start retention time of the frame plot X-axis
To Defines the end retention time of the frame plot X-axis

Autoscale Automatically defines the retention time range o f t he f ram e

plot X-axis
Intensity Axis From Defines the lowest signal count value of the frame plot Y-axis

To Defines the highest signal count value of the frame plot Y-axis
Autoscale Automatically defines the signal count range of the frame plo t
Y-axis.

5.5.3.2 Frame & Axes

This section allow s the user to define the displayed properties of the frame plot.

Parameter Sub Parameter Description

Axes Time axis Enables or disables the X-axis of the frame plot

Intensity axis Enables or disables the Y-axis of the frame plot

Font Defines font style, size and font emphasis of the axes
Axis to plot gap Defines distance between plot and axis

Frame Enables or disables a black border around the frame plot

Axis Titles Axis titles Enables or disables axis labeling

Units Enables or disables axis units labeling

Font Defines font style, size and font emphasis of the axis titles
Grid Horizontal grid lines Enables or disables horizontal grid lines in the frame plot

Vertical grid lines Enables or disables vertical grid lines in the frame plot

5.5.3.3 Title
This section allow s the user to define the displayed titles of the frame plot.

Parameter Sub Parameter Description

Title Draw titles Enables or disables the titles displayed above the frame plot

Font Defines the font style, size, and emphasis of the titles

Legend Draw legend Enables or disables the frame plot legend

5.5.3.4 Data
This section allow s the user to define the type of data displayed on the frame plot.

Parameter Sub Parameter Description

Reconstructed Ion Chromatogram Draw reference Enables or disables display of the reference injection XIC

Draw unaligned Enables or disables display of the unaligned unknown XIC

Thumbnails Show spectral thumbnails Enables or disables thumbnails of mass spectra displayed on
Mass Spectra pane

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5.5.3.5 Interactive Settings

This section allow s the user to define w hich interactive controls on the plot are displayed on the frame plot.

Parameter Sub Parameter Description

Interactive Settings Show overview plot Enables or disables the miniature full frame plot vi ew wh e n
zoomed in on the main frame plot
Show popup controls Enables or disables the zoom and resize controls when
mousing over the lower left corner of the plot or in the ce nte r
of the frame axes

5.5.4 Frame Report Pane

Note: This pane is only available via the Non-Targeted MS Processing category (see section 5, 1.d.).

The Frame Report pane consists of 2 sections – the Frame Table and the Frame Filter (see section 5.5.4.1). There is a
dedicated Interactive Results pane (see section 5.4.9) for Non-Targeted MS Processing. The report columns available for
display are listed in section 7.38. See section 5.4.9 for more information regarding the operation and functionality of
interactive results.
The Frame Table and Frame List in the Navigation Pane are updated dynamically based on the Frame Filter applied w hich
can be accessed and exposed from the bottom of the Frame Report Pane by clicking on the chevron or by editing the
Frame Table properties. The behavior is described in more detail in section 5.5.4.1.

5.5.4.1 Frame Filter

The Frame Filter and the Frame Filter table property in the Frame Report pane serve the same purpose.

Parameter Sub Parameter Description

Custom Conditions ALL Restrict the data shown based on comparin g a ll ru le s wi t h
user-defined numerical values and using the following l ogica l
arguments:
Is equal to (=)
Is not equal to (<>)
Is larger than (>)
Is smaller than (<)
Is larger than or equal to (=>)
Is smaller than or equal to (=<)
Is between
Is not between

ANY [Any field from the sequence As for the previous parameter.
table – including user defined
columns]
or Allows for matching based on only one comparison in the rule

and Forces matching based on every rule in the list . T he o r su b

parameter overrides the requirement to match every
comparison in the specific rule list.

5.5.5 Chromatogram Plot Pane

Note: This pane is only available via the Non-Targeted MS Processing category (see section 5, 1.d.).

The Chromatogram Plot consists of a subset of functions from the Chromatogram pane used in the Data Processing
category of the studio. See section 5.4.1 for details.

5.5.6 Mass Spectra Pane

The Mass Spectra pane allow s the user to view the mass spectra for a selected Frame in the Frame Plot

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5.5.7 Processing Parameters Pane

Note: This pane is only available via the Non-Targeted MS Processing category

The Processing Parameters pane show s the parameter values that w ere used to process each individual injection. This is a
read-only pane that show s the values for parameters that w ere defined in the processing method, but w ere subject to
change based on the actual data for that injection

Parameter Sub - Parameter Shown Description

Global Setting Description Actual description of the experiment, which m ay

be updated form the processing method default.
Max Threads Minimum of (the Maximum number of logical CPU
cores which the algorithm is allowed t o ru n o n )
and (the number of logical CPU cores available)
Relative Reference Injection Path to reference injection if refere nce m o de i s
set to Fixed.
Alignment Parameters Alignment Bypass Whether the alignment step is bypassed or not
Alignment Min Intensity Maximum of (Minimum signal intensity spec ifie d
by the processing method) and (minimum va lue
of the data)
Correlation Bin Width Maximum, in Daltons, of (Width specified in t he
processing method for the MS segment to
correlate reference TIC to unknown TIC data
point) and (minimum of the data being processed)
Max RT Shift Minimum of (Maximum allowable retentio n t ime
shift of a datapoint when align ing a n u nkn o wn
against a reference TIC specified in the
processing method) and (maximu m RT o f t h e
data)
RT Limits for Alignment Maximum of (the Maximum allowed retention time
transformation of unknown TIC datapoin t wh e n
aligning to reference TIC) and (the RT limit o f t e
data)
Tile Size Initial size (in number of scans) of a tile that
correlates base peak alignment across the
reference and unknown injections
Frame Parameters Frame Time Width [min] The effective retention time widt h, i n m in, o f a
frame that is created to evaluate whether si g n al
meets or exceeds the peak intensity t h resh o ld,
based on the processing method and the data
m/z Max Minimum of (the start of the m/z range in wh ic h
the algorithm is permitted to cre at e a f ra me a s
specified in the processing method) and (the m/ z
max of the data)
m/z Min Maximum of (the end of the m/z range i n wh ich
the algorithm is permitted to create a f ra me, a s
specified in the method) and (the minimum m/z of
the data)
m/z Width [ppm] The effective m/z width, in ppm, of a frame that is
created to evaluate whether signal meets or
exceeds the peak intensity threshold, b ase d on
the processing method and the data
Maximum Number of Frames Minimum of (the maximum number of frames th e
algorithm will detect before stopping, as specified
in the processing method) and (the limit of
possible frames in the data)
Peak Intensity Threshold The minimum signal intensity in a frame in o rde r
to designate a frame as valid based on a selected
value, as auto computed or defined in the
processing method

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Parameter Sub - Parameter Shown Description

Retention Time Start [min] Maximum of (the start time of the range in wh ich
the algorithm is permitted to create a f ra me, a s
defined in the processing method) and (the
starting RT of the data)
Retention Time Stop [min] Minimum of (the end time of the range i n wh ich
the algorithm is permitted to create a f ra me, a s
defined in the processing method) and (the
ending RT of the data)
Scan Filter(s) The MS TIC filter the algorithm uses to eva lua te
and create frames.

5.6 Non-Targeted MS Processing Category (BioPharma Finder)

The Non-Targeted MS Processing Category has tw o similar but different user interfaces, depending on the choice of new
peak detection algorithm. This section describes the functionality w hen the BioPharma Finder Algorithm is used. For a
description of the functionality w hen the SIEVE Algorithm is used, see 5.5)

5.6.1 Ribbon Bar

In the BioPharma Finder Non-Targeted MS Processing category, the buttons on the “Panes” section of the ribbon allow
show ing or hiding of panes. The follow ing panes are available:
• Processing Method (see section 5.6.2)
• Component Results Plot (see section 5.6.3)

• Component Results Table (see section 5.6.4

• Chromatogram Plot (see section 5.6.55.5.5)
• MS Plot (see section 5.6.6)
• Processing Method Parameters (see section )5.6.7

5.6.2 Processing Method Pane

Note: This pane is only available via the BioPharma Finder Non-Targeted MS Processing category

The Processing Method pane is populated w ith elements for specifying individual parameter values used during NTMS data
processing.

Section Parameter Description

General Displays the number and the name o f in jectio n
Control Injection #, Name that was used in the processing run as the
reference injection.

Corresponds to the type of processing t h at wa s

selected in the Processing Method pane using the
Select Task to be Performed drop-down list. This
parameter can have one of the following two
values:
Processing Type
Find All Ions in the Run: Result are presented a s
each ion representing a separate en try. Th is i s
the default.
Find All Masses in the Run: Combines m u lt iple
charge states into a single entry

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Section Parameter Description

Basic Auto-Compute Basic Parameters Corresponds to the selection made in t he A ut o-

Populate check box of the Processi n g Me th od
pane:
True: The check box was checked and the
parameter values were filled automatically, based
on the specific injection data.
False: The check box was cleared checke d a nd
the parameters values were selected
Corresponds to the Absolute MS Signal
Absolute MS Signal Threshold
Threshold parameter.

This parameter represents the noise level i n t h e

MS data, in terms of absolute intensities.
It is one of the two factors affecting the va lu e o f
MS Noise Level the Absolute MS Signal Threshold used for
distinguishing signals from noise. The fact or, b y
which the noise level has to be surpassed to
recognize an absolute intensity value as a signal,
is specified by the S/N Threshold.
This parameters represents the signal-t o-n oise
threshold used when interpreting the raw MS
data, to distinguish a signal from noise.
The value specifies the factor by which a value of
S/N Threshold the MS absolute intensity has to surpass the M S
Noise Level, in order to be considere d a si g na l
and not noise. This parameter is one of t h e t wo
factors affecting the value of t h e A b so lut e M S
Signal Threshold.

This parameter represents the typical wi dt h o f

peaks near the beginning of the chromatographic
run. It complements the Typical
Beginning Peak Width (min) Chromatographic Peak Width to take into
account the tendency of chromatographic p ea ks
to broaden during the course of a
chromatographic run.
This parameter represents the typical wi dt h o f
chromatographic peaks in the analyze d L C/ MS
run.
Note: When the Auto-populate check box is
selected in the Processing Method pane, the
value of Typical Chromatographic Peak Wid th is
set to the width of the highest peak in the
Typical Chromatographic Pk Width (min)
chromatogram.
To take into account the tendency of
chromatographic peaks to broa d en d uring t he
course of a chromatographic run, the Typical
Chromatographic Peak Width is compl emen te d
with the Beginning Peak Width and t he E nd ing
Peak Width.

This parameter represents the typical wi dt h o f

peaks near the end of the chromatographic run. It
Ending Peak Width (min) complements the Typical Chromatographic
Peak Width to take into account the tendency o f
chromatographic peaks to broa d en d uring t he
course of a chromatographic run.

This parameter represents the maximum width of

chromatographic peaks in the LC/ MS ru n . A n y
peak wider than this value will be consi de red t o
be part of the background and will not be includ e
it in the results.
Max Chromatographic Pk Width (min)
Note: When the Auto-populate check box is
selected in the Processing Method pane, the
value of Maximum Chromatographic Peak Wid t h
is set to the geometric mean of the wi dth o f t h e
highest peak and the range of the chromatogram.

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Section Parameter Description

This parameter specifies the start retention t i me

of a truncated chromatogram time ran ge t h at is
Time Limit Start (min)
used to reduce the NTMS processing to an
appropriate area.

This parameter specifies the end retention time of

a truncated chromatogram time range that is used
Time Limit End (min)
to reduce the NTMS processing to an appropriate
area.

This parameter represents the maximum allowed

mass difference of the same ion in different
scans. Depending on the resolut ion o f t h e M S
Mass Tolerance
data, the value is reported in ppm (for high-
resolution data) or in daltons (for low-re so lu tio n
data).

This parameter represents the maximum allowed

mass deviation when comparing the theo ret ical
Mass Accuracy
mass to the calculated mass of a particular ion t o
determine identification.

This parameter specifies the maximum

considered retention time shift when co mp arin g
Maximum RT Shift (min) two or more LC/MS runs. It is one of the basic Ion
Alignment parameters of the BioPharma Fin de r
NTMS Processing Method pane
Advanced This parameter represents the lowest relative
abundance of a component in the MS signal, as a
percentage of the base peak, required to d et ec t
an ion at a given point in the chromatogram.
Unlike the Absolute MS Signal Threshold, wh ic h
sets the minimum MS signal for detection of a ny
Relative MS Signal Threshold
ion in the MS data, the Relative MS Signal
Threshold defines the minimum relative
abundance for detection o f a comp on ent t ha t
coelutes with a larger compone nt in t he sa m e
LC/MS run.

This parameter represents the lowest signal

Relative Analog Threshold value, relative to the highest peak in the
chromatogram, that the application can detect.

This parameter represents the factor used to

divide the Typical Chromatographic Peak Wi d t h
value to obtain the width of the G au ssi a n f ilt er
used to average nearby full MS scans. For
example, a value of 4 means the filter width is one
fourth of the typical chromatographic peak width.
Filtering improves the signal-to-noise ratio (S / N)
Width of Gaussian Filter of each scan by reducing noise, but this may
decrease chromatographic resolution. Lower th is
parameter value to improve sensitivity by
suppressing noise and increase th e n umb er t o
improve chromatographic resolution. A value of 1
represents maximum noise suppression using the
Gaussian filter width equal to t he t ypical p e ak
width.

This parameter represents the minimum size of a

valley between a pair of peaks, as a perce n t ag e
Minimum Chromatography Valley (%)
value, for considering the pair as t wo se p a ra te
peaks.

This parameters represents the minimum width of

Minimum MS Peak Width (Da) MS peaks used to generate a range for the
isotopic envelope of the ion

This parameters represents the maxmum width of

Maximum MS Peak Width (Da) MS peaks used to generate a range for the
isotopic envelope of the ion

This parameter represents the maximum mass to

Maximum Mass (Da) change the calculation of the average mass of an
ion.

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Section Parameter Description

This parameter represents a percen ta ge va lue

Mass Centroid Cutoff (% from base) cutoff to change the calculation of t h e a ve rage
mass of an ion.

5.6.3 Component Results Plot Pane

Note: This pane is only available via the Non-Targeted MS Processing category

The Component Results Plot displays the XIC of the selected component from the Control and selected Sample injections.
To aid in identifying the XIC peak, a colored box representing the peak start/stop range is overlaid on the plot. The plot is
also automatically zoomed to a range of =/- 1 minute around the peak.

A limited context menu and Properties dialog are available..

Item Function
Context Menu item Copy
Context Menu item Full Size
Context Menu item Zoom
Property Page Plot Details
Property Page Time Axis
Property Page Signal Axis
Property Page Interactive Settings

See section 5.4.1 for a description of the functionality.

5.6.4 Component Results Pane

Note: This pane is only available via the Non-Targeted MS Processing category

The Component Results pane consists of 2 sections – the Component Results Table (see 5.6.4.1) and the Component
Results Filter (See 5.6.4.2). The Component Results Table and Component Results List in the Navigation Pane are updated
dynamically based on the applied Component Results Filter. The filter can be accessed from the bottom of the Component
Results Report Pane by clicking on the chevron.

5.6.4.1 Component Results Table

The Component Results Table contain a list of peaks found perhaps filtered by rules from the Components Results Filter
below ).
The table has the follow ing columns:

Column Description

Component Number Component number of the nth result component.

Control RT (min) Retention time of the peak corresponding to the nth result component from the control injection.

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Chromeleon 7

Retention time of the start of the peak corresponding to the nth result component f rom t he co n tro l
Control RT Start (min)
injection.
Control RT Stop (min) Retention time of the end of the peak corresponding to nth result component from the control injection.

Retention time of the peak corresponding to the nth result component from th e t arg et i nject ion . I t
RT (min)
displays the retention time for the component from the first raw data file.

Retention time of the start of the peak corresponding to the nth result comp one nt f rom t he t a rg et
RT Start (min)
injection. It displays the retention time for the component from the first raw data file.

Retention time of the end of the peak corresponding to the nth result co mpo nen t f ro m t h e t a rge t
RT Stop (min)
injection.
Control M/Z Mass-to-charge ratio of the nth result component from the control injection.

M/Z Mass-to-charge ratio of the nth result component from the target injection.

Control Charge State Charge state of the nth result component from the control injection.
Charge State Charge state of the nth result component from the target injection.

Control Mono Mass Exp Experimental (observed) monoisotopic mass of the nth result component from the control injection.
Mono Mass Exp Experimental (observed) monoisotopic mass of the nth result component from the target injection.

Control Avg Mass Exp Average experimental (observed) mass of the nth result component from the control injection.

Average Mass Exp Average experimental (observed) mass of the nth result component from the target injection.
Max MS Area Maximum MS area of the nth result component from the target injection.

Control MS Area MS area of the nth result component from the control injection.

MS Area MS area of the nth result component from the target injection. It displays the area for the component ,
specific to each individual raw data file.
MS Area Ratio MS ratio of the target vs. control injection of the nth result component from the target injection.

The follow ing context menu items are available by right-clicking on the table header

Menu Item Description

Table Sort Allows reordering of table columns as well as showing and hiding various columns.

Remove Sort Re-sorts the table based on Component Number (the default sort)
Rest to Default Columns Re-draws the table using all of the default columns and layouts

5.6.4.2 Component Results Filter

Initially after processing, the Components Results Table contain a list of all peaks found. The Components Results Filter is
used to remove expected peaks, thus leaving only new /unexpected peaks.
The Components Results Filter ha tw o sections:

Parameter Sub Parameter Description

Filter target components which (Checkbox) Tick the box to enable filter the results using items in the it em
match within the following MS Components table. In order to be filtered, the RT and Mass
tolerances of an entry in the Component Results Table must ma tch t h at
MS Components table within the limits specified below.
Retention Time (min or %) Select either a maximum RT differen ce o r a m aximum RT
percent difference in order for a component to be considered a
match
M/Z (amu or %) Select either a maximum amu difference or a maximum am ua
percent difference in order for a component to be considered a
match
Match Match XXX of the following rules ALL is equivalent to the AND logical operator. Finds table rows
with variable values that match all of the criteria specified in the
rules that are assigned the AND logical operator.
ANY is equivalent to the OR logical operator. Finds table ro ws
with variable values that match any of the criteria specifie d i n
the rules that are assigned the OR logical operator.

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Variable Selects a variable from the list.

Comparison operator Select the operator to be used for comparing variable values:
= (is equal to)
<> (is not equal to)
< (is less than)
<= (is less than or equal to)
> (is greater than)
>= (is greater than or equal to)
is between
is not between
is during previous
is not during previous
is like (use with wildcards) (for Quick Search only)
is not like (use with wildcards) (for Quick Search only)
contains
does not contain
starts with
does not start with
ends with
does not end with
is any
is not any
is empty
is not empty
Value Select the compare value.

5.6.5 Chromatogram Plot Pane

The Chromatogram Plot displays the chromatogram for the selected injection. It w ill be either the TIC or BPC, depending on
the selection in the Channel list of the Navigation Pane.
The same context menu and properties are available for this plot pane as are available for the Chromatogram Pane of the
Data Process category. See section 5.4.1 for details.

5.6.6 MS Plot Pane

When a processed injection and component result are selected, the Mass Spectra pane displays the peak mass spectrum
of both the control and sample.

5.6.6.1 Zooming and Navigating in the Mass Spectrum

The mass spectrum view allow s zooming and navigating as required w ith the follow ing options:

Function Description

Zoom When active it is possible to zoom into the chromatogram by dragging an area.
Undo Zoom Reverts the recent zoom operation and returns to the previous view. Accesse d b y
right-clicking on the plot and selecting Unzoom
Full Scale Reverts the recent all zooming and re-plots the data full scale. Accessed b y ri gh t-
clicking on the plot and selecting Full Scale
Y axis zoom tools Shown when moving the cursor over the Y axis. The following functions are
available:
+ zooms into the plot vertically
Autoscale Signal resizes the plot height to the highest mass abundance cu rre nt ly
visible
- zooms out of the plot vertically

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Function Description

X axis zoom tools Shown when moving the cursor over the X axis. The following functions are
available:
+ zooms into the plot horizontally
Autoscale Time resizes the plot to the complete mass range of the acquired data.
- zooms out of the plot horizontally
Full size button Shown when moving the cursor to the bottom left corner of the plot. Click t h e f u ll-
size button to autoscale both axes simultaneously.

In addition, the follow ing zoom operations are available:

Function Description
Double Click on the abundance axis Automatically resizes the plot height to the highest m a ss a b u nd an ce cu rren tly
visible.
Double Click on the m/z axis Automatically resizes the plot width to the complete mass pane of the acquired data

Undo Zoom Reverts the recent zoom operation and returns to the previous view.

Drag the abundance axis Scrolls the y axis limits

Drag the m/z axis Scrolls the x axis limits

The follow ing context menu operations are also available:

5.6.6.2 Copy
Copies the mass spectrum plot to the clipboard as an image. This is also possible by using the Ctrl + C hotkey.

5.6.6.3 Find in Library

This menu item performs an ad hoc library search on the displayed mass spectrum using the parameters specified on the
MS Library Search tab of the processing method. Refer to 5.4.12.9 for an explanation of this w indow.

5.6.6.4 Scale

Parameter Sub Parameter Description

Apply scaling to all plots N/A Allows the user to apply the same scaling to all plots
simultaneously when checked.
Mass From Defines the start value of the mass axis.
To Defines the end value of the mass axis.

Autoscale When this is selected the plot is scaled to show the ful l ma ss
range of the data
Fixed intervals of tick marks Chromeleon automatically determines t h e i nt erva l o f t ick
marks (the small lines that mark values) on the time axis. T o
customize the intervals, select the Fixed intervals of tick marks
check box and then type or select a number in the Majo r t ick
mark and/or Minor tick mark box. A tick mark inte rva l o f 0 . 0
removes the tick marks.
Intensity From Defines the start value of the intensity axis.

To Defines the end value of the intensity axis.

Autoscale When this is selected the plot is scaled to show the full
intensity range of the mass spectrum.
Fixed intervals of tick marks Chromeleon automatically determines t h e i nt erva l o f t ick
marks (the small lines that mark values) on the time axis. T o
customize the intervals, select the Fixed intervals of tick marks
check box and then type or select a number in the Majo r t ick
mark and/or Minor tick mark box. A tick mark inte rva l o f 0 . 0
removes the tick marks.

5.6.6.5 Frame & Axes

This section allow s defining axes, grid and normalization of the mass spec plot.

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Parameter Sub Parameter Description

Axes Mass axis Displays a mass axis on the mass spec plot.
Intensity axis Displays an abundance axis on the mass spec plot.

Font Allows the font type and size of the axes to be defined.

Axis to Plot Gap Defines the distance in mm between the axes and the plot.
Frame Displays a frame around the plot

Axis Titles Axis Titles Applies titles to the mass spec plot axes.

Units Displays units on the axes of the mass spec plot.

Font Allows the font type and size of the axis titles to be defined

Grid Horizontal grid lines Applies horizontal grid lines to the mass spec plot.
Vertical grid lines Applies vertical grid lines to the mass spec plot.

Orientation Horizontal Scan type is the horizontal axis, and signal is the vertical axis

Vertical Scan type is the vertical axis, and signal is the horizontal axis.
Normalization None No normalization is performed.

Absolute maximum Performs spectra normalization relative to the absolute

maximum of the spectra.

5.6.6.6 Label
This section allow s defining how labels are show n in the mass spectral plot.

Parameter Sub Parameter Description

Peak Label Rotation Defines the angle the mass spectrum label is shown at.

Maximum threshold The threshold intensity (in %) at which ma ss p e a ks wi l l b e

labeled
Font Defines the font for the mass spectrum label.

Show detected mass info for time Checking this box will cause the detected mass f o r t h e t i me
spectra spectrum to be displayed horizontally on top of the mass peak.
If the monitored mass is not detected, no information is
displayed.

5.6.6.7 Comparison
This section allow s defining how multiple mass spectra are arranged

Group Sub Parameter Description

Arrangement Stacked Plots are stacked on a single plot and share the sa m e sca n a xis;
each stacked plot has a separate intensity axis.
Overlaid Plots are overlaid on a single plot and share t h e sa m e sca n a n d
intensity axes
Offset Scan Offset To offset overlaid plots on the scan axis, select the check b o x a nd
enter the offset percentage in the box.
Intensity Offset To offset overlaid plots on the intensity axis, select t he c he c k b o x
and enter the offset percentage in the box
Overlay Overlay with right signal axis When plots are overlaid, select this check box to include a se co n d
signal axis on the right side of the plot
Mirror Mirror Signal Select this check box to invert the intensity axis of t h e o verla id o r
stacked plots. The plots "mirror" the main spectrum or I-t plot.

5.6.6.8 Interactive Settings

This section defines w hat optional zoom/unzoom tools are displayed on the mass spec plot

Function Description

Show overview plot When this check box is selected, the miniature overview of the mass spectrum plot
is displayed when zooming into the chromatogram.

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Chromeleon 7

Function Description

Show popup controller When this check box is selected, the full-size button, vertical and horizontal z o om
toolbars on the chromatogram axes are visible.

5.6.7 Processing Parameters

Note: This pane is only available via the Non-Targeted MS Processing category

The Processing Parameters pane show s the parameter values that w ere used to process each individual injection. This is a
read-only pane that show s the values for parameters that w ere defined in the processing method, but w ere subject to
change based on the actual data for that injection

Section Parameter Description

General Displays the number and the name o f in jectio n

Control Injection #, Name that was used in the processing run as the
reference injection.

Corresponds to the type of processing t h at wa s

selected in the Processing Method pane using the
Select Task to be Performed drop-down list. This
parameter can have one of the following two
values:
Processing Type
Find All Ions in the Run: Result are presented a s
each ion representing a separate en try. Th is i s
the default.
Find All Masses in the Run: Combines m u lt iple
charge states into a single entry
Basic Auto-Compute Basic Parameters Corresponds to the selection made in t he A ut o-
Populate check box of the Processi n g Me th od
pane:
True: The check box was checked and the
parameter values were filled automatically, based
on the specific injection data.
False: The check box was cleared checke d a nd
the parameters values were selected

Corresponds to the Absolute MS Signal

Absolute MS Signal Threshold
Threshold parameter.

This parameter represents the noise level i n t h e

MS data, in terms of absolute intensities.
It is one of the two factors affecting the va lu e o f
MS Noise Level the Absolute MS Signal Threshold used for
distinguishing signals from noise. The fact or, b y
which the noise level has to be surpassed to
recognize an absolute intensity value as a signal,
is specified by the S/N Threshold.

This parameters represents the signal-t o-n oise

threshold used when interpreting the raw MS
data, to distinguish a signal from noise.
The value specifies the factor by which a value of
S/N Threshold the MS absolute intensity has to surpass the M S
Noise Level, in order to be considere d a si g na l
and not noise. This parameter is one of t h e t wo
factors affecting the value of t h e A b so lut e M S
Signal Threshold.

This parameter represents the ty pical wi dt h o f

peaks near the beginning of the chromatographic
run. It complements the Typical
Beginning Peak Width (min) Chromatographic Peak Width to take into
account the tendency of chromatographic p ea ks
to broaden during the course of a
chromatographic run.

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Section Parameter Description

This parameter represents the typical wi dt h o f

chromatographic peaks in the analyze d L C/ MS
run.
Note: When the Auto-populate check box is
selected in the Processing Method pane, the
value of Typical Chromatographic Peak Wid th is
set to the width of the highest peak in the
Typical Chromatographic Pk Width (min)
chromatogram.
To take into account the tendency of
chromatographic peaks to broa d en d uring t he
course of a chromatographic run, the Typical
Chromatographic Peak Width is compl emen te d
with the Beginning Peak Width and t he E nd ing
Peak Width.
This parameter represents the typical wi dt h o f
peaks near the end of the chromatographic run. It
complements the Typical Chromatographic
Ending Peak Width (min)
Peak Width to take into account the tendency o f
chromatographic peaks to broa d en d uring t he
course of a chromatographic run.

This parameter represents the maximum width of

chromatographic peaks in the LC/ MS ru n . A n y
peak wider than this value will be consi de red t o
be part of the background and will not be includ e
it in the results.
Max Chromatographic Pk Width (min)
Note: When the Auto-populate check box is
selected in the Processing Method pane, the
value of Maximum Chromatographic Peak Wid t h
is set to the geometric mean of the wi dth o f t h e
highest peak and the range of the chromatogram.
This parameter specifies the start retention t i me
of a truncated chromatogram time ran ge t h at is
Time Limit Start (min)
used to reduce the NTMS processing to an
appropriate area.

This parameter specifies the end retention time of

a truncated chromatogram time range that is used
Time Limit End (min)
to reduce the NTMS processing to an appropriate
area.

This parameter represents the maximum allowed

mass difference of the same ion in different
scans. Depending on the resolut ion o f t h e M S
Mass Tolerance
data, the value is reported in ppm (for high-
resolution data) or in daltons (for low-re so lu tio n
data).

This parameter represents the maximum allowed

mass deviation when comparing the theo ret ical
Mass Accuracy
mass to the calculated mass of a particular ion t o
determine identification.

This parameter specifies the maximum

considered retention time shift when co mp arin g
Maximum RT Shift (min) two or more LC/MS runs. It is one of the basic Ion
Alignment parameters of the BioPharma Fin de r
NTMS Processing Method pane
Advanced This parameter represents the lowest relative
abundance of a component in the MS signal, as a
percentage of the base peak, required to d et ect
an ion at a given point in the chromatogram.
Unlike the Absolute MS Signal Threshold, wh ic h
sets the minimum MS signal for detection of a ny
Relative MS Signal Threshold
ion in the MS data, the Relative MS Signal
Threshold defines the minimum relative
abundance for detection o f a comp on ent t ha t
coelutes with a larger compone nt in t he sa m e
LC/MS run.

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Chromeleon 7

Section Parameter Description

This parameter represents the lowest signal

Relative Analog Threshold value, relative to the highest peak in the
chromatogram, that the application can detect.
This parameter represents the factor used to
divide the Typical Chromatographic Peak Wi d t h
value to obtain the width of the G au ssi a n f ilt er
used to average nearby full MS scans. For
example, a value of 4 means the filter width is one
fourth of the typical chromatographic peak width.
Filtering improves the signal-to-noise ratio (S / N)
Width of Gaussian Filter of each scan by reducing noise, but this may
decrease chromatographic resolution. Lower th is
parameter value to improve sensitivity by
suppressing noise and increase th e n umb er t o
improve chromatographic resolution. A value of 1
represents maximum noise suppression using the
Gaussian filter width equal to t he t ypical p e ak
width.

This parameter represents the minimum size of a

valley between a pair of peaks, as a perce n t ag e
Minimum Chromatography Valley (%)
value, for considering the pair as t wo se p a ra te
peaks.

This parameters represents the minimum width of

Minimum MS Peak Width (Da) MS peaks used to generate a range for the
isotopic envelope of the ion

This parameters represents the maxmum width of

Maximum MS Peak Width (Da) MS peaks used to generate a range for the
isotopic envelope of the ion
This parameter represents the maximum mass to
Maximum Mass (Da) change the calculation of the average mass of an
ion.

This parameter represents a percen ta ge va lue

Mass Centroid Cutoff (% from base) cutoff to change the calculation of t h e a ve rage
mass of an ion.

5.7 Intact Protein Deconvolution Category

5.7.1 Ribbon Bar

The Ribbon bar provides access to various panes, method creation, and data processing.

In the Intact Protein Deconvolution category, the buttons on the “Panes” section of the ribbon allow show ing or hiding of
panes. The follow ing panes are available:

• Processing Method (see section 5.7.2)

• Processing Parameters (see section 5.7.3)
• Component Results (see section 0)
• Chromatogram (see section )

• Deconvoluted Spectrum (see section 5.7.6)

• Source Spectrum (see section 5.7.7)

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 Chromeleon 7

5.7.2 Processing Method Pane

Note: This pane is only available via the Intact Protein Deconvolution category

The parameters on this pane w ill be used to deconvolve the injection data. They are stored as part of the overall
Chromeleon processing method. It is divided into 4 tabs: Chromatogram Parameters, Source Spectra Parameters,
Algorithm Parameters and Multiconsensus. The IPD processing w orkflow is such that a user w ould typically setup the
processing method and then select Start or Start All on the ribbon. The tabs in this pane are described below .

5.7.2.1 Chromatogram Parameters

Parameter Sub Parameter Description

Use Restricted Time Checked Parameters defined under Range Display Type are
used for calculations
Unchecked Full time scale is used for calculations

Range Display Type Scan Range Uses the defined scan range for calculations

Time Limit Uses the time limit range for calculations

Chromatogram Settings m/z Range Mass range used in the calculation

Chromatogram Trace Type The type of Chromatogram used:

TIC Total ion intensity or
PBC Base Peak

Sensitivity Type of Sensitivity for the calculation

High or Low

Rel. Intensity Threshold (%) Intensity Threshold to be used in the calculation

5.7.2.2 Source Spectrum Parameters

Note: This pane is only available via the Intact Protein Deconvolution category

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Chromeleon 7

Parameter Sub Parameter Description

Source Spectra Parameters Sliding Windows Select this option to use the Sliding Windows deconvo lut ion
algorithm to generate source spectra
Average over Selected Retention Time Select this option to use the Average over Selected Retention
Time deconvolution algorithm to generate source spectra

5.7.2.3 Algorithm Parameters

Note: This pane is only available via the Intact Protein Deconvolution category

Parameter Sub Parameter Description

Deconvolution Algorithm ReSpect Isotopically Unresolved deconvolution algorithm

Xtract Isotopically Resolved deconvolution algorithm

Deconvolution Results Filter Output Mass Range Definable mass range for the output

Deconvoluted Spectra Display Mode Spectra will be displayable in either an I so t opic vi ew o r i n

Mass Probability Distribution Profile
Charge State Distribution Model Mass Range Total Mass Range
Deconvolution Mass Tolerance Mass tolerance in either Da or PPM

Sensitivity Type of Sensitivity for the calculation

High or Low
Rel. Intensity Threshold (%) Intensity Threshold to be used in the calculation

Choice of Peak Model Intact Protein Appropriate peak model for the data. Peaks wi l l b e m od el
based on the intact protein model
Nucleotide Appropriate peak model for the data. Peaks wi l l b e m od el
based on the Nucleotide model
Resolution at 400 m/z Raw File Specific Resolution of the source spectrum at an m/z value of 400.
Method Specific

Generate XIC for each Checked XIC will be calculated for each component
Component
Calculate XIC
Unchecked XIC will not be calculated for each component
Advanced Settings Access to advanced parameters

5.7.2.4 Advanced Settings

Parameter Sub Parameter Description

Intact Protein Deconvolution Charge Carrier Number of adduct ions used during electrospray (ESI)
Parameters processing.
Charge High Maximum charge state to be deconvolved.

Charge Low Minimum charge state to be deconvolved.

End Time End time

High Number of Adjacent Charges Maximum number of charge state peaks that must appear i n
a row for components of the minimum output mass and
maximum output mass.
Intensity Threshold Scale Intensity threshold scale required to display peaks in a
chromatogram.
Low Number of Adjacent Charges Minimum number of charge state peaks that must appear in a
row for components of the minimum and m a xim um o ut pu t
masses.

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 Chromeleon 7

Parameter Sub Parameter Description

Min Peak Significance Numerical value (in standard deviatio ns) t h a t d e te rmine s
whether a peak is considered legitimate and retained.
Negative Charge Whether the data was acquired in n eg at ive ch arg e m ode
during the electrospray (ESI) process.
Noise Compensation Whether the ReSpect algorithm improves si g n al d e te ct ion
where the noise level varies across the data.
Noise Rejection Degree of confidence that a peak is plausible.

Number of Peak Models Number of peak models generated to determine the width that
a peak must have to be associated with a compound.
Peak Model Width Scale Number of regions used to determine the peak width required
for a peak to be associated with a compound.
Quality Score Threshold Minimum protein quality score required for a component to be
considered valid.
Relative Abundance Threshold Height of the smaller overlapping isoto pic clu st e r u se d t o
resolve overlapping isotopic clusters.
Start Time Start time

Target Peak Mass Expected target mass to use when calculating the peak
model.
Target Peak Shape Left Numerical value for the left side of the peak (determines t h e
peak sharpness required for a peak to be associat ed wi t h a
compound).
Target Peak Shape Right Numerical value for the right side of the peak (determines th e
peak sharpness required for a peak to be associat ed wi t h a
compound).

5.7.2.5 M ulticonsensus

Note: This pane is only available via the Intact Protein Deconvolution category

Parameter Sub Parameter Description

Multiconsensus Injections Include Select the check box before an injection name to include t he
injection in Multiconsensus deconvolution processing.

When the Multiconsensus result format is selected for

experiments with multiple loaded raw data files, Chrome leon
processes one experiment and then merges the
deconvolution results from all of the l oa ded ra w d at a f i les
together.
Name The name of an injection in the current inje ctio n l ist o f t he
sequence.
Condition (Optional) Enter information about an injection. This
information is retained in list form. To assign an existing
condition to any other injection, click the down a rro w f o r a n
injection and select the preferred condition from the list.

Note: If you assign a condition to one i nje ctio n, you m ust

assign a condition to all of the injections
Multiconsensus Component Mass Tolerance Specifies the mass tolerance that components from individual
Merge files must satisfy to be merged into a Multiconsensus
component.
Click the down arrow to select the unit: ppm (parts per million)
or Da (Daltons).
RT Tolerance Specifies the maximum separation in re t ent ion t ime t h at
components from individual files must satisfy t o b e m erg ed
into a Multiconsensus component.

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Chromeleon 7

Parameter Sub Parameter Description

Minimum Number of Required Specifies the minimum number of injectio ns t h a t mu st b e

Occurrences included in a Multiconsensus component for it to be
considered valid.

5.7.3 Processing Parameters Pane

Note: This pane is only available via the Intact Protein Deconvolution category

The Processing Parameters pane show s the parameter values that w ere used to process each individual injection. This is a
read-only pane that show s the values for parameters that w ere defined in Section 5.6.2, but w ere subject to change bas ed
on the actual data for that injection

Parameter Sub - Parameter Shown Description

Chromatogram Parameters End Scan Number This is the ending scan number of the data use d
by the deconvolution algorithm. It i s co m put ed
based on the actual End Time (see belo w) a nd
the actual injection data.
End Time This is the actual ending reten tio n t ime o f t h e
data that is supplied to the deconvolution
algorithm. It is the lesser of (a) the time specifie d
in the processing method and (b) the end time o f
the injection data.
Mass Range High This is the actual maximum mass of the data
used by the deconvolution al gorit hm . I t i s t h e
greater of (a) the high mass specified in the
processing method and (b) the actual max imu m
mass of the injection data.
Mass Range Low This is the actual minimum mass of the data used
by the deconvolution algorithm. It is the greater of
(a) the low mass specified in the processing
method and (b) the actual minimum mass of t h e
injection data.
Start Scan Number This is the starting scan number of the data used
by the deconvolution algorithm. It i s co m put ed
based on the actual Start Time (see belo w) a nd
the actual injection data.
Start Time This is the actual starting retention t i me o f t he
data that is supplied to the deconvolution
algorithm. It is the greater of (a) the time specified
in the processing method and (b) the start time of
the injection data.
ReSpect Parameters End Time When the option to use the ReSpect algorithm i s
specified in the processing method , t h is i s t h e
actual Ending retention time used for
deconvolution. It is the lesser of (a) the time
specified in the processing method a nd (b ) t h e
end time of the injection data.
Start Time When the option to use the ReSpect algorithm i s
specified in the processing method , t h is i s t h e
actual Starting retention time used for
deconvolution. It is the greate r o f (a ) t he t ime
specified in the processing method a nd (b ) t h e
start time of the injection data.
Sliding Window Parameters Start Time When the option to use the Sliding Window
algorithm is specified in the processing met ho d,
this is the actual Starting retention time use d f o r
deconvolution. It is the greate r o f (a ) t he t ime
specified in the processing method a nd (b ) t h e
start time of the injection data.

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 Chromeleon 7

Parameter Sub - Parameter Shown Description

Stop Time When the option to use the Sliding Window
algorithm is specified in the processing met ho d,
this is the actual Ending retention time u se d f o r
deconvolution. It is the lesser of (a) the time
specified in the processing method a nd (b ) t h e
end time of the injection data.
Xtract Parameters End Time When the option to use the Xtract Window
algorithm is specified in the processing met ho d,
this is the actual Ending retention time u se d f o r
deconvolution. It is the lesser of (a) the time
specified in the processing method a nd (b ) t h e
end time of the injection data.
Start Time When the option to use the Xtract a lg orit hm i s
specified in the processing method , t h is i s t h e
actual Starting retention time used for
deconvolution. It is the greate r o f (a ) t he t ime
specified in the processing method a nd (b ) t h e
start time of the injection data.

5.7.4 Component Results Pane

Note: This pane is only available via the Intact Protein Deconvolution category

The Component Results pane displays a nested table of the deconvolution results.

For non-Multiconsensus data, clicking the “+” icon next to a Result Component w ill expand the table to show a sub-table of
individual charge states and the associated results.
For Multiconsensus data, clicking the “+” icon next to a Result Component w ill expand the table to show a sub-table of the
results for the individual injections that w ere included in the multi-consensus experiment. Clicking the “+” icon next to an
injection w ill display a sub-table of the individual charge states and the associated results.

5.7.4.1 Table Columns

Parameter Description

Result Component Shows “Result Component 1” for the first component, “Result Component 2” for the second, and so on.
Monoisotopic Mass Displays a weighted average of the monoisotopic masses of each charge state
Sum Intensity Displays the sum of the intensities of the isotopic clusters in a charge state.

Relative Abundance Displays the relative abundance of the peaks in the sample that are above the threshold set by the Rel.
Abundance Threshold (%) (for Xtract) or Rel. Abundance Threshold (%) (for ReSpect) parameter.
Fractional Abundance Displays the fractional abundance of a component, which is the abundance for that peak relative to the
total abundance of all peaks in the spectrum, expressed as a percentage.
Score Displays the quality score of the deconvolved component.

Number of Charge States Displays the number of detected isotopic clusters for a given deconvolved mass.
This is the same number as the number of rows at the charge state level below the component level.
Charge State Distribution Displays the range of charge states detected for the component, from the lowest to the highest charge
state.
Mass Std. Dev. Displays the standard deviation, in Daltons, of the delta masses for all the charge states of a
component (for example, the standard deviation of Delta Mass (Da)).
Delta Mass Displays the difference between the mass of a specific component a nd t he ma ss o f t h e h igh est -
intensity component.
Start Time (min) Displays the start of the retention time range for of the Results Component in the selected injection

Stop Time (min) Displays the end of the retention time range for of the Results Component in the selected injection
RT Range Displays the range of the Results Component in the selected injection

Apex RT Displays the Apex RT of the Results Component in the selected injection

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Chromeleon 7

Number of Detected Intervals Displays the number of sliding windows within the specified tolerances where the application found the
component of interest
Scan Range (Visible only for sliding windows deconvolution experiments.) Displays t h e S t art Time (m in) f o r a
specific raw data file.
Protein Name The Protein Name variable returns the name of the target sequence that mat ch es t h i s co mp one nt
within a given tolerance.
Modification Modification of the target sequence that best matches a specific component within a given tolerance.
Matched Mass Error (ppm) Error associated with the best target sequence that matches this component.

Theoretical Mass (Da) Theoretical mass of a component.

Drug Load Drug load of a component.

Average Charge The weighted average charge, based on abundance of each charge state

Monoisotopic Mass CV CV (coefficient of variation) of the monoisotopic masses for each charge state
Apex RT %CV CV (coefficient of variation) percentage of the apex retention time of a component.

Sum Intensity %CV CV (coefficient of variation) percentage of the apex intensities of a component.

Number of Files Observed Number of raw data files in which the component was detected.
Score %CV CV (coefficient of variation) percentage of the score of a component.

Condition Condition of a component.

5.7.4.2 Table Header Properties

Right-clicking on the table header provides access to a Properties dialog w ith the follow ing tabs:

Table Columns…
Allow s definition of w hich columns should be displayed and in w hich order. Note that this applies only to the main table, not
the injection or charge state sub-tables.

Remove Sort
Restores the sort order to the default order (by Results Component)

Filter Bar
Toggles display of an additional table row in the first position. To filter (limit) the display of the results row s to those meeting
specific criteria, type criteria in the cell

Reset to Default Columns

Restores the table column configuration to the system default

5.7.4.3 Table Body Properties

Right-clicking on the table body provides access to a Properties dialog w ith the follow ing tabs:

Copy
Copies the selected information to the clipboard

Add to Component Table

Adds a new entry to the MS Component Table of the Processing Method, based on the selected entry.

5.7.5 Chromatogram Pane

Note: This pane is only available via the Intact Protein Deconvolution category

The Chromatogram pane displays the TIC or BPC Chromatogram and the Results XIC for a selected injection.

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 Chromeleon 7

5.7.5.1 Zooming and Navigating

The chromatogram view allow s zooming and navigating in the chromatogram as required w ith the follow ing options:

Function Description

Automatic Tool When active it is possible to zoom into the chromatogram by dragging an a re a. I n
addition, other actions can be performed.
Zoom When active it is possible to zoom into the chromatogram by dragging an area.
Undo Zoom Reverts the recent zoom operation and returns to the previous view.

In addition the following zoom operations are available:

Function Description

Double Click on the signal axis Automatically resizes the chromatogram height to the highest peak currently visible.
Double Click on the retention axis Automatically resizes the chromatogram width to the co mp let e d ura tio n o f t he
chromatogram.
Signal axis zoom tools Shown when moving the cursor over the signal axis. The following f u nc t ions a re
available:
+ zooms into the chromatogram vertically
Autoscale Signal resizes the chromatogram height to the highest p ea k cu rre nt ly
visible
- zooms out of the chromatogram vertically

Retention time axis zoom tools Shown when moving the cursor over the retention time axis. The following functions
are available:
+ zooms into the chromatogram horizontally
Autoscale Time resizes the chromatogram to the complete duration of the
chromatogram.
- zooms out of the chromatogram horizontally
Full size button Shown when moving the cursor to the bottom left corner of the chromatogram plot .
Click the full size button to autoscale both axes simultaneously.

Undo Zoom Reverts the recent zoom operation and returns to the previous view.

The following context menu operations are also available:

Function Description
Right Click select Full Size Automatically resizes the chromatogram height to the full size.
Right Click select Autoscale Automatically resizes the chromatogram height to the highest peak currently visible.

Right Click select Unzoom Reverts the recent zoom operation and returns to the previous view.

Holding down the right-hand mouse button and Zooms into the chromatogram area selected.
selecting an area of the chromatogram select Zoom

5.7.5.2 Properties
The follow ing properties are available:

Plot Details

Parameter Sub Parameter Description

Axes Time Axis Displays a time axis on the chromatogram.

Signal Axis Displays a signal axis on the chromatogram.

Font Allows the font type and size of the axes to be defined.

Axis to plot gap Defines the distance in mm between the axes and the
chromatogram plot.
Frame Frame that is drawn around the plot area.
Axes Descriptions Axes Titles Applies titles to the chromatogram axes.

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Chromeleon 7

Units Displays units on the axes of the chromatogram.

Font Allows the font type and size of the axes titles to be defined.
Grid Signal axis grid lines Applies horizontal grid lines to the chromatogram.

Time axis grid lines Applies vertical grid lines to the chromatogram.

Orientation Horizontal Displays the chromatogram in the portrait orientation.

Vertical Displays the chromatogram in the landscape orientation.

Signal details Raw data points Shows the raw data points.

Time Axis
This section allow s the user to define the scaling used for the time axis. The follow ing options are available:

Parameter Sub Parameter Description

Time Axis Share time axes If your chromatogram plot includes overlaid ch rom at ogra ms
and you have selected a Stacked arrangement on the
Comparison page, you can select whether to use a co mmo n
(shared) time axis for the chromatogram stripes, or se p a ra t e
time axes. The unit on the time axis is always identica l f or a ll
chromatogram stripes.
Select the Share time axis check box to display a sin gle t ime
axis for all chromatograms (default). Clear the ch eck b o x t o
display separate time axes for each chromatogram.
If you have cleared the Share time axis check box, select t he
chromatogram from the Settings for chromatogram plot list f o r
which the settings under Range (see below) shall apply.
Range Autoscale or Fixed Determines the method for selecting the range. Can be set t o:
Autoscale or Fixed, Autoscale on Peak, or Fixed using
Autoscale on Peak Formula.
Fixed using Formula
Autoscale or Fixed From Defines the start time of the chromatogram. Eithe r A ut o o r a
specific time can be selected.
To Defines the end time of the chromatogram. Eit her A u to o r a
specific time can be selected.
Autoscale on Peak Selected Allows the user to select the peak by Name, Greatest He igh t,
Greatest Area, Number, or Component Table Number
Width Defines the width by which to pad the se l ecte d a ut osca le d
peak range. This can be defined or set to Autosize width.
Fixed using Formula From Defines the start time of the chromatogram using a formula
To Defines the end time of the chromatogram using a formula

Tick mark intervals Fixed intervals of tick marks Defines whether tick marks should appear at selected intervals

Major tick mark Defines the interval for major tick marks
Minor tick mark Defines the interval for minor tick marks

Time axis units Minutes (min) The units for the time axis are minutes.
Seconds (s) The units for the time axis are seconds.

Signal Axis
This section allow s the user to define the scaling used for the signal axis. The follow ing options are available.

Parameter Sub Parameter Description

Signal Axis Settings for chromatogram Determines the signal axis for which to define the setti ngs. T o b e
plot able to select between different signal axes, you h ave t o lo ad a t
least one Overlay. In addition, two signal axes must be displayed.
Range for selected plot Autoscale or Fixed Determines the method for selecting the ra ng e. Ca n b e se t t o:
Autoscale or Fixed, or Fixed using Formula.
Fixed using formula

Autoscale or Fixed To Defines the end value of the signal axis. Either Auto or a sp e cif ic
time can be selected.

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Parameter Sub Parameter Description

From Defines the start value of the signal axis. Either Auto or a sp e ci fic
time can be selected.
Fixed using Formula From Defines the start value of the signal axis using a formula

To Defines the end value of the signal axis using a formula

Autoscale in time range or peak Autoscale in visible time Determines the signal autoscale options for the current
range chromatogram. Following options are enabled only fo r t he si gn al
scale mode ‘Autoscale or fixed’; Autoscale in visi ble t ime ra n ge,
Autoscale in fixed time range Autoscale in fixed time range, Autoscale on peak.
Autoscale on peak

Autoscale in visible time range N/A Calculates the signal minimum and / or maximum on th e b asi s o f
the current time range specified on the Time Axis properties page.
Autoscale in fixed time range From Custom start value to calculate signal minimum and / or maximum.
To Custom end value to calculate signal minimum and / or maximum.

Autoscale on peak Selected Calculates the signal minimum and / or maximum on th e b asi s o f
the range between peak start and end time. Following peak
selection modes are available; by name, by g rea te st h ei ght , b y
greatest area, by number, by component number.
Time mark intervals Fixed intervals of tick marks Defines whether tick marks should appear at selected intervals

Major tick mark Defines the interval for major tick marks
Minor tick mark Defines the interval for minor tick marks

Title
This section defines the caption that w ill be displayed in the chromatogram header. Left, middle and right captions can be
selected either based on simple text values or on user-defined formulas. The formula can be based on variables from the
follow ing sections:

• Global Functions (see section 7.1)

• General (see section 7.2)
• Sequence (see section 7.3)
• Injection (see section 7.4)

• Audit Trail (see section 7.5)

• Preconditions (see section 7.6)
• Chromatogram (see section 7.8)
• Processing Method (see section 7.21)
• Instrument Method (see section 7.31)
• Custom Formulas (see section 5.8.31)

In addition, the follow ing options are available:

Parameter Sub Parameter Description
Title Draw Titles Displays chromatogram titles.
Font Allow s the font type and size of the titles to be defined
Left title Draw left title Displays the left part of the title.
When checked the left part of the title can be defined
based on formulas as described above.
Middle title Draw middle title Displays the middle part of the title.
When checked the middle part of the title can be
defined based on formulas as described above.

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Parameter Sub Parameter Description

Right title Draw right title Displays the right part of the title.
When checked the right part of the title can be defined
based on formulas as described above.
Legend Draw legend Displays a legend for overlaid chromatograms.
When checked the format of the legend can be defined
based on formulae as described above.

Line & Fill Styles

This section allow s a consistent color scheme for the objects in the chromatogram plot to be defined. The follow ing items
can have their line color defined:
• Chromatograms 1-8 • Peak w idth • Errors
• Peak delimiter • Raw data points • Peak purity index
• Peak separation • Detection parameters • Peak match index

• Baseline • Gradients • Tubes

• Rider baseline • Signal Parameters • Fractions
• Free baseline • Triggers •
• Peak tangents • Manual Commands •

The follow ing items can have their fill color defined:
• Background • Peak label • Detection parameter label
• Tube Label • Tubes • Fractions

Interactive Settings
This section defines the interactive settings in the chromatogram. The follow ing options are available:

Function Description

Maximum hit test distance Specify the distance when the shape of the mouse point er ch an ge s wh e n y o u
approach an object in the chromatogram plot.
Show overview plot When this check box is selected, the miniature overview of the chromatogram plot
is displayed when zooming into the chromatogram.
Show popup controller When this check box is selected, the full size button, vertical and horizonta l zoo m
toolbars on the chromatogram axes are visible.
Visualize selections When this check box is selected, visualization of selected objects, such as a
selected peak, is enabled.
Highlight selected chromatogram Enables or disables the highlighting of the selected chromatogram.

5.7.6 Deconvoluted Spectrum Pane

Note: This pane is only available via the Intact Protein Deconvolution category

The Deconvoluted Spectrum pane displays the Deconvoluted mass spectrum for the selected injection.

5.7.6.1 Zooming and Navigating in the Mass Spectrum

The mass spectrum view allow s zooming and navigating as required w ith the follow ing options:

Function Description

Zoom When active it is possible to zoom into the chromatogram by dragging an area.
Undo Zoom Reverts the recent zoom operation and returns to the previous view. Accesse d b y
right-clicking on the plot and selecting Unzoom

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Function Description

Full Scale Reverts the recent all zooming and re-plots the data full scale. Accessed b y ri gh t-
clicking on the plot and selecting Full Scale
Y axis zoom tools Shown when moving the cursor over the Y axis. The following functions are
available:
+ zooms into the plot vertically
Autoscale Signal resizes the plot height to the highest mass abundance cu rre nt ly
visible
- zooms out of the plot vertically

X axis zoom tools Shown when moving the cursor over the X axis. The following functions are
available:
+ zooms into the plot horizontally
Autoscale Time resizes the plot to the complete mass range of the acquired data.
- zooms out of the plot horizontally
Full size button Shown when moving the cursor to the bottom left corner of the plot. Cli ck t h e f u ll
size button to autoscale both axes simultaneously.

In addition, the follow ing zoom operations are available:

Function Description

Double Click on the abundance axis Automatically resizes the plot height to the highest m a ss a b u nd an ce cu rren tly
visible.
Double Click on the m/z axis Automatically resizes the plot width to the complete mass pane of the acquired data

Undo Zoom Reverts the recent zoom operation and returns to the previous view.
Drag the abundance axis Scrolls the y axis limits

Drag the m/z axis Scrolls the x axis limits

The follow ing context menu operations are also available:

5.7.6.2 Copy
Copies the mass spectrum plot to the clipboard as an image, This is also possible by using the Ctrl + C hotkey.

5.7.6.3 Export Spectrum

Exports the mass spectrum to a text file. The follow ing options are available:

Parameter Sub Parameter Description

Destination Clipboard Exports a textual description of the mass spectrum dat a i nt o
the clipboard.
File Exports a textual description of the mass spectrum data into a
text file.
Format CM-ASCII The exported mass spectrum contains complete information
STIP-ASCII The exported mass spectrum plot contains condensed
information
Parameters Use baseline correction settings Uses the baseline correction settings from MS settings tab o f
from Processing method the processing method
Use fixed scan step Changes the resolution for the exported mass spectrum

5.7.6.4 Full Size

Completely unzooms both the x-axis and y-axis

5.7.6.5 Autoscale Intensity

Completely unzooms the y-axis

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5.7.6.6 Undo Zoom

Reverts the recent zoom operation and returns to the previous view .

5.7.6.7 Properties
The follow ing sections describe the tabs of the Properties dialog accessed from the context menu.

Scale

Parameter Sub Parameter Description

Apply scaling to all plots N/A Allows the user to apply the same scaling to all plots
simultaneously when checked.
Mass From Defines the start value of the mass axis.

To Defines the end value of the mass axis.

Autoscale When this is selected the plot is scaled to show the ful l ma ss
range of the data
Fixed intervals of tick marks Chromeleon automatically determines t h e i nt erva l o f t ick
marks (the small lines that mark values) on the time axis. T o
customize the intervals, select the Fixed intervals of tick marks
check box and then type or select a number in the Majo r t ick
mark and/or Minor tick mark box. A tick mark inte rva l o f 0 . 0
removes the tick marks.
Intensity From Defines the start value of the intensity axis.
To Defines the end value of the intensity axis.

Autoscale When this is selected the plot is scaled to show the full
intensity range of the mass spectrum.
Fixed intervals of tick marks Chromeleon automatically determines t h e i nt erva l o f t ick
marks (the small lines that mark values) on the time axis. T o
customize the intervals, select the Fixed intervals of tick marks
check box and then type or select a number in the Majo r t ick
mark and/or Minor tick mark box. A tick mark inte rva l o f 0 . 0
removes the tick marks.

Frame & Axes

This section allow s defining axes, grid and normalization of the mass spec plot.

Parameter Sub Parameter Description

Axes Mass axis Displays a mass axis on the mass spec plot.

Intensity axis Displays an abundance axis on the mass spec plot.

Font Allows the font type and size of the axes to be defined.
Axis to Plot Gap Defines the distance in mm between the axes and the plot.

Frame Displays a frame around the plot

Axis Titles Axis Titles Applies titles to the mass spec plot axes.

Units Displays units on the axes of the mass spec plot.

Font Allows the font type and size of the axis titles to be defined
Grid Horizontal grid lines Applies horizontal grid lines to the mass spec plot.

Vertical grid lines Applies vertical grid lines to the mass spec plot.

Orientation Horizontal Scan type is the horizontal axis, and signal is the vertical axis
Vertical Scan type is the vertical axis, and signal is the horizontal axis.

Normalization None No normalization is performed.

Absolute maximum Performs spectra normalization relative to the absolute
maximum of the spectra.
Charge States Specifies if charge state lines should be superimposed on th e
plot

Title

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This section defines if titles are displayed and how titles should be displayed:

Parameter Sub Parameter Description

Draw titles Shows a title for the fluorescence spectra plot.

Font Allows the font for the fluorescence sp e ctra p lot t it le t o b e

defined.
Left title Draw left title Displays the left part of the title.

Use default When checked left part of the title is shown as in Chrome leon
7.2.
When not checked the left part of t he t i tle can b e d e fin ed
based on formulas in the edit field.
Center title Draw center title Displays the middle part of the title.
Use default When checked middle part of the title is shown as in
Chromeleon 7.2.
When not checked the middle part of the title can b e d ef ine d
based on formulas in the edit field.
Right title Draw right title Displays the right part of the title.

Use default When checked right part of the title is shown as in Chromeleon
7.2.
When not checked the right part of the t i tle can b e d ef ine d
based on formulas in the edit field.

Comparison
This section allow s defining how multiple mass spectra are arranged

Group Sub Parameter Description

Arrangement Stacked Plots are stacked on a single plot and share the sa m e sca n a xis;
each stacked plot has a separate intensity axis.
Overlaid Plots are overlaid on a single plot and share t h e sa m e sc a n a n d
intensity axes
Offset Scan Offset To offset overlaid plots on the scan axis, select the check b o x a nd
enter the offset percentage in the box.
Intensity Offset To offset overlaid plots on the intensity axis, select t he c he ck b o x
and enter the offset percentage in the box
Overlay Overlay with right signal axis When plots are overlaid, select this check box to include a se co n d
signal axis on the right side of the plot
Mirror Mirror Signal Select this check box to invert the intensity axis of t h e o verla id o r
stacked plots. The plots "mirror" the main spectrum or I-t plot.

Line & Fill Styles

This section allow s the color of each item in the mass spec plot to be defined. The follow ing items can have their color
defined:
• Grid lines • Axes • Spectrum 1-8

The follow ing items can have their fill color defined:
• Background • •

Interactive Settings
This section defines w hat optional zoom/unzoom tools are displayed on the mass spec plot

Function Description
Show overview plot When this check box is selected, the miniature overview of the mass spectrum plot
is displayed when zooming into the chromatogram.

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Function Description

Show popup controller When this check box is selected, the full size button, vertical and horizonta l zoo m
toolbars on the chromatogram axes are visible.
.

5.7.7 Source Spectrum Pane

Note: This pane is only available via the Intact Protein Deconvolution category

The Source Spectrum pane show s the spectrum extracted from the source injection data. The charge states for the spectral
peaks are optionally overlaid on the plot.

5.7.7.1 Zooming and Navigating in the Mass Spectrum

The mass spectrum view allow s zooming and navigating as required w ith the follow ing options:

Function Description

Zoom When active it is possible to zoom into the chromatogram by dragging an area.

Undo Zoom Reverts the recent zoom operation and returns to the previous view. Accesse d b y
right-clicking on the plot and selecting Unzoom
Full Scale Reverts the recent all zooming and re-plots the data full scale. Accessed b y ri gh t-
clicking on the plot and selecting Full Scale
Y axis zoom tools Shown when moving the cursor over the Y axis. The following functions are
available:
+ zooms into the plot vertically
Autoscale Signal resizes the plot height to the highest mass abundance cu rre nt ly
visible
- zooms out of the plot vertically

X axis zoom tools Shown when moving the cursor over the X axis. The following functions are
available:
+ zooms into the plot horizontally
Autoscale Time resizes the plot to the complete mass range of the acquired data.
- zooms out of the plot horizontally
Full size button Shown when moving the cursor to the bottom left corner of the plot. Cli ck t h e f u ll
size button to autoscale both axes simultaneously.

In addition, the following zoom operations are available:

Function Description
Double Click on the abundance axis Automatically resizes the plot height to the highest m a ss a b u nd an ce cu rren tly
visible.
Double Click on the m/z axis Automatically resizes the plot width to the complete mass pane of the acquired data

Undo Zoom Reverts the recent zoom operation and returns to the previous view.

Drag the abundance axis Scrolls the y axis limits

Drag the m/z axis Scrolls the x axis limits

The follow ing context menu operations are also available:

5.7.7.2 Copy
Copies the mass spectrum plot to the clipboard as an image, This is also possible by using the Ctrl + C hotkey.

5.7.7.3 Export Spectrum

Exports the mass spectrum to a text file. The follow ing options are available:

Parameter Sub Parameter Description

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Destination Clipboard Exports a textual description of the mass spectrum dat a i nt o

the clipboard.
File Exports a textual description of the mass spectrum data into a
text file.
Format CM-ASCII The exported mass spectrum contains complete information

STIP-ASCII The exported mass spectrum plot contains condensed

information
Parameters Use baseline correction settings Uses the baseline correction settings from MS settings tab o f
from Processing method the processing method
Use fixed scan step Changes the resolution for the exported mass spectrum

5.7.7.4 Full Size

Completely unzooms both the x-axis and y-axis

5.7.7.5 Autoscale Intensity

Completely unzooms the y-axis

5.7.7.6 Undo Zoom

Reverts the recent zoom operation and returns to the previous view .

5.7.7.7 Properties
The follow ing sections describe the tabs of the Properties dialog accessed from the context menu.

Scale

Parameter Sub Parameter Description

Apply scaling to all plots N/A Allows the user to apply the same scaling to all plots
simultaneously when checked.
Mass From Defines the start value of the mass axis.

To Defines the end value of the mass axis.

Autoscale When this is selected the plot is scaled to show the ful l ma ss
range of the data
Fixed intervals of tick marks Chromeleon automatically determines t h e i nt erva l o f t ick
marks (the small lines that mark values) on the time axis. T o
customize the intervals, select the Fixed intervals of tick marks
check box and then type or select a number in the Majo r t ic k
mark and/or Minor tick mark box. A tick mark inte rva l o f 0 . 0
removes the tick marks.
Intensity From Defines the start value of the intensity axis.
To Defines the end value of the intensity axis.

Autoscale When this is selected the plot is scaled to show the full
intensity range of the mass spectrum.
Fixed intervals of tick marks Chromeleon automatically determines t h e i nt erva l o f t ick
marks (the small lines that mark values) on the time axis. T o
customize the intervals, select the Fixed intervals of tick marks
check box and then type or select a number in the Majo r t ick
mark and/or Minor tick mark box. A tick mark inte rva l o f 0 . 0
removes the tick marks.

Frame & Axes

This section allow s defining axes, grid and normalization of the mass spec plot.

Parameter Sub Parameter Description

Axes Mass axis Displays a mass axis on the mass spec plot.

Intensity axis Displays an abundance axis on the mass spec plot.

Font Allows the font type and size of the axes to be defined.

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Parameter Sub Parameter Description

Axis to Plot Gap Defines the distance in mm between the axes and the plot.
Frame Displays a frame around the plot

Axis Titles Axis Titles Applies titles to the mass spec plot axes.

Units Displays units on the axes of the mass spec plot.

Font Allows the font type and size of the axis titles to be defined

Grid Horizontal grid lines Applies horizontal grid lines to the mass spec plot.

Vertical grid lines Applies vertical grid lines to the mass spec plot.
Orientation Horizontal Scan type is the horizontal axis, and signal is the vertical axis

Vertical Scan type is the vertical axis, and signal is the horizontal axis.
Normalization None No normalization is performed.

Absolute maximum Performs spectra normalization relative to the absolute

maximum of the spectra.
Charge States Specifies if charge state lines should be superimposed on th e
plot

Title
This section defines if titles are displayed and how titles should be displayed:

Parameter Sub Parameter Description

Draw titles Shows a title for the fluorescence spectra plot.

Font Allows the font for the fluorescence sp e ctra p lot t it le t o b e

defined.
Left title Draw left title Displays the left part of the title.

Use default When checked left part of the title is shown as in Chrome leon
7.2.
When not checked the left part of t he t i tle can b e d e fin ed
based on formulas in the edit field.
Center title Draw center title Displays the middle part of the title.
Use default When checked middle part of the title is shown as in
Chromeleon 7.2.
When not checked the middle part of the title can b e d ef ine d
based on formulas in the edit field.
Right title Draw right title Displays the right part of the title.

Use default When checked right part of the title is shown as in Chromeleon
7.2.
When not checked the right part of the t i tle can b e d ef ine d
based on formulas in the edit field.

Comparison
This section allow s defining how multiple mass spectra are arranged

Group Sub Parameter Description

Arrangement Stacked Plots are stacked on a single plot and share the sa m e sca n a xis;
each stacked plot has a separate intensity axis.
Overlaid Plots are overlaid on a single plot and share t h e sa m e sca n a n d
intensity axes
Offset Scan Offset To offset overlaid plots on the scan axis, select the check b o x a nd
enter the offset percentage in the box.
Intensity Offset To offset overlaid plots on the intensity axis, select t he che ck b o x
and enter the offset percentage in the box
Overlay Overlay with right signal axis When plots are overlaid, select this check box to include a se co n d
signal axis on the right side of the plot

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Group Sub Parameter Description

Mirror Mirror Signal Select this check box to invert the intensity axis of t h e o verla id o r
stacked plots. The plots "mirror" the main spectrum or I-t plot.

Line & Fill Styles

This section allow s the color of each item in the mass spec plot to be defined. The follow ing items can have their color
defined:
• Grid lines • Axes • Spectrum 1-8

The follow ing items can have their fill color defined:

• Background • •

Interactive Settings
This section defines w hat optional zoom/unzoom tools are displayed on the mass spec plot

Function Description
Show overview plot When this check box is selected, the miniature overview of the mass spectrum plot
is displayed when zooming into the chromatogram.
Show popup controller When this check box is selected, the full size button, vertical and horizonta l zoo m
toolbars on the chromatogram axes are visible.

5.8 Report Template

Report Template Files define how data w ill be printed. Figure 56 show s a typical report definition file.

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Chromeleon 7

Figure 56: Report Template in the Chromatography Studio

All Chromeleon objects are highlighted using a red flag. Any cells containing user entered text or equations show no flags.
The follow ing objects can be displayed in a report definition file:

5.8.1 Chromatogram Plot

The follow ing display options are available for Chromatograms:

5.8.1.1 Plot Details

Parameter Sub Parameter Description

Axes Time Axis Displays a time axis on the chromatogram.

Signal Axis Displays a signal axis on the chromatogram.

Font Allows the font type and size of the axes to be defined.

Axis to plot gap Defines the distance in mm between the axes and the
chromatogram plot.
Frame Frame that is drawn around the plot area.

Axes Descriptions Axes Titles Applies titles to the chromatogram axes.

Units Displays units on the axes of the chromatogram.

Font Allows the font type and size of the axes titles to be defined.

Grid Signal axis grid lines Applies horizontal grid lines to the chromatogram.
Time axis grid lines Applies vertical grid lines to the chromatogram.

Orientation Horizontal Displays the chromatogram in the portrait orientation.

Vertical Displays the chromatogram in the landscape orientation.

Signal details Raw data points Shows the raw data points.

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5.8.1.2 Time Axis

This section allow s the user to define the scaling used for the time axis. The follow ing options are available:

Parameter Sub Parameter Description

Time Axis Share time axes If your chromatogram plot includes overlaid ch rom at ogra ms
and you have selected a Stacked arrangement on the
Comparison page, you can select whether to use a co mmo n
(shared) time axis for the chromatogram stripes, or se p a ra t e
time axes. The unit on the time axis is always identica l f or a ll
chromatogram stripes.
Select the Share time axis check box to display a sin gle t ime
axis for all chromatograms (default). Clear the ch eck b o x t o
display separate time axes for each chromatogram.
If you have cleared the Share time axis check box, select t he
chromatogram from the Settings for chromatogram plot list f o r
which the settings under Range (see below) shall apply.
Range Autoscale or Fixed Determines the method for selecting the range. Can be set t o:
Autoscale or Fixed, Autoscale on Peak, or Fixed using
Autoscale on Peak Formula.
Fixed using Formula
Autoscale or Fixed From Defines the start time of the chromatogram. Eithe r A ut o o r a
specific time can be selected.
To Defines the end time of the chromatogram. Eit her A u to o r a
specific time can be selected.
Autoscale on Peak Selected Allows the user to select the peak by Name, Greatest He igh t,
Greatest Area, Number, or Component Table Number
Width Defines the width by which to pad the se l ecte d a ut osca le d
peak range. This can be defined or set to Autosize width.
Fixed using Formula From Defines the start time of the chromatogram using a formula
To Defines the end time of the chromatogram using a formula

Tick mark intervals Fixed intervals of tick marks Defines whether tick marks should appear at selected intervals

Major tick mark Defines the interval for major tick marks
Minor tick mark Defines the interval for minor tick marks

Time axis units Minutes (min) The units for the time axis are minutes.
Seconds (s) The units for the time axis are seconds.

5.8.1.3 Signal Axis

This section allow s the user to define the scaling used for the signal axis. The follow ing options are available.

Parameter Sub Parameter Description

Signal Axis Settings for chromatogram Determines the signal axis for which to define the setti ngs. T o b e
plot able to select between different signal axes, you h ave t o lo ad a t
least one Overlay. In addition, two signal axes must be displayed.
Range for selected plot Autoscale or Fixed Determines the method for selecting the ra ng e. Ca n b e se t t o:
Autoscale or Fixed, or Fixed using Formula.
Fixed using formula

Autoscale or Fixed To Defines the end value of the signal axis. Either Auto or a sp e cif ic
time can be selected.
From Defines the start value of the signal axis. Either Auto or a sp e ci fic
time can be selected.
Fixed using Formula From Defines the start value of the signal axis using a formula

To Defines the end value of the signal axis using a formula

Autoscale in time range or peak Autoscale in visible time Determines the signal autoscale options for the current
range chromatogram. Following options are enabled only fo r t he si gn al
scale mode ‘Autoscale or fixed’; Autoscale in visi ble t ime ra n ge,
Autoscale in fixed time range Autoscale in fixed time range, Autoscale on peak.
Autoscale on peak

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Parameter Sub Parameter Description

Autoscale in visible time range N/A Calculates the signal minimum and / or maximum on th e b asi s o f
the current time range specified on the Time Axis properties page.
Autoscale in fixed time range From Custom start value to calculate signal minimum and / or maximum.

To Custom end value to calculate signal minimum and / or maximum.

Autoscale on peak Selected Calculates the signal minimum and / or maximum on th e b asi s o f
the range between peak start and end time. Following peak
selection modes are available; by name, by g rea te st h ei ght , b y
greatest area, by number, by component number.
Time mark intervals Fixed intervals of tick marks Defines whether tick marks should appear at selected intervals

Major tick mark Defines the interval for major tick marks

Minor tick mark Defines the interval for minor tick marks

5.8.1.4 Title
This section defines the caption that w ill be displayed in the chromatogram header. Left, middle and right captions can be
selected either based on simple text values or on user-defined formulas. The formula can be based on variables from the
follow ing sections:
• Global Functions (see section 7.1)
• General (see section 7.2)
• Sequence (see section 7.3)
• Injection (see section 0)
• Audit Trail (see section 7.5)
• Preconditions (see section 7.6)
• Chromatogram (see section 7.8)
• Processing Method (see section 7.21)

• Instrument Method (see section 7.31)

• Custom Formulas (see section 5.8.31)

Note: If a chromatogram is manually integrated the text “[manipulated]” is alw ays shown in the left caption.

In addition, the follow ing options are available:

Parameter Sub Parameter Description

Title Draw Titles Displays chromatogram titles.
Font Allows the font type and size of the titles to be defined

Left title Draw left title Displays the left part of the title.
When checked the left part of the title can be defin ed b a se d
on formulas as described above.
Middle title Draw middle title Displays the middle part of the title.
When checked the middle part of th e t i tle can b e d ef ine d
based on formulas as described above.
Right title Draw right title Displays the right part of the title.
When checked the right part of the title can be defined ba se d
on formulas as described above.
Legend Draw legend Displays a legend for overlaid chromatograms.
When checked the format of the legend can be defined based
on formulae as described above.

5.8.1.5 Peak Characterization

This section defines how detailed peaks are characterized in the chromatogram plot. The follow ing options are available:

Parameter Sub Parameter Description

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Parameter Sub Parameter Description

Peak delimiter N/A Shows the peak delimiters.
Delimiter Allows defining color and line style for peak delimiters.

Separation Allows defining color and line style for the separation.

Baseline N/A Shows the baseline.

Main peak Allows defining color and line style for the base line un de r a
main peak.
Rider peak Allows defining color and line style for the base line un de r a
rider peak.
Peak tangents N/A Shows the peak tangents.
N/A Allows defining color and line style for peak tangents.

Peak widths N/A Shows peak widths.

N/A Allows defining color and line style for peak widths.

Draw peak width at Draws a line at the given height. Default s h e ig ht s a re 5 % ,

10%, 50%.
Peak Highlight Do not highlight any peaks The identified peak will not be shaded unless it has the focus

Highlight all identified peaks All identified peaks will be shaded in all plots
Highlight all detected peaks All detected peaks will be shaded in all plots

5.8.1.6 Peak Label

This section defines how peaks should be labeled. The follow ing options are available:

Parameter Sub Parameter Description

Identified peaks Label identified peaks Labels all identified peaks with details generated by the use r-
defined formula.

(Formula) The formula can be based on variables f ro m a ll t he a rea s

detailed in section 7.
Unidentified peaks Label unidentified peaks Labels all unidentified peaks with details g e n era te d b y t he
user-defined formula.

(Formula) The formula can be based on variables f ro m a ll t he a rea s

detailed in section 7.
Label style Font Defines the font for peak labels.

Rotation Defines the angle the peak label is shown at.

5.8.1.7 Peak Purity

This section defines plot options for peak purity and peak match.

Parameter Sub Parameter Description

Peak Purity Index Overlay peak purity index Shows the peak purity index in the chromatogram plot.
Line Style Allows defining line color, width and style for the p eak p u ri ty
index.
Peak Match Overlay peak match factor Shows the peak match factor in the chromatogram plot.

Line Style Allows defining line color, width and style for the p eak m a t ch
factor.

5.8.1.8 Peak Windows

This section defines how peak w indow s are displayed.
Formulas used in this section can combine variables from the follow ing categories:
• Global Functions (see section 7.1)

• General (see section 7.2)

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Chromeleon 7

• Sequence (see section 7.3)

• Injection (see section 0)
• Audit Trail (see section 7.5)
• Preconditions (see section 7.6)
• Chromatogram (see section 7.8)

• Processing Method (see section 7.21)

• Component (see section 7.29)
• Instrument Method (see section 7.31)
• Custom Formulas (see section 5.8.31)
The follow ing options are available:

Parameter Sub Parameter Description

Component table windows Show component table windows Displays peak windows for components from the co mpo ne nt
table (dotted lines indicating the width of the retention win dow
for the peak). Note: peak windows allow the retention time and
retention window of peaks to be adjusted graphically.
(Formula) Labels all peak calipers for identified peaks with details
generated by the user-defined formula.
Unidentified peak group windows Show unidentified peak group Displays peak windows for unidentified peak groups.
windows
(Formula) Labels all peak windows for unidentified p eaks wi t h d e t ails
generated by the user-defined formula.
Other Options Show all peak window drop lines Displays dotted lines for all peaks, not only the currently
selected peak.

Font Defines the font for peak windows.

5.8.1.9 Comparison
This section defines how chromatogram overlays are displayed. The follow ing options are available:

Parameter Sub Parameter Description

Arrangement Overlaid All overlaid chromatograms are shown in one window.

Stacked All overlaid chromatograms are shown in stacked windows.

Grouped by detector All overlaid chromatograms from a given detector are shown in
one stripe.
Overlay order Sorted by injection list order Sorts the chromatograms in the order in which th ey o c cu r i n
the injection list
Current chromatogram always o n Ensures that the current chromatogram is always at th e f ro nt
top (overlaid) or the top (stacked).
Offset Time Offset Offsets the overlaid chromatogram by the % time value
selected.
Signal Offset Offsets the overlaid chromatogram by the % signal value
selected.
Overlay Overlay with peak characterization If selected the peak characterization settings such as peak
names, peak delimiters or the baseline apply not only to the
active chromatogram but also to all overlaid chromatograms.
Overlay with right signal axis. If selected the overlaid chromatogram is measured against a
right signal axis.
Mirror last overlaid chromatogram Mirrors the chromatogram that was added to the overla y l ast
on the time axis.
Normalization Normalize signal Normalizes the signal against the reference peak.

Peak Allows specification of the reference peak

Retention time Allows specification of the retention time to be used for
normalization

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Parameter Sub Parameter Description

Normalize time Allows to normalize the signal in x direction either by shifting or
stretching all chromatograms so that the retention time o f t h e
selected component matches for each overlaid chromatogram.
First peak Allows specification of the start peak for normalization

Second peak Allows specification of the end peak for normalization

Normalize signal Off No signal normalization

Peak Normalizes overlaid signal to height of specified peak

Retention time Normalizes overlaid signal to height of a specific data point

Full range Normalizes overlaid signal to maximum peak height

Normalize time Off No normalization by time

Shift to peak Shifts the overlaid chromatogram to overlay a specific peak

Stretch between start and peak Stretches the overlaid chromatogram between t h e st a rt a n d
specified peak
Stretch between two peaks Stretches the overlaid chromatogram between the two
selected peaks
Stretch between start and end Stretches the overlaid chromatogram between t h e st a rt a n d
end, in order that the run times match

5.8.1.10 Events
This section allow s defining w hich events that occurred during the data acquisition or data processing are display ed on the
chromatogram. The follow ing options are available:

Parameter Sub Parameter Description

Detection Parameters N/A Indicates the Detection Parameters.

Gradients Dwell time Defines the dwell time. This will draw a gradient profile that i s
in accordance with the retention time.
For this device only: Choose the device for which the gradients should b e sh o wn
for. By default, gradients are displayed for <All devices>.
Signal parameters N/A Displays signal parameters in the chromatogram.
Triggers N/A Hide or show triggers from the instrument method in the
chromatogram.
Manual commands N/A Displays manual commands in the chromatogram.
Errors N/A Displays errors in the chromatogram.

Label Style Label events Displays event labels in the chromatogram.

Font Defines the event label font.

5.8.1.11 Fraction Tubes

This section defines how fraction tubes should be displayed. The follow ing options are available:

Parameter Sub Parameter Description

Tubes Show tubes Displays the tubes collected

Label tubes Displays a label for the tube based on a formula using
Chromeleon Report Variables
Fractions Show fractions Displays the fractions collected

Hide tubes inside fractions Removes distinctions between tubes collected as part o f t he
same fraction
Label fractions Displays a label for the fraction base d o n a f orm ula u si n g
Chromeleon Report Variables
Label Style Font Allows the font type and size of the labels to be determined
Rotation Allows the orientation of the label to be determined

Alignment Allows the location of the label to be determined

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5.8.1.12 M S Quantitation Channel

This section defines special plot and display options to be applied w hen the MS Quantitation trace is displayed.

Parameter Sub Parameter Description

Trace visualization Trace offset If selected, each XIC is plot with a vertical offset compared t o
the previous XIC; otherwise, all XICs are plotted on a common
using their true y-axis values

Show only display range of If selected, the XIC plot range is limited to the display range as
extracted ion trace defined in the component table of the processing method.
If not selected, the full-time range of the XIC is plotted.
Use alternating colors If selected, the XICs are drawn using a rotating color p a llet e
as defined in the Line and Fill Styles tab.
If not selected, the XICs are drawn usi ng t h e p rim ary p lot
color, as defined in the Line and Fill Styles tab.
Show peak characterization If selected, the MS Quantitation plot is annotat ed wi t h p ea k
characterizations (peak delimiters, peak tangen ts, b a se lin e
and width.)
Label traces Label quantitation peaks Shows or hides the XIC peak labels
(Formula) The formula can be based on variables f ro m a ll t he a rea s
detailed in section 7.
Label style Alignment Defines if the peak labels should be placed abo ve t h e p ea k
apex or at the lower right of each peak trace.
Draw Frames If selected, a box is drawn around the peak labels
Font Defines the font for peak labels.

Rotation Defines the angle the peak label is shown at.

5.8.1.13 Channel
Allow s selecting the channel for the chromatogram. The options are:
• Use channel selected at print time
• Fixed channel

5.8.1.14 Injection Overlay

Allow s selection of an injection to be compared w ith the main chromatogram. The options are:

Parameter Sub Parameter Description

Dynamic overlays from current Add overlay rule Allows a rule for the overlay to be defined
sequence
Calibration standards Allows overlay of defined calibration standards. Options
available are: None, All, First, Recent and Last
Injection replicates Allows overlay of defined injection replicates. Options
available are: None, All, First, Recent and Last. The inject ion
can further be defined by a query (see section 4.4)
Empty injection query Allows overlay of an injection defined b y a q uery. O pt ion s
available are: None, All, First, Recent and Last i nje ct ion a s
defined by a query. (see section 4.4)
Fixed injection and signal overlays N/A Allows selection of any injection and any chan ne l f rom t h at
injection.

5.8.1.15 Channel Overlay

Defines w hich chromatograms w ill be overlaid
Specific channels and specific injections can be overlaid.

5.8.1.16 Line & Fill Styles

This section allow s a consistent color scheme for the objects in the chromatogram plot to be defined. The follow ing items
can have their line color defined:

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• Chromatograms 1-8 • Peak w idth • Errors

• Peak delimiter • Raw data points • Peak purity index
• Peak separation • Detection parameters • Peak match index
• Baseline • Gradients • Tubes
• Rider baseline • Signal Parameters • Fractions

• Free baseline • Triggers

• Peak tangents • Manual Commands •
The follow ing items can have their fill color defined:
• Background • Peak label • Detection parameter label
• Tube Label • Tubes • Fractions

5.8.1.17 SmartLink
Show s a list of all report objects that are linked w ith the chromatogram plot. An object can be unlinked by selecting the
object and clicking Unlink or pressing DELETE.

5.8.2 Calibration Plot

The follow ing calibration plot display options are available:

5.8.2.1 Component

Parameter Sub Parameter Description

Component Use component selected at p ri nt Displays the calibration plot of the component selected at prin t
time time

Fixed component selected by Displays the calibration plot of the component with the selected
name name
Fixed component selected by Displays the calibration plot of the component with the selected
component table number component number.
Compatibility Option Use the first component in the Default option – If the “First Component Selec t ed b y Na m e”
component table if the sp e cif ied option is enabled but if no associated component is found, t he
component is not found. calibration curve is displayed for the first component in the list.

5.8.2.2 Channel
Allow s selection of the channel for the calibration plot. The options are:
• Use channel selected at print time

• Fixed channel

5.8.2.3 Scale

Parameter Sub Parameter Description

Proportional N/A Allows the user to scale all plots proportionally to one anot he r
when checked.
Amount Axis From Defines the start value of the amount axis.

To Defines the end value of the amount axis.

Autoscale If selected the full range is shown and the values are not
considered.
Logarithmic scale Applies the logarithmic scale to the amount axis.
Fixed intervals of tick marks Customizes the interval of tick marks via typing or select ing a
number in the Major tick mark and/or Minor tick mark boxes.
Response Axis From Defines the start value of the response axis.

To Defines the end value of the response axis.

Autoscale If selected the full range is shown and the values are not
considered.

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Chromeleon 7

Parameter Sub Parameter Description

Logarithmic scale Applies the logarithmic scale to the response axis.
Fixed intervals of tick marks Customizes the interval of tick marks via typing or select ing a
number in the Major tick mark and/or Minor tick mark boxes.
Log-log linear transformation N/A Applies a log-log linear transformation to the current plot.

5.8.2.4 Frame & Axes

Parameter Sub Parameter Description

Axes Amount Axis Displays an amount axis on the calibration plot.

Response Axis Displays a response axis on the calibration plot.

Font Allows the font type and size of the axes to be defined

Axis to Plot Gap Defines the distance in mm between the axes and the
chromatogram plot.
Frame Allows the user to display the plot frame.

Axis Titles Axis Titles Applies titles to the calibration plot axes.
Units Displays units on the axes of the calibration plot.

Font Allows the font type and size of the axis titles to be defined
Grid Horizontal grid lines Applies horizontal grid lines to the calibration plot.

Vertical grid lines Applies vertical grid lines to the calibration plot.

5.8.2.5 Title
This section defines if and how titles should be displayed.

Parameter Sub Parameter Description

Title Draw Titles Displays chromatogram titles.
Font Allows the font type and size of the titles to be defined

Left title Draw left title Displays the left part of the title.
When checked the left part of the title can be defined based on
formulas as described above.
Middle title Draw middle title Displays the middle part of the title.
When checked the middle part of t h e t i tle can b e d ef ine d
based on formulas as described above.
Right title Draw right title Displays the right part of the title.
When checked the right part of the title can be defined b a se d
on formulas as described above.

5.8.2.6 Options
The follow ing options are available:

Parameter Sub Parameter Description

Check Standard & Current Draw check standard Draws points for check standard injection points on the calibration plot.
Injection injection points
Draw level tolerance lines Displays concentration level tolerance lines on the ca libra t ion p lo t wh e n
check standard/QC sample injection points are displayed.

Draw response / amount Draws a horizontal line from the from the response axis (response va lu e o f
quantification lines of the current injection). Where the line hits the calibration curve, a vertical line
current injection is drawn to the amount axis.
Confidence Interval Draw upper and lower Draws the upper and lower confidence limits of the calibration curve.
confidence limits

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Parameter Sub Parameter Description

Upper probability, Lower The confidence probability to be used when calculating the confidence limits.
probability The following values can be selected:
• 95 %
• 97.5 %
• 99 %
• 99.5 %
• 99.9 %
• 99.95
%
• 99.995
%
Draw Hubaux-Vos detection Draws the Hubaux-Vos detection limits for the calibration curve.
limit

5.8.2.7 Line & Fill Styles

This section allows a consistent color scheme for the objects in the calibration plot to be defined. The following items can have their line color
defined:
• Grid • Markers • Original markers
• Axes • Selected marker • Hubaux-Vos lines
• Calibration curve • Disabled markers • Quantification lines
• Confidence interval curves • Check standard markers

• Prediction limit curve • Check standard outlier markers

The follow ing items can have their fill color defined:
• Background

5.8.2.8 SmartLink
The follow ing options are available:

Parameter Sub Parameter Description

Select the chromatogram plot to link None No link is selected

with
Interactive Chromatogram Links with the interactive chromatogram in the data processing
category.
Chromatogram Plot (sheet name) Allows the user to link with a chromatogram plot on any o t he r
sheet within the current report.
Multiple Peak Selection N/A Shows calibration plot for selected components

Zoom Area N/A Shows calibration plot for components wh o se p e ak a p e x is

within the zoom area.

5.8.3 UV-Vis Spectra Plot

The follow ing peak spectra display options are available:

5.8.3.1 Spectra

Parameter Sub Parameter Description

Currently selected spectra N/A Peak and time spectra of current spectra plot.
(interactive mode only!)
Peak Spectra Name Displays the spectra plot for the peak of the selected name.
Greatest height Displays the spectra plot for the peak with the greatest height.

Greatest area Displays the spectra plot for the peak with the greatest area.

Number Displays the spectra plot for the peak with the selected
number in the chromatogram.

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Chromeleon 7

Parameter Sub Parameter Description

Component table number Displays the spectra plot for the peak with the selected
number in the component table.
SLS hit number Displays the spectra plot for the peak with the sel ect ed S L S
hit number.

Time scans at fixed retent ion t i me N/A Displays the spectrum at a fixed retention time (o r b u nche d
(or bunched over a range) over a time range).

5.8.3.2 Channel
This section defines w hich channel is show n. There are tw o options:
• Currently selected channel (interactive mode only!)
• Fixed Channel (Channel is specified by the user)

5.8.3.3 Scale

Parameter Sub Parameter Description

Apply scaling to all plots N/A Allows the user to apply the same scaling to all plots
simultaneously when checked.
Wavelength From Defines the start value of the wavelength axis.
To Defines the end value of the wavelength axis.

Autoscale When this is selected the plot is scaled to show the full
wavelength range of the spectrum.
Fixed intervals of tick marks Customizes the interval of tick marks via typing or select ing a
number in the Major tick mark and/or Minor tick mark boxes.
Absorbance From Defines the start value of the absorbance axis.

To Defines the end value of the absorbance axis.

Autoscale When this is selected the plot is scaled to show the full
absorbance range of the spectrum.
Fixed intervals of tick marks Customizes the interval of tick marks via typing or select ing a
number in the Major tick mark and/or Minor tick mark boxes.

5.8.3.4 Frame & Axes

This section allow s defining axes, grid and normalization of the spectral plot.

Parameter Sub Parameter Description

Axes Wavelength axis Displays a wavelength axis on the spectra plot.

Absorbance axis Displays a response axis on the spectra plot.

Font Allows the font type and size of the axes to be defined

Axis to Plot Gap Defines the distance in mm between the axes and the spect ra
plot.
Frame Displays plot frame when selected

Axis Titles Axis Titles Applies titles to the spectra plot axes.
Units Displays units on the axes of the spectra plot.

Font Allows the font type and size of the axis titles to be defined
Grid Horizontal grid lines Applies horizontal grid lines to the spectra plot.

Vertical grid lines Applies vertical grid lines to the spectra plot.

Orientation Horizontal Displays the chromatogram horizontally with re sp ect t o t h e

wavelength axis.
Vertical Displays the chromatogram vertically with respect to the
wavelength axis.
Normalization None No normalization is performed. Signal response is reported in
mAU.

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Parameter Sub Parameter Description

Absolute Maximum Performs spectra normalization relative to the absolute
maximum of the spectra.
Relative Maximum Performs spectra normalization relative to the relative
maximum of the spectra.
Fixed Wavelength at Performs spectra normalization relative to the fixed wavelength
selected.

5.8.3.5 Title
This section allow s controlling the titles for the spectral plot.

Parameter Sub Parameter Description

Title Draw Titles Displays UV-Vis spectral plot, mass spectral p lo t, o r I -t p lot
titles.
Font Allows the font type and size of the titles to be defined

Left title Draw left title Displays the left part of the title.
When checked the left part of the title can be defined based on
formulas as described above.
Center title Draw center title Displays the center part of the title.
When checked the center part of the title can be defined based
on formulas as described above.
Right title Draw right title Displays the right part of the title.
When checked the right part of the title can be defined b a se d
on formulas as described above.

5.8.3.6 Peak Spectra

This section allow s selecting w hich spectra should be show n.

Parameter Sub Parameter Description

Spectra Sampling Points Apex Spectrum Displays the spectrum at the peak apex.

Front 1 (%) Displays the spectrum at the selected % he igh t o f t he p eak

ascending flank.
Front 2 (%) Displays the spectrum at the selected % he igh t o f t he p eak
ascending flank.
Tail 1 (%) Displays the spectrum at the selected % he igh t o f t he p eak
tailing flank.
Tail 2 (%) Displays the spectrum at the selected % he igh t o f t he p eak
tailing flank.
Reference Spectrum None No reference overly is displayed.

Apex spectrum of recent The spectrum of the currently displayed peak is overl aid wi th
calibration standard the spectrum of the peak with the same name f ro m t h e l ast
calibration standard injection of the sequence.
Apex spectrum of a fixed injection The spectrum of the currently displayed peak is overl aid wi th
the spectrum of the peak with the same name from the
selected injection.

Reference spectrum in The spectrum of the currently displayed peak is overl aid wi th
corresponding component table the reference spectrum from the component table of the
processing method.
Spectral library screening results The spectrum of the currently displayed peak is overl aid wi th
the spectra of the results of the spectral library screening (t h e
number of hits to be shown can be selected).

5.8.3.7 Label
This section allow s defining how labels are show n in the spectral plot.

Parameter Sub Parameter Description

Label Maxima Rotation Defines the angle the spectrum label is shown at.

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Chromeleon 7

Parameter Sub Parameter Description

Maxima Count Defines how many maxima should be labeled.
Font Defines the font for the spectrum label.

Options Show match factor Displays the match of each spectrum with the correspo nd ing
main spectrum. The main spectrum is either the peak
spectrum, or a reference spectrum (spectra compariso n), o r
the top spectrum in a spectra library selection.
Show baseline correction info Displays information about the base lin e co rre ct ion in t he
header.

5.8.3.8 Analysis
This section controls how spectra analysis is performed.

Parameter Sub Parameter Description

Spectra Analysis None No analysis is performed.

Difference Forms the difference between the main sp e ct ru m a nd t h e

remaining individual spectra of the pane. Depending on
whether normalization is performed (see Frame & Axes),
representation of the difference spectra is in percent or in t he
corresponding dimension; for example, mAU.
First derivative Calculates and displays the first derivative of each sp e ct rum
displayed.
Second derivative Calculates and displays the second derivative of each
spectrum displayed.

Background spectra used for Displays the subtracted background spectrum in a se p ara te
baseline correction spectra plot.
Overlay Overlay background spectra used Overlays the spectrum with the spectrum used f o r b ase l ine
for baseline correction correction.
Overlay spectra without base line Overlays each spectrum with the corresp on ding sp e ctru m
correction without baseline correction.

5.8.3.9 Comparison
This section defines Arrangement, Offset, Overlay and Mirror settings.

Parameter Sub Parameter Description

Arrangement Stacked All overlaid spectra are shown in stacked plots
Overlaid All overlaid spectra are shown in one plot

Offset Scan offset Offsets the overlaid spectra by the scan value selected
Intensity offset Offsets the overlaid spectra by the intensity value selected

Overlay Overlay with right signal axis If selected the overlaid spectrum is measured against a ri gh t
signal axis.
Mirror Mirror signal If selected displays the overlaid spectrum as a mirror of
existing spectrum.

5.8.3.10 Line & Fill Styles

This section allow s the color of each item in the peak spectra plot to be defined. The follow ing items can have their color
defined:
• Grid lines • Uncorrected spectrum • First front spectrum
• Axes • Spectrum 1-8 • Second front spectrum
• Reference Spectrum • Library Spectrum 1-7 • First tail spectrum

• Background spectrum • Apex Spectrum • Second tail spectrum

The follow ing items can have their fill color defined:
• Background

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5.8.3.11 SmartLink
The follow ing options are available:

Link to Chromatogram

Parameter Sub Parameter Description

Select the chromatogram plot to link None No link is selected

with
Interactive Chromatogram Links with the interactive chromatogram in the data processing
category.
Chromatogram Plot (sheet name) Allows the user to link with a chromatogram plot on any o t he r
sheet within the current report.
Multiple Peak Selection N/A Shows spectra for selected components
Zoom Area N/A Shows spectra for components whose peak apex is within t h e
zoom area.

Link to Injection

Parameter Sub Parameter Description

Link to Injections Allows multiple injections to be included in the array of SmartLink objects

Include Current Selections/Pins In addition to those injections specified by type or by custom c on dit ion
(below), the currently selected and pinned injections will be includ ed in
the list of SmartLink injections
Include Injection Types Unknown Displays values from unknown injections.

Calibration Standard Displays values from calibration standard injections.

Check Standard Displays values from check standard injections.

Matrix Displays values from matrix blank injections.

Blank Displays values from blank run injections.

Spiked Displays values from spiked injections.

Unspiked Displays values from unspiked injections.

Custom Conditions Only include injections that match Displays only injections that fulfill certain conditio ns, b a se d o n re port
the following conditions variables.

ALL (Any field from the inje ctio n Restrict the data points shown based on comparing the selected variable
list – including user defined with a user-defined value and using the following logical arguments:
columns) Is equal to (=)
Is not equal to (<>)
Is larger than (>)
Is smaller than (<)
Is larger than or equal to (=>)
Is smaller than or equal to (=<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty

AND [Any field from the injection As for the previous parameter.
list – including user defined
columns]

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Chromeleon 7

Parameter Sub Parameter Description

Link to Injections Allows multiple injections to be included in the array of SmartLink objects
Include Current Selections/Pins In addition to those injections specified by type or by custom con dit ion
(below), the currently selected and pinned injections will be includ ed in
the list of SmartLink injections
or Allows for matching based on only one comparison in the rule

and Forces matching based on every rule in the list. The or sub p a ra met er
overrides the requirement to match every comparison in the specific rule
list.

Display By
Defines how the SmartLink objects w ill be ordered.

Parameter Description
Peaks per injection When a single injection is selected, the peak objects for that injection are plotted in horizontal order.
When multiple injections are selected, each injection has its own row and each peak has its own column.
Injections per peak When a single peak is selected, the peak objects for each injection are plotted in horizontal order.
When multiple peaks are selected, each peak has its own row and each injection has its own column.

5.8.4 Contour Plot

The follow ing contour plot display options are available:

5.8.4.1 Scale

Parameter Sub Parameter Description

Time Axis From: Defines the start value of the time axis.
To: Defines the end value of the time axis.

Autoscale When selected the contour plot and th e ch roma to gra m p lot a re
scaled to show the whole chromatogram. This option is also
available in the layout ribbon.
Units Minutes [mins] or Seconds [s]
Scan Axis From: Defines the start value of the scan axis.

To: Defines the end value of the scan axis.

Autoscale When selected the contour plot and the spectra plot a re sca l ed t o
show the whole scan range. This option is a l so a vaila ble in t he
layout ribbon.
Signal Axis From: Defines the start value of the signal axis.

To: Defines the end value of the signal axis.

Autoscale When selected the contour plot and th e ch roma to gra m p lot a re
scaled to show the whole signal range.
Gradient Linear Scale Signal values are colored using a linear scale.

Logarithmic Scale Signal values are colored using a logarithmic scale. Thi s o p tio n i s
also available in the layout ribbon.

5.8.4.2 General

Parameter Sub Parameter Description

View 3D View Displays 3D contour view when selected
Data 3D data field If more than one type of 3D data field is available, the required f ield
can be selected from the list.
Axes Axis to plot gap Defines the distance in mm between the axes and the contour plot.
Font N/A Allows defining the font to be used for axes and labels in the Contour
Plot.

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Parameter Sub Parameter Description

Options Use black for zero Black represents a signal value of zero on the plot. This option
generates the fewest possible color repeats. A point’s color can
change when the scale changes.
Draw optimum integration path Draws the optimum integration path for the chromatogram (i .e . t h e
optimum wavelength profile). This option is a lso a va ilab le i n t h e
layout ribbon.
Spectra Retrieval Use raw spectra When selected raw spectra are shown and the UV settings from t h e
processing method are ignored. This option is also available i n t h e
layout ribbon.
Apply baseline correction settings from When selected the settings selected on the UV Spectra tab page o f
current processing method the processing method are applied to the raw data and include pea k
spectrum bunching and baseline correction options. This o p t ion is
also available in the layout ribbon.

5.8.4.3 3D View Settings

Parameter Sub Parameter Description

Show Grid 3D View Shows a grid on the 3D plot.

Rotation X Type or select the angle of rotation around X axis of the 3D plot.

Y Type or select the angle of rotation around Y axis of the 3D plot.

Z Type or select the angle of rotation around Z axis of the 3D plot.

Reset Returns the axes to their default angles of rotation.

Performance N/A Best Quality using the same number of spectra used by the contour
plot. Best Performance using the fewest number of spectra.

5.8.4.4 Title
This section defines if titles are displayed and how titles should be displayed:

Parameter Sub Parameter Description

Draw titles Shows a title for the contour/3D plot.

Font Allows the font for the contour/3D plot title to be defined.
Left title Draw left title Displays the left part of the title.

Use default When checked left part of the title is shown as in Chrome leon
7.2.
When not checked the left part of t he t i tle can b e d e fin ed
based on formulas in the edit field.
Center title Draw center title Displays the middle part of the title.
Use default When checked middle part of the title is shown as in
Chromeleon 7.2.
When not checked the middle part of the title can b e d ef ine d
based on formulas in the edit field.
Right title Draw right title Displays the right part of the title.

Use default When checked right part of the title is shown as in Chromeleon
7.2.
When not checked the right part of the t i tle can b e d ef ine d
based on formulas in the edit field.

5.8.5 Mass Spectrum Plot

The follow ing sections describe the tabs of the Properties dialog accessed from the context menu.

5.8.5.1 Spectra
This section defines w hich mass spectra are show n. There are three options:
• Currently selected mass spectrum (interactive mode only!)

• Peak spectrum (Peak is specified by the user)

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Chromeleon 7

• Time Scan at a fixed retention time (as specified by the user)

5.8.5.2 Channel
This section defines w hich channel is show n. There are tw o options:

• Currently selected channel (interactive mode only!)

• Fixed Channel (Channel is specified by the user)

5.8.5.3 Scale

Parameter Sub Parameter Description

Apply scaling to all plots N/A When linking is enabled and multiple spectral are disp la yed,
this option determines whether or not the scaling se t t ing s o f
the currently selected plot apply to all linked plots.
Mass From Defines the start value of the wavelength axis.

To Defines the end value of the wavelength axis.

Zero mass offset When selected a particular mass can be specified as the zero
mass which resets the masses of other ions re l a tiv e t o t h e
selected zero mass.
Autoscale When this is selected the plot is scaled to show the full
wavelength range of the spectrum.
Fixed intervals of tick marks Chromeleon automatically determines t h e i nt erva l o f t ick
marks (the small lines that mark values) on the time axis. T o
customize the intervals, select the Fixed intervals of tick marks
check box and then type or select a number in the Majo r t ick
mark and/or Minor tick mark box. A tick mark inte rva l o f 0 . 0
removes the tick marks.
Intensity From Defines the start value of the absorbance axis.

To Defines the end value of the absorbance axis.

Autoscale When this is selected the plot is scaled to show the full
absorbance range of the spectrum.
Fixed intervals of tick marks Chromeleon automatically determines t h e i nt erva l o f t ick
marks (the small lines that mark values) on the time axis. T o
customize the intervals, select the Fixed intervals of tick marks
check box and then type or select a number in the Majo r t ick
mark and/or Minor tick mark box. A tick mark inte rva l o f 0 . 0
removes the tick marks.

5.8.5.4 Frame & Axes

This section allow s defining axes, grid and normalization of the mass spec plot.

Parameter Sub Parameter Description

Axes Mass axis Displays a mass axis on the mass spec plot.

Intensity axis Displays an abundance axis on the mass spec plot.

Font Allows the font type and size of the axes to be defined.

Axis to Plot Gap Defines the distance in mm between the axes and the plot.
Frame Displays a frame around the plot

Axis Titles Axis Titles Applies titles to the mass spec plot axes.

Units Displays units on the axes of the mass spec plot.

Font Allows the font type and size of the axis titles to be defined

Grid Horizontal grid lines Applies horizontal grid lines to the mass spec plot.

Vertical grid lines Applies vertical grid lines to the mass spec plot.
Orientation Horizontal Scan type is the horizontal axis, and signal is the vertical axis

Vertical Scan type is the vertical axis, and signal is the horizontal axis.

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Parameter Sub Parameter Description

Normalization None No normalization is performed.
Absolute maximum Performs spectra normalization relative to the absolute
maximum of the spectra.

5.8.5.5 Title
This section allow s controlling the titles for the mass spec plot.

Parameter Sub Parameter Description

Draw titles Shows a title for the fluorescence spectra plot.
Font Allows the font for the fluorescence sp e ctra p lot t it le t o b e
defined.
Left title Draw left title Displays the left part of the title.

Use default When checked left part of the title is shown as in Chrome leon
7.2.
When not checked the left part of t he t i tle can b e d e fin ed
based on formulas in the edit field.
Center title Draw center title Displays the middle part of the title.

Use default When checked middle part of the title is shown as in

Chromeleon 7.2.
When not checked the middle part of the title can b e d ef ine d
based on formulas in the edit field.
Right title Draw right title Displays the right part of the title.

Use default When checked right part of the title is shown as in Chromeleon
7.2.
When not checked the right part of the t i tle can b e d ef ine d
based on formulas in the edit field.

5.8.5.6 Peak Spectra

This section allow s selecting w hich auxiliary mass spectra should be show n.

Parameter Sub Parameter Description

Spectra Sampling Points Apex Spectrum Displays the mass spectrum at the peak apex as a thumbnail

Front 1 (%) Displays the mass spectrum at the selected % h e ight o f t he

peak ascending flank as a thumbnail.
Front 2 (%) Displays the mass spectrum at the selected % h e ight o f t he
peak ascending flank as a thumbnail.
Tail 1 (%) Displays the mass spectrum at the selected % h e ight o f t he
peak tailing flank as a thumbnail.
Tail 2 (%) Displays the mass spectrum at the selected % h e ight o f t he
peak tailing flank as a thumbnail.
Reference Spectrum None No reference overly is displayed.

Apex spectrum of recent The mass spectrum of the currently displayed peak is overlaid
calibration standard with the mass spectrum of the peak with the same name f rom
the last calibration standard injection of the sequence.
Apex spectrum of a fixed injection The mass spectrum of the currently displayed peak is overlaid
with the mass spectrum of the peak with the same name f rom
the selected injection.
Spectral library screening results The mass spectrum of the currently displayed peak is overlaid
with the mass spectra of the results of the spectral library
screening (the number of hits to be shown can be selected).

5.8.5.7 Label
This section allow s defining how labels are show n in the mass spectral plot.

Parameter Sub Parameter Description

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Chromeleon 7

Peak Label Rotation Defines the angle the mass spectrum label is shown at.

Maximum threshold The threshold intensity (in %) at which ma ss p e a ks wi l l b e

labeled
Font Defines the font for the mass spectrum label.

Options Show baseline correction info Displays information about the baseline correction in the
header.

Show detected mass info for peak Checking this box will cause the detected mass f o r t h e p e ak
spectra spectrum to be displayed horizontally on top of the mass peak.
If the monitored mass is not detected, no information is
displayed.

Show detected mass info for time Checking this box will cause the detected mass f o r t h e t i me
spectra spectrum to be displayed horizontally on top of the mass peak.
If the monitored mass is not detected, no information is
displayed.

5.8.5.8 Analysis
This section controls how mass spectra analysis is performed.

Parameter Sub Parameter Description

Spectra Analysis None No analysis is performed.

Difference Forms the difference between the main mass spect ru m a n d

the remaining individual mass spectra of the pane. Depending
on whether normalization is performed (see Frame & A xes),
representation of the difference mass spectra is in percen t o r
in the corresponding dimension;

Background spectra used for Displays the subtracted background spectrum in a se p ara te
baseline correction spectra plot.
Overlay Overlay background spectra used Overlays the mass spectrum with the mass spectrum used for
for baseline correction baseline correction.

Overlay spectra without base line Overlays each mass spectrum with the correspond ing ma ss
correction spectrum without baseline correction.

5.8.5.9 Comparison
This section allow s defining how multiple mass spectra are arranged

Group Sub Parameter Description

Arrangement Stacked Plots are stacked on a single plot and share the sa m e sca n a xis;
each stacked plot has a separate intensity axis.
Overlaid Plots are overlaid on a single plot and share t h e sa m e sca n a n d
intensity axes
Offset Scan Offset To offset overlaid plots on the scan axis, select the check b o x a nd
enter the offset percentage in the box.
Intensity Offset To offset overlaid plots on the intensity axis, select t he che ck b o x
and enter the offset percentage in the box
Overlay Overlay with right signal axis When plots are overlaid, select this check box to include a se co n d
signal axis on the right side of the plot
Mirror Mirror Signal Select this check box to invert the intensity axis of t h e o verla id o r
stacked plots. The plots "mirror" the main spectrum or I-t plot.

5.8.5.10 Line & Fill Styles

This section allow s the color of each item in the mass spec plot to be defined. The follow ing items can have their color
defined:
• Grid lines • Uncorrected spectrum • Second front spectrum
• Axes • Spectrum 1-8 • First Tail spectrum
• Reference spectrum • Apex Spectrum • Second tail spectrum

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• Background spectrum • First front spectrum

The follow ing items can have their fill color defined:
• Background

5.8.5.11 M S Settings

Group Sub Parameter Description

TIC Spectrum Filter Filter This option works in combination with t he Time S pe ct ra T oo l t o
select a mass spectrum from a specific acquisition filter.
Select the acquisition filter in the Filter list (or type a filter definit ion),
and then use the Time Spectra Tool to select a retention time on the
chromatogram. The spectrum from the selected filter at the selected
retention time is shown on the plot.
If the selected filter was not in use at the selected retention time, the
spectrum at the retention time nearest to when the selected filter was
in effect is shown.
Noise Reduction Use setting of processing method Use the parameters from the MS Settings page of t h e p ro cessi n g
method.
Do not reduce Noise No noise reduction calculations will be performed

Relative Threshold Allows masses below a specified percentage of the base peak to b e
ignored
Fixed Threshold Limits spectra to only N largest mass intensities for a peak

5.8.5.12 Data Presentation

Group Sub Parameter Description

Plot Mode Automatic Select this option to display the mass spectral data in the f orm at in
which it was acquired. For centroid format data, the plot d isp la ys a
discrete vertical line for each mass peak. For profile format data, th e
plot is a continuous curve, with each mass peak consisting of
multiple data points.
Centroid Select this option to always display the data in centroid format, even
if profile data was acquired.
Mass precision N/A Select whether to use the mass precision defined on the MS
Settings tab page of the processing method, or to define a cu st o m
number of significant figures to include in the mass peak l a b els o n
the plot.
Mass tolerance N/A Select whether to use the default mass tolerance range defin ed o n
the MS Settings page of the processing method, or to define a
custom range.

5.8.5.13 SmartLink
This section defines how the SmartLink functionality applies to the mass spec plot

Link to Chromatogram

Group Sub Parameter Description

Link to Chromatogram N/A When this option is selected, the plot will adapt to sho w o nly t h e
spectra for peaks visible in the chromatogram plot. When the p lot
is linked, the plot pane splits into several panes to show plots from
multiple peaks
Multiple Peak Selection When selected, the peaks that are selected in the chromato gra m
plot define which peaks are displayed in the mass spec plot
Zoom Area When selected, the zoom area of the chromatogram plot d ef ines
which peaks are shown in the mass spec plot

Link to Injection

Parameter Sub Parameter Description

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Chromeleon 7

Link to Injections Allows multiple injections to be included in the array of SmartLink objects

Include Current Selections/Pins In addition to those injections specified by type or by custom con dit ion
(below), the currently selected and pinned injections will be includ ed in
the list of SmartLink injections
Include Injection Types Unknown Displays values from unknown injections.

Calibration Standard Displays values from calibration standard injections.

Check Standard Displays values from check standard injections.

Matrix Displays values from matrix blank injections.

Blank Displays values from blank run injections.

Spiked Displays values from spiked injections.

Unspiked Displays values from unspiked injections.

Custom Conditions Only include injections that match Displays only injections that fulfill certain conditio ns, b a se d o n re port
the following conditions variables.

ALL (Any field from the inje c tio n Restrict the data points shown based on comparing the selected variable
list – including user defined with a user-defined value and using the following logical arguments:
columns) Is equal to (=)
Is not equal to (<>)
Is larger than (>)
Is smaller than (<)
Is larger than or equal to (=>)
Is smaller than or equal to (=<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
AND [Any field from the injection As for the previous parameter.
list – including user defined
columns]
or Allows for matching based on only one comparison in the rule
and Forces matching based on every rule in the list. The or sub p a ra met er
overrides the requirement to match every comparison in the specific rule
list.

Display By
Defines how the SmartLink objects w ill be ordered.

Parameter Description

Peaks per injection When a single injection is selected, the peak objects for that injection are plotted in horizontal order.
When multiple injections are selected, each injection has its own row and each peak has its own column.
Injections per peak When a single peak is selected, the peak objects for each injection are plotted in horizontal order.
When multiple peaks are selected, each peak has its own row and each injection has its own column.

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5.8.6 MS Components Plot

The follow ing sections describe the tabs of the Properties dialogue accessed from the context menu.

5.8.6.1 Plot Details

This section defines w hich parts of the plot framew ork are show n. The parameters available are:

Parameter Sub Parameter Description

Axes Time Axis Displays a time axis on the chromatogram.
Signal Axis Displays a signal axis on the chromatogram.

Font Allows the font type and size of the axes to be defined.
Axis to Plot Gap Defines the distance in mm between the axes and the
chromatogram plot.
Frame Frame that is drawn around the plot area.
Axes Descriptions Axes Titles Applies titles to the chromatogram axes.

Units Displays units on the axes of the chromatogram.

Font Allows the font type and size of the axes titles to be defined

Grid Signal axis grid lines Applies horizontal grid lines to the chromatogram.

Time axis grid lines Applies vertical grid lines to the chromatogram
Orientation Horizontal Displays the chromatogram in the landscape orientation.

Vertical Displays the chromatogram in the portrait orientation.

Signal details Raw data points Shows the raw data points.

5.8.6.2 Time Axis

The time w indow for MS Component plots is defined in the component table of the processing method and cannot be
changed on this page. Separate time axes and tick mark intervals are not supported for MS Components. Please refer to
section 5.3.2.20 for more details.

5.8.6.3 Signal Axis

This section allow s the user to define the scaling used for the signal axis. The follow ing options are available:

Parameter Sub Parameter Description

Range for component XICs Autoscale or Fixed Determines the method for selecting the ra ng e. Ca n b e se t t o:
Autoscale or Fixed, Autoscale using reference injectio n o r Fi xed
Autoscale using reference using Formula.
injection
Fixed using formula

Autoscale or Fixed To Defines the end value of the signal axis. Either Auto or a sp e cif ic
time can be selected.
From Defines the start value of the signal axis. Either Auto or a sp e ci fic
time can be selected.
Fixed using Formula From Defines the start value of the signal axis using a re p ort va riab le
formula
To Defines the end value of the signal axis usi n g a re p ort vari able
formula

5.8.6.4 Title
This section defines the title that w ill be displayed in the chromatogram header. Left, middle and right titles can be selected
either based on simple text values or on user-defined formulas. The formula can be based on variables from the follow ing
sections:
• Global Functions (7.1)
• General (7.2)
• Sequence (7.3)

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Chromeleon 7

• Injection (0)
• Audit Trail (see section 7.5)
• Preconditions (see section 7.6)
• Chromatogram (7.8)
• Processing Method (7.21)

• Instrument Method (7.31)

• Custom Formulas (5.8.31)
In addition, the follow ing options are available:

Parameter Sub Parameter Description

Draw titles Displays chromatogram titles.
Font Allows the font type and size of the titles to be defined

Left title Draw left title Displays the left part of the title.
When checked the left part of the title can be defined based on
formulas as described above.
Middle title Draw middle title Displays the middle part of the title.
When checked the middle part of t h e t i tle can b e d ef ine d
based on formulas as described above.
Right title Draw right title Displays the right part of the title.
When checked the right part of the title can be defined b a se d
on formulas as described above.
Legend Draw legend Displays the user-defined legend string in a legend box on t he
MS Component plot.

5.8.6.5 Peak Characterization

This section defines how detailed peaks are characterized in the MS Components plot. The follow ing options are available:

Parameter Sub Parameter Description

Peak delimiter Shows the peak delimiters.

Delimiter Allows defining color and line style for peak delimiters.

Separation Allows defining color and line style for the separation drop line.
Baseline Shows the baseline.

Main peak Allows defining color and line style for the base line un de r a
main peak.
Rider peak Allows defining color and line style for the base line un de r a
rider peak.
Peak tangents Shows the peak tangents.

Allows defining color and line style for peak tangents.

Peak widths Shows peak widths.

Allows defining color and line style for peak widths.

Draw peak width at Draws a line at the given height. Default s h e ig ht s a re 5 % ,

10%, 50%, but are user definable
Peak Highlight Do not highlight peaks The identified peak will not be shaded in any pa ne u n less i t
has the focus

Highlight identified peaks in all The identified peak will be shaded in all sub-panes
plots

5.8.6.6 Peak Label

This section defines how peaks should be labeled. The follow ing options are available:

Parameter Sub Parameter Description

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Parameter Sub Parameter Description

Identified peaks Label identified peaks Labels all identified peaks with details generated by the use r-
defined formula.
(Formula) The formula can be based on variables f ro m a ll t he a rea s
detailed in section 7.
Unidentified peaks Label unidentified peaks Labels all unidentified peaks with details g e n era te d b y t he
user-defined formula.
(Formula) The formula can be based on variables f ro m a ll t he a rea s
detailed in section 7.
Label style Font Defines the font for peak labels.

Rotation Defines the angle the peak label is shown at.

5.8.6.7 Peak Windows

This section defines the caption that w ill be displayed in the MS Components plot peak w indow indicator. Caption can be
selected either based on simple text values or on user-defined formulas. The formula can be based on variables from the
follow ing sections:
• Global Functions (7.1)

• General (7.2)
• Sequence (7.3)
• Injection (0)
• Audit Trail (see section 7.5)
• Preconditions (see section 7.6)
• Chromatogram (7.8)
• Processing Method (7.21)
• Component (7.29)
• Instrument Method (7.31)
In addition, the follow ing options are available:

Parameter Sub Parameter Description

Component table windows Show component table windows Shows the component retention time window

Other options Show all peak window drop lines Shows the peak window start and stop times as dashed lin es
on the MS Component plot
Font Defines the font for component table window indicator

5.8.6.8 Comparison
This section defines how MS Components plot overlays are displayed. The follow ing options are available:

Parameter Sub Parameter Description

Arrangement Overlaid All overlaid MS Component plots are shown in one window.

Stacked All overlaid MS Component plots are shown in stacked

windows.
Overlay order Sorted by injection list order Not applicable for MS Component Plots

Current chromatogram always o n Not applicable for MS Component Plots

top
Offset Time Offset Offsets the overlaid chromatogram by the % time value
selected.
Signal Offset Offsets the overlaid chromatogram by the % signal value
selected.
Overlay Overlay with peak characterization If selected the peak characterization sett in gs su ch a s p e a k
names, peak delimiters or the baseline apply not o nly t o t h e
active chromatogram but also to all overlaid chromatograms.

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Chromeleon 7

Parameter Sub Parameter Description

Overlay with right signal axis. If selected the overlaid chromatogram is measured a g ainst a
right signal axis.
Mirror last overlaid chromatogram Plots the last confirmation peak mirrored against quanti tat ion
and all other confirmation peak(s) (if applicable).
Normalization Normalize signal Normalizes the signal against the reference peak.

Internal Standard Show the XICs of the ISTD When checked, the quantitation and confirming i on p lo ts f o r
associated with the component. the ISTD of a component are also plotted.

5.8.6.9 Reference Injection

This section defines an optional reference injection w hich can be used for scaling and overlays.:

Parameter Sub Parameter Description

Specify dynamic or fixed injection Use injection in current sequence If selected, one can specify a series of ru le s t o ch oose t h e
that matches this rule injection of interest. If multiple injections match the ru le, t he n
one can further specify the first, most recent or last m a tchin g
injection be used.
Use fixed injection from arb it rary If selected, the browse button may be used to navigat e t o a n
sequence injection in a sequence from elsewhere in a data vault.
Options Show as an overlay in every If selected, then the data from the specified reference injection
component tile is plotted as an overlay on each data tile.

Show as a separate component If selected, then the data from the specified reference injection
tile in the first position of the v ie w is plotted in a separate tile in the upper left p osi t ion o f e a ch
pane or plot group of tiles.

5.8.6.10 Events
This section allow s defining w hich events that occurred during the data acquisition or data processing are display ed on the
MS Components plot. The follow ing options are available:

Parameter Sub Parameter Description

Detection Parameters Show detection parameters Indicates the Detection Parameters.

Label Style Label events Displays event labels in the chromatogram.

Font Defines the event label font.

5.8.6.11 Component
This section allow s defining of w hich component(s) should be displayed in the MS Components plot. The follow ing options
are available:

Parameter Description
Currently selected component(s) Displays the MS Components plot for the currently selected component in the navi gat ion p ane o r
components dictated by SmartLink (if enabled).
Fixed component selected by name Displays the MS Components plot for the selected named component.

Fixed component selected by Displays the MS Components plot for the component matching the selected number in the
component table number component table.

5.8.6.12 Line & Fill Styles

This section allow s a consistent color scheme for the objects in the MS Components plot to be defined. The follow ing items
can have their line color defined:

• Chromatograms 1-8 • Peak delimiter • Peak separation

• Peak tangents • Peak w idth • Baseline
• Rider baseline • Free baseline • Raw data points
• Detection parameters • •
The follow ing items can have their fill color defined:

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• Background • Peak label • Detection parameter label

5.8.6.13 SmartLink
This section defines how the SmartLink functionality applies to the MS Components plot

Link to Chromatogram

Group Sub Parameter Description

Select the chromatogram N/A When a chromatogram in the dropdown is selected, the MS
plot to link with Components plot will adapt to show only the MS component traces
within the chromatogram plot time range. When the plot is li nke d ,
the plot pane splits into several panes to show plots from multip le
peaks

Note: Interactive Chromatogram refers to the current

chromatogram of the Data Processing category.
Chromatogram Overlays When this option is selected, the MS Components plot will adapt to
show the component traces for injections that are overlaid in t he
chromatogram plot.
Multiple Peak Selection When selected, the components that are selected in the
chromatogram plot or pinned in the Components se ct i o n o f t he
navigation pane define which peaks a re d i sp l ayed in t he MS
Components plot
Zoom Area When selected, the zoom area of the chromatogram plot d ef ines
which peaks are shown in the mass spec plot

Link to Injection

Parameter Sub Parameter Description

Link to Injections Allows multiple injections to be included in the array of SmartLink objects

Include Current Selections/Pins In addition to those injections specified by type or by custom c on dit ion
(below), the currently selected and pinned injections will be includ ed in
the list of SmartLink injections
Include Injection Types Unknown Displays values from unknown injections.

Calibration Standard Displays values from calibration standard injections.

Check Standard Displays values from check standard injections.

Matrix Displays values from matrix blank injections.

Blank Displays values from blank run injections.

Spiked Displays values from spiked injections.

Unspiked Displays values from unspiked injections.

Custom Conditions Only include injections that match Displays only injections that fulfill certain conditio ns, b a se d o n re port
the following conditions variables.

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Chromeleon 7

Parameter Sub Parameter Description

Link to Injections Allows multiple injections to be included in the array of SmartLink objects
Include Current Selections/Pins In addition to those injections specified by type or by custom con dit ion
(below), the currently selected and pinned injections will be includ ed in
the list of SmartLink injections

ALL (Any field from the inje c tio n Restrict the data points shown based on comparing the selected variable
list – including user defined with a user-defined value and using the following logical arguments:
columns) Is equal to (=)
Is not equal to (<>)
Is larger than (>)
Is smaller than (<)
Is larger than or equal to (=>)
Is smaller than or equal to (=<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty

AND [Any field from the injection As for the previous parameter.
list – including user defined
columns]
or Allows for matching based on only one comparison in the rule
and Forces matching based on every rule in the list. The or sub p a ra met er
overrides the requirement to match every comparison in the specific rule
list.

Display By
Defines how the SmartLink objects w ill be ordered.

Parameter Description
Peaks per injection When a single injection is selected, the peak objects for that injection are plotted in horizontal order.
When multiple injections are selected, each injection has its own row and each peak has its own column.
Injections per peak When a single peak is selected, the peak objects for each injection are plotted in horizontal order.
When multiple peaks are selected, each peak has its own row and each injection has its own column.

5.8.7 IPD Chromatogram Plot

The follow ing display options are available for IPD Chromatograms:

5.8.7.1 Select Component

Parameter Sub Parameter Description

Components Match XXX of the following rules ALL is equivalent to the AND logical operator. Finds injections
with variable values that match all of the criteria sp e cifie d i n
the rules that are assigned the AND logical operator.
ANY is equivalent to the OR logical operator. Finds injection s
with variable values that match any of the criteria specifie d i n
the rules that are assigned the OR logical operator.
Variable Selects an IPD Results variable from the list.

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Comparison operator Select the operator to be used for comparing variable values:
= (is equal to)
<> (is not equal to)
< (is less than)
<= (is less than or equal to)
> (is greater than)
>= (is greater than or equal to)
is between
is not between
is during previous
is not during previous
is like (use with wildcards) (for Quick Search only)
is not like (use with wildcards) (for Quick Search only)
contains
does not contain
starts with
does not start with
ends with
does not end with
is any
is not any
is empty
is not empty
Value Select the compare value.

Injection Components Match XXX of the following rules ALL is equivalent to the AND logical operator. Finds injections
with variable values that match all of the criteria sp e cifie d i n
the rules that are assigned the AND logical operator.
ANY is equivalent to the OR logical operator. Finds injection s
with variable values that match any of the criteria specifie d i n
the rules that are assigned the OR logical operator.
Variable Selects an IPD Results variable from the list.
Comparison operator Select the operator to be used for comparing variable values:
= (is equal to)
<> (is not equal to)
< (is less than)
<= (is less than or equal to)
> (is greater than)
>= (is greater than or equal to)
is between
is not between
is during previous
is not during previous
is like (use with wildcards) (for Quick Search only)
is not like (use with wildcards) (for Quick Search only)
contains
does not contain
starts with
does not start with
ends with
does not end with
is any
is not any
is empty
is not empty
Value Select the compare value.
Total Number of Plots Specifies how many component XIC plots will be displayed

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Show Chromatogram Trace Shows the TIC/BPC plot stacked above the compone nt X IC
plot.

5.8.7.2 Plot Details

Parameter Sub Parameter Description

Axes Time Axis Displays a time axis on the chromatogram.

Signal Axis Displays a signal axis on the chromatogram.

Font Allows the font type and size of the axes to be defined.

Axis to plot gap Defines the distance in mm between the axes and the
chromatogram plot.
Frame Frame that is drawn around the plot area.

Axes Descriptions Axes Titles Applies titles to the chromatogram axes.

Units Displays units on the axes of the chromatogram.

Font Allows the font type and size of the axes titles to be defined.

Grid Signal axis grid lines Applies horizontal grid lines to the chromatogram.
Time axis grid lines Applies vertical grid lines to the chromatogram.

Orientation Horizontal Displays the chromatogram in the portrait orientation.

Vertical Displays the chromatogram in the landscape orientation.

Signal details Raw data points Shows the raw data points.

5.8.7.3 Time Axis

This section allow s the user to define the scaling used for the time axis. The follow ing options are available:

Parameter Sub Parameter Description

Time Axis Share time axes If your chromatogram plot includes overlaid ch rom at ogra ms
and you have selected a Stacked arrangement on the
Comparison page, you can select whether to use a co mmo n
(shared) time axis for the chromatogram stripes, or se p a ra t e
time axes. The unit on the time axis is always identica l f or a ll
chromatogram stripes.
Select the Share time axis check box to display a sin gle t ime
axis for all chromatograms (default). Clear the ch eck b o x t o
display separate time axes for each chromatogram.
If you have cleared the Share time axis check box, select t he
chromatogram from the Settings for chromatogram plot list f o r
which the settings under Range (see below) shall apply.
Range Autoscale or Fixed Determines the method for selecting the range. Can be set t o:
Autoscale or Fixed, Autoscale on Peak, or Fixed using
Autoscale on Peak Formula.
Fixed using Formula
Autoscale or Fixed From Defines the start time of the chromatogram. Eithe r A ut o o r a
specific time can be selected.
To Defines the end time of the chromatogram. Eit her A u to o r a
specific time can be selected.
Autoscale on Peak Selected Allows the user to select the peak by Name, Greatest He igh t,
Greatest Area, Number, or Component Table Number
Width Defines the width by which to pad the se l ecte d a ut osca le d
peak range. This can be defined or set to Autosize width.
Fixed using Formula From Defines the start time of the chromatogram using a formula
To Defines the end time of the chromatogram using a formula

Tick mark intervals Fixed intervals of tick marks Defines whether tick marks should appear at selected intervals

Major tick mark Defines the interval for major tick marks
Minor tick mark Defines the interval for minor tick marks

Time axis units Minutes (min) The units for the time axis are minutes.

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Parameter Sub Parameter Description

Seconds (s) The units for the time axis are seconds.

5.8.7.4 Signal Axis

This section allow s the user to define the scaling used for the signal axis. The follow ing options are available.

Parameter Sub Parameter Description

Signal Axis Settings for chromatogram Determines the signal axis for which to define the setti ngs. T o b e
plot able to select between different signal axes, you h ave t o lo ad a t
least one Overlay. In addition, two signal axes must be displayed.
Range for selected plot Autoscale or Fixed Determines the method for selecting the ra ng e. Ca n b e se t t o:
Autoscale or Fixed, or Fixed using Formula.
Fixed using formula
Autoscale or Fixed To Defines the end value of the signal axis. Either Auto or a sp e cif ic
time can be selected.
From Defines the start value of the signal axis. Either Auto or a sp e ci fic
time can be selected.
Fixed using Formula From Defines the start value of the signal axis using a formula
To Defines the end value of the signal axis using a formula

Autoscale in time range or peak Autoscale in visible time Determines the signal autoscale options for the current
range chromatogram. Following options are enabled only fo r t he si gn al
scale mode ‘Autoscale or fixed’; Autoscale in visi ble t ime ra n ge,
Autoscale in fixed time range Autoscale in fixed time range, Autoscale on peak.
Autoscale on peak
Autoscale in visible time range N/A Calculates the signal minimum and / or maximum on th e b asi s o f
the current time range specified on the Time Axis properties page.
Autoscale in fixed time range From Custom start value to calculate signal minimum and / or maximum.

To Custom end value to calculate signal minimum and / or maximum.

Autoscale on peak Selected Calculates the signal minimum and / or maximum on th e b asi s o f
the range between peak start and end time. Following peak
selection modes are available; by name, by g rea te st h ei ght , b y
greatest area, by number, by component number.
Time mark intervals Fixed intervals of tick marks Defines whether tick marks should appear at selected intervals
Major tick mark Defines the interval for major tick marks

Minor tick mark Defines the interval for minor tick marks

5.8.7.5 Title
This section defines the caption that w ill be displayed in the chromatogram header. Left, middle and right captions can be
selected either based on simple text values or on user-defined formulas. The formula can be based on variables from the
follow ing sections:
• Global Functions (see section 7.1)

• General (see section 7.2)

• Sequence (see section 7.3)
• Injection (see section 0)
• Audit Trail (see section 7.5)
• Preconditions (see section 7.6)

• Chromatogram (see section 7.8)

• Processing Method (see section 7.21)
• Instrument Method (see section 7.31)
• Custom Formulas (see section 5.8.31)

In addition, the follow ing options are available:

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Chromeleon 7

Parameter Sub Parameter Description

Title Draw Titles Displays chromatogram titles.

Font Allows the font type and size of the titles to be defined

Left title Draw left title Displays the left part of the title.
When checked the left part of the title can be defin ed b a se d
on formulas as described above.
Middle title Draw middle title Displays the middle part of the title.
When checked the middle part of th e t i tle can b e d ef ine d
based on formulas as described above.
Right title Draw right title Displays the right part of the title.
When checked the right part of the title can be defined ba se d
on formulas as described above.
Legend Draw legend Displays a legend for overlaid chromatograms.
When checked the format of the legend can be defined based
on formulae as described above.

5.8.7.6 Line & Fill Styles

This section allow s a consistent color scheme for the objects in the chromatogram plot to be defined. The follow ing items
can have their line color defined:
• Chromatograms 1-8 • Peak w idth • Errors
• Peak delimiter • Raw data points • Peak purity index
• Peak separation • Detection parameters • Peak match index
• Baseline • Gradients • Tubes
• Rider baseline • Signal Parameters • Fractions
• Free baseline • Triggers

• Peak tangents • Manual Commands

The follow ing items can have their fill color defined:
• Background • Peak label • Detection parameter label
• Tube Label • Tubes • Fractions

5.8.8 IPD Mass Deconvoluted Spectra Plot

This object show s the spectrum extracted from the source injection data. The charge states for the spectral peaks are
optionally overlaid on the plot.
The follow ing properties are available:

5.8.8.1 Select Deconvoluted Component

Parameter Sub Parameter Description

Components Match XXX of the following rules ALL is equivalent to the AND logical operator. Finds injections
with variable values that match all of the criteria sp e cifie d i n
the rules that are assigned the AND logical operator.
ANY is equivalent to the OR logical operator. Finds injection s
with variable values that match any of the criteria specifie d i n
the rules that are assigned the OR logical operator.
Variable Selects an IPD Results variable from the list.

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Comparison operator Select the operator to be used for comparing variable values:
= (is equal to)
<> (is not equal to)
< (is less than)
<= (is less than or equal to)
> (is greater than)
>= (is greater than or equal to)
is between
is not between
is during previous
is not during previous
is like (use with wildcards) (for Quick Search only)
is not like (use with wildcards) (for Quick Search only)
contains
does not contain
starts with
does not start with
ends with
does not end with
is any
is not any
is empty
is not empty
Value Select the compare value.

Injection Components Match XXX of the following rules ALL is equivalent to the AND logical operator. Finds injections
with variable values that match all of the criteria sp e c ifie d i n
the rules that are assigned the AND logical operator.
ANY is equivalent to the OR logical operator. Finds injection s
with variable values that match any of the criteria specifie d i n
the rules that are assigned the OR logical operator.
Variable Selects an IPD Results variable from the list.
Comparison operator Select the operator to be used for comparing variable values:
= (is equal to)
<> (is not equal to)
< (is less than)
<= (is less than or equal to)
> (is greater than)
>= (is greater than or equal to)
is between
is not between
is during previous
is not during previous
is like (use with wildcards) (for Quick Search only)
is not like (use with wildcards) (for Quick Search only)
contains
does not contain
starts with
does not start with
ends with
does not end with
is any
is not any
is empty
is not empty
Value Select the compare value.
Total Number of Plots Specifies how many component XIC plots will be displayed

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Chromeleon 7

Show Chromatogram Trace Shows the TIC/BPC plot stacked above the compone nt X IC
plot.

5.8.8.2 Scale

Parameter Sub Parameter Description

Apply scaling to all plots N/A Allows the user to apply the same scaling to all plots
simultaneously when checked.
Mass From Defines the start value of the mass axis.

To Defines the end value of the mass axis.

Autoscale When this is selected the plot is scaled to show the ful l ma ss
range of the data
Fixed intervals of tick marks Chromeleon automatically determines t h e i nt erva l o f t ick
marks (the small lines that mark values) on the time axis. T o
customize the intervals, select the Fixed intervals of tick marks
check box and then type or select a number in the Majo r t ick
mark and/or Minor tick mark box. A tick mark inte rva l o f 0 . 0
removes the tick marks.
Intensity From Defines the start value of the intensity axis.
To Defines the end value of the intensity axis.

Autoscale When this is selected the plot is scaled to show the full
intensity range of the mass spectrum.
Fixed intervals of tick marks Chromeleon automatically determines t h e i nt erva l o f t ick
marks (the small lines that mark values) on the time axis. T o
customize the intervals, select the Fixed intervals of tick marks
check box and then type or select a number in the Majo r t ic k
mark and/or Minor tick mark box. A tick mark inte rva l o f 0 . 0
removes the tick marks.

5.8.8.3 Frame & Axes

This section allow s defining axes, grid and normalization of the mass spec plot.

Parameter Sub Parameter Description

Axes Mass axis Displays a mass axis on the mass spec plot.

Intensity axis Displays an abundance axis on the mass spec plot.

Font Allows the font type and size of the axes to be defined.

Axis to Plot Gap Defines the distance in mm between the axes and the plot.

Frame Displays a frame around the plot

Axis Titles Axis Titles Applies titles to the mass spec plot axes.

Units Displays units on the axes of the mass spec plot.

Font Allows the font type and size of the axis titles to be defined
Grid Horizontal grid lines Applies horizontal grid lines to the mass spec plot.

Vertical grid lines Applies vertical grid lines to the mass spec plot.
Orientation Horizontal Scan type is the horizontal axis, and signal is the vertical axis

Vertical Scan type is the vertical axis, and signal is the horizontal axis.

Normalization None No normalization is performed.

Absolute maximum Performs spectra normalization relative to the absolute
maximum of the spectra.

5.8.8.4 Title
This section defines if titles are displayed and how titles should be displayed:

Parameter Sub Parameter Description

Draw titles Shows a title for the fluorescence spectra plot.

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Parameter Sub Parameter Description

Font Allows the font for the fluorescence sp e ctra p lot t it le t o b e

defined.
Left title Draw left title Displays the left part of the title.

Use default When checked left part of the title is shown as in Chrome leon
7.2.
When not checked the left part of t he t i tle can b e d e fin ed
based on formulas in the edit field.
Center title Draw center title Displays the middle part of the title.

Use default When checked middle part of the title is shown as in

Chromeleon 7.2.
When not checked the middle part of the title can b e d ef ine d
based on formulas in the edit field.
Right title Draw right title Displays the right part of the title.

Use default When checked right part of the title is shown as in Chromeleon
7.2.
When not checked the right part of the t i tle can b e d ef ine d
based on formulas in the edit field.

5.8.8.5 Comparison
This section allow s defining how multiple mass spectra are arranged

Group Sub Parameter Description

Arrangement Stacked Plots are stacked on a single plot and share the sa m e sca n a xis;
each stacked plot has a separate intensity axis.
Overlaid Plots are overlaid on a single plot and share t h e sa m e sca n a n d
intensity axes
Offset Scan Offset To offset overlaid plots on the scan axis, select the check b o x a nd
enter the offset percentage in the box.
Intensity Offset To offset overlaid plots on the intensity axis, select t he c he ck b o x
and enter the offset percentage in the box
Overlay Overlay with right signal axis When plots are overlaid, select this check box to include a se co n d
signal axis on the right side of the plot
Mirror Mirror Signal Select this check box to invert the intensity axis of t h e o verla id o r
stacked plots. The plots "mirror" the main spectrum or I-t plot.

5.8.8.6 Line & Fill Styles

This section allow s the color of each item in the mass spec plot to be defined. The follow ing items can have their color
defined:
• Grid lines • Axes • Spectrum 1-8
•
The follow ing items can have their fill color defined:

• Background • •

5.8.9 IPD Mass Source Spectra Plot

This object show s the spectrum extracted from the source injection data. The charge states for the spectral peaks are
optionally overlaid on the plot.
The follow ing properties are available:

5.8.9.1 Scale

Parameter Sub Parameter Description

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Chromeleon 7

Parameter Sub Parameter Description

Apply scaling to all plots N/A Allows the user to apply the same scaling to all plots
simultaneously when checked.
Mass From Defines the start value of the mass axis.

To Defines the end value of the mass axis.

Autoscale When this is selected the plot is scaled to show the ful l ma ss
range of the data
Fixed intervals of tick marks Chromeleon automatically determines t h e i nt erva l o f t ick
marks (the small lines that mark values) on the time axis. T o
customize the intervals, select the Fixed intervals of tick marks
check box and then type or select a number in the Majo r t ick
mark and/or Minor tick mark box. A tick mark inte rva l o f 0 . 0
removes the tick marks.
Intensity From Defines the start value of the intensity axis.

To Defines the end value of the intensity axis.

Autoscale When this is selected the plot is scaled to show the full
intensity range of the mass spectrum.
Fixed intervals of tick marks Chromeleon automatically determines t h e i nt erva l o f t ick
marks (the small lines that mark values) on the time axis. T o
customize the intervals, select the Fixed intervals of tick marks
check box and then type or select a number in the Majo r t ick
mark and/or Minor tick mark box. A tick mark inte rva l o f 0 . 0
removes the tick marks.

5.8.9.2 Frame & Axes

This section allow s defining axes, grid and normalization of the mass spec plot.

Parameter Sub Parameter Description

Axes Mass axis Displays a mass axis on the mass spec plot.

Intensity axis Displays an abundance axis on the mass spec plot.

Font Allows the font type and size of the axes to be defined.

Axis to Plot Gap Defines the distance in mm between the axes and the plot.

Frame Displays a frame around the plot

Axis Titles Axis Titles Applies titles to the mass spec plot axes.

Units Displays units on the axes of the mass spec plot.

Font Allows the font type and size of the axis titles to be defined

Grid Horizontal grid lines Applies horizontal grid lines to the mass spec plot.

Vertical grid lines Applies vertical grid lines to the mass spec plot.
Orientation Horizontal Scan type is the horizontal axis, and signal is the vertical axis

Vertical Scan type is the vertical axis, and signal is the horizontal axis.

Normalization None No normalization is performed.

Absolute maximum Performs spectra normalization relative to the absolute
maximum of the spectra.
Charge States Specifies if charge state lines should be superimposed on th e
plot

5.8.9.3 Title
This section defines if titles are displayed and how titles should be displayed:

Parameter Sub Parameter Description

Draw titles Shows a title for the fluorescence spectra plot.

Font Allows the font for the fluorescence sp e ctra p lot t it le t o b e
defined.
Left title Draw left title Displays the left part of the title.

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 Chromeleon 7

Parameter Sub Parameter Description

Use default When checked left part of the title is shown as in Chrome leon
7.2.
When not checked the left part of t he t i tle can b e d e fin ed
based on formulas in the edit field.
Center title Draw center title Displays the middle part of the title.
Use default When checked middle part of the title is shown as in
Chromeleon 7.2.
When not checked the middle part of the title can b e d ef ine d
based on formulas in the edit field.
Right title Draw right title Displays the right part of the title.

Use default When checked right part of the title is shown as in Chromeleon
7.2.
When not checked the right part of the t i tle can b e d ef ine d
based on formulas in the edit field.

5.8.9.4 Comparison
This section allow s defining how multiple mass spectra are arranged

Group Sub Parameter Description

Arrangement Stacked Plots are stacked on a single plot and share the sa m e sca n a xis;
each stacked plot has a separate intensity axis.
Overlaid Plots are overlaid on a single plot and share t h e sa m e sca n a n d
intensity axes
Offset Scan Offset To offset overlaid plots on the scan axis, select the check b o x a nd
enter the offset percentage in the box.
Intensity Offset To offset overlaid plots on the intensity axis, select t he c he ck b o x
and enter the offset percentage in the box
Overlay Overlay with right signal axis When plots are overlaid, select this check box to include a se co n d
signal axis on the right side of the plot
Mirror Mirror Signal Select this check box to invert the intensity axis of t h e o verla id o r
stacked plots. The plots "mirror" the main spectrum or I-t plot.

5.8.9.5 Line & Fill Styles

This section allow s the color of each item in the mass spec plot to be defined. The follow ing items can have their color
defined:
• Grid lines • Axes • Spectrum 1-8

The follow ing items can have their fill color defined:
• Background • •

5.8.10SIEVE Frame Plot

The follow ing sections describe the tabs of the Properties dialogue accessed from the context menu

5.8.10.1 Frame Filter

This section defines w hich frames are displayed in the plot:

Parameter Sub Parameter Description

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Chromeleon 7

Parameter Sub Parameter Description

Custom Conditions ALL Restrict the data shown based on comparin g a ll ru le s wi t h
user-defined numerical values and using the following l ogica l
arguments:
Is equal to (=)
Is not equal to (<>)
Is larger than (>)
Is smaller than (<)
Is larger than or equal to (=>)
Is smaller than or equal to (=<)
Is between
Is not between
ANY [Any field from the sequence As for the previous parameter.
table – including user defined
columns]
Or Allows for matching based on only one comparison in the rule

And Forces matching based on every rule in the list . T he o r su b

parameter overrides the requirement to match every
comparison in the specific rule list.

5.8.10.2 Scale
This section allow s the user to define the scaling used for the time (X) and signal count (Y) axes of the frame plot. The
follow ing options are available:

Parameter Sub Parameter Description

Time axis From Defines the start retention time of the frame plot X-axis

To Defines the end retention time of the frame plot X-axis

Autoscale Automatically defines the retention time range o f t he f ram e

plot X-axis
Intensity Axis From Defines the lowest signal count value of the frame plot Y-axis
To Defines the highest signal count value of the frame plot Y-axis

Autoscale Automatically defines the signal count range of the frame plo t
Y-axis.

5.8.10.3 Frame & Axes

This section allow s the user to define the displayed properties of the frame plot.

Parameter Sub Parameter Description

Axes Time axis Enables or disables the X-axis of the frame plot

Intensity axis Enables or disables the Y-axis of the frame plot

Font Defines font style, size and font emphasis of the axes

Axis to plot gap Defines distance between plot and axis

Frame Enables or disables a black border around the frame plot

Axis Titles Axis titles Enables or disables axis labeling

Units Enables or disables axis units labeling

Font Defines font style, size and font emphasis of the axis titles
Grid Horizontal grid lines Enables or disables horizontal grid lines in the frame plot

Vertical grid lines Enables or disables vertical grid lines in the frame plot

5.8.10.4 Title
This section allow s the user to define the displayed titles of the frame plot.

Parameter Sub Parameter Description

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 Chromeleon 7

Parameter Sub Parameter Description

Title Draw titles Enables or disables the titles displayed above the frame plot

Font Defines the font style, size, and emphasis of the titles

Legend Draw legend Enables or disables the frame plot legend

5.8.10.5 Data
This section allow s the user to define the type of data displayed on the frame plot.

Parameter Sub Parameter Description

Reconstructed Ion Chromatogram Draw reference Enables or disables display of the reference injection XIC

Draw unaligned Enables or disables display of the unaligned unknown XIC

Thumbnails Show spectral thumbnails Enables or disables thumbnails of mass spectra displayed on
Mass Spectra pane

5.8.11Injection Rack View

The follow ing injection rack view plot options are available:

5.8.11.1 General

Parameter Sub Parameter Description

Show Overview Displays the rack overview in the top right corner of t he ra ck
view.
Positions Displays the vial positions in the rack view. (Only visible when
zoom allows.)

Tray name Displays the tray names on the rack view.

Visible Trays Show all trays Shows all configured trays for the select ed a ut osa mp ler i f
supported.
Hide inactive tray Hides trays that are configured but do not contain any
injections (i.e. are not used) in the current sequence.

5.8.11.2 Title

Parameter Sub Parameter Description

Draw Title N/A Displays the title in the top center of the plot.

Font N/A Allows defining the font to be used for the title of the plot.

5.8.12Fraction Tray Plot

The fraction tray pane provides a graphical display of the fraction tube positions for the current sequence in the assigned
instruments autosampler. The follow ing options are available:

Function Description
Copy to Clipboard Copies the current rack image to the clipboard.
Full Size Scale the rack view to full size.

Zoom in (+) Zoom into the rack view.

Zoom out (-) Zoom out of the rack view.

In the Fraction Tray plot properties dialog, there are several options:

5.8.12.1 General

Parameter Sub Parameter Description

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Chromeleon 7

Parameter Sub Parameter Description

Show Overview Displays the rack overview in the top right corner of t he ra c k
view.

Positions Displays the vial positions in the rack view. (Only visible when
zoom allows.)

Tray name Displays the tray names on the rack view.

5.8.12.2 Title

Parameter Sub Parameter Description

Draw Title N/A Displays the title in the top center of the plot.

Font N/A Allows defining the font to be used for the title of the plot.

5.8.12.3 Fill styles

In the fraction tray, the fill colors of various objects can be defined. The follow ing options are available:

Parameter Sub Parameter Description

Tubes collected during sequence run N/A Defines the color for all tubes collected during the current sequence

Tubes collected from current injection N/A Defines the color for all tubes from the currently selected injection

Currently selected tube/fraction N/A Defines the color of the currently selected tube or fraction

5.8.12.4 Tooltip

Function Description
Enable tooltip Displays information about a vial/tube.

Tooltip formula The content of the tooltip can be adapted depending on the context the Tray V ie w
control is used, based on variables contained in the Injection category section 7. X.

5.8.12.5 Interactive Settings

Parameter Sub Parameter Description

Scaling Enable scaling Disables zooming of the rack view.

Rotation Enable rotation Disables rotation of the rack view.

5.8.13Fluorescence Spectra Plot

The follow ing fluorescence spectra display options are available:

5.8.13.1 Spectra

Parameter Sub Parameter Description

Currently selected spectra N/A Peak and time spectra of current spectral plot.
(interactive mode only!)
Peak Spectra Name Displays the spectra plot for the peak of the selected name.

Greatest height Displays the spectra plot for the peak with the greatest height.

Greatest area Displays the spectra plot for the peak with the greatest area.
Number Displays the spectra plot for the peak with the selected
number in the chromatogram.
Component table number Displays the spectra plot for the peak with the selected
number in the component table.
SLS hit number Displays the spectra plot for the peak with the sel ect ed S L S
hit number.

Time scans at fixed retent ion t i me N/A Displays the spectrum at a fixed retention time (o r b u nche d
(or bunched over a range) over a time range).

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5.8.13.2 Channel
This section defines w hich channel is show n. There are tw o options:
• Currently selected channel (interactive mode only!)

• Fixed Channel (Channel is specified by the user)

5.8.13.3 Scale

Parameter Sub Parameter Description

Apply scaling to all plots N/A Allows the user to apply the same scaling to all plots
simultaneously when checked.
Wavelength From Defines the start value of the wavelength axis.

To Defines the end value of the wavelength axis.

Autoscale When this is selected the plot is scaled to show the full
wavelength range of the spectrum.
Fixed intervals of tick marks Chromeleon automatically determines the interval of tick marks
(the small lines that mark values) on the time axis. To
customize the intervals, select the Fixed intervals of tick marks
check box and then type or select a number in the M ajo r t ick
mark and/or Minor tick mark box. A tick mark i n te rva l o f 0 . 0
removes the tick marks.
Intensity From Defines the start value of the intensity axis.
To Defines the end value of the intensity axis.

Autoscale When this is selected the plot is scaled to show the full
intensity range of the spectrum.
Fixed intervals of tick marks Chromeleon automatically determines the interval of tick marks
(the small lines that mark values) on the time axis. To
customize the intervals, select the Fixed intervals of tick marks
check box and then type or select a number in the M ajo r t ic k
mark and/or Minor tick mark box. A tick mark i n te rva l o f 0 . 0
removes the tick marks.

5.8.13.4 Frame & Axes

This section allow s defining axes, grid and normalization of the spectral plot.

Parameter Sub Parameter Description

Axes Wavelength axis Displays a wavelength axis on the spectra plot.

Intensity axis Displays an intensity axis on the spectra plot.

Font Allows the font type and size of the axes to be defined
Axis to Plot Gap Defines the distance in mm between the axes and the spect ra
plot.
Frame Displays plot frame when selected

Axis Titles Axis Titles Applies titles to the spectra plot axes.

Units Displays units on the axes of the spectra plot.

Font Allows the font type and size of the axis titles to be defined

Grid Horizontal grid lines Applies horizontal grid lines to the calibration plot.
Vertical grid lines Applies vertical grid lines to the calibration plot.

Orientation Horizontal Displays the chromatogram horizontally with re sp ect t o t h e

wavelength axis.
Vertical Displays the chromatogram vertically with respect to the
wavelength axis.
Normalization None No normalization is performed. Signal response is reported in
mAU.
Absolute Maximum Performs spectra normalization relative to the absolute
maximum of the spectra.

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Chromeleon 7

Parameter Sub Parameter Description

Relative Maximum Performs spectra normalization relative to the relative
maximum of the spectra.
Fixed Wavelength at Performs spectra normalization relative to the fixed wavelength
selected.

5.8.13.5 Title
This section allow s controlling the caption for the spectral plot.

Parameter Sub Parameter Description

Draw titles Shows a title for the fluorescence spectra plot.

Font Allows the font for the fluorescence sp e ctra p lot t it le t o b e

defined.
Left title Draw left title Displays the left part of the title.

Use default When checked left part of the title is shown as in Chrome leon
7.2.
When not checked the left part of t he t i tle can b e d e fin ed
based on formulas in the edit field.
Center title Draw center title Displays the middle part of the title.

Use default When checked middle part of the title is shown as in

Chromeleon 7.2.
When not checked the middle part of the title can b e d ef ine d
based on formulas in the edit field.
Right title Draw right title Displays the right part of the title.

Use default When checked right part of the title is shown as in Chromeleon
7.2.
When not checked the right part of the t i tle can b e d ef ine d
based on formulas in the edit field.

5.8.13.6 Spectra Filter

This section allow s defining w hich fluorescence spectra are show n.

Parameter Sub Parameter Description

Scan type Any Displays any spectrum found, regardless of the scan type.
Emission Displays emission scans only.
Excitation Displays excitation scans only.
Synchronous Displays synchronous scans only.

Photomultiplier Any Displays any spectrum found, regardless of which

photomultiplier tube (PMT) measured the spectrum.
Photomultiplier 1 Displays spectra measured by the primary PMT only.

Photomultiplier 2 Displays spectra measured by the secondary PMT only.

More Options N/A Adds additional filter criteria.

5.8.13.7 Overlay
This section allow s selecting w hich spectra should be overlaid.

Parameter Sub Parameter Description

Reference Overlay None No reference overly is displayed.

Peak spectra of recent calibratio n The spectrum of the currently displayed peak is overl aid wi th
standard the spectrum of the peak with the same name f ro m t h e l ast
calibration standard injection of the sequence.
Peak spectra of a fixed injection The spectrum of the currently displayed peak is overl aid wi th
the spectrum of the peak with the same name from the
selected injection.

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 Chromeleon 7

5.8.13.8 Label
This section allow s defining how labels are show n in the spectral plot.

Parameter Sub Parameter Description

Label Maxima Rotation Defines the angle the spectrum label is shown at.
Maxima Count Defines how many maxima should be labeled.

Font Defines the font for the spectrum label.

Options Show match factor Displays the match of each spectrum with the correspo nd ing
main spectrum. The main spectrum is either the peak
spectrum, or a reference spectrum (spectra compariso n), o r
the top spectrum in a spectra library selection.
Show baseline correction info Displays information about the base lin e co rre ct ion in t he
header.

5.8.13.9 Analysis
This section controls how spectra analysis is performed.

Parameter Sub Parameter Description

Spectra Analysis None No analysis is performed.

Difference Forms plots representing the difference b et ween t he ma in

spectrum and the remaining individual spectra o f t h e p an e.
Depending on whether normalization is performed (see Frame
& Axes), representation of the difference spectra is in percen t
or in the corresponding dimension.
First derivative Calculates and displays the first derivative of each sp e ct rum
displayed.
Second derivative Calculates and displays the second derivative of each
spectrum displayed.

5.8.13.10 Comparison
This section defines Arrangement, Offset, Overlay and Mirror settings.

Parameter Sub Parameter Description

Arrangement Stacked All overlaid spectra are shown in stacked plots
Overlaid All overlaid spectra are shown in one plot

Offset Scan offset Offsets the overlaid spectra by the scan value selected
Intensity offset Offsets the overlaid spectra by the intensity value selected

Overlay Overlay with right signal axis If selected the overlaid spectrum is measured against a ri gh t
signal axis.
Mirror Mirror signal If selected displays the overlaid spectrum as a mirror of
existing spectrum.

5.8.13.11 Line & Fill Styles

This section allow s the color of each item in the peak spectra plot to be defined. The follow ing items can have their color
defined:
• Grid lines • Uncorrected spectrum • Second front spectrum
• Axes • Spectrum 1-8 • First tail spectrum
• Reference spectrum • Apex Spectrum • Second tail spectrum
• Background spectrum • First front spectrum •
The follow ing items can have their fill color defined:
• Background

5.8.13.12 SmartLink
The follow ing options are available:

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Chromeleon 7

Link to Chromatogram

Parameter Sub Parameter Description

Select the chromatogram plot to link None No link is selected
with
Interactive Chromatogram Links with the interactive chromatogram in the data processing
category.
Chromatogram Plot (sheet name) Allows the user to link with a chromatogram plot on any o t he r
sheet within the current report.
Multiple Peak Selection N/A Shows spectra for selected components

Zoom Area N/A Shows spectra for components whose peak apex is within t h e
zoom area.

Link to Injection

Parameter Sub Parameter Description

Link to Injections Allows multiple injections to be included in the array of SmartLink objects
Include Current Selections/Pins In addition to those injections specified by type or by custom con dit ion
(below), the currently selected and pinned injections will be includ ed in
the list of SmartLink injections
Include Injection Types Unknown Displays values from unknown injections.
Calibration Standard Displays values from calibration standard injections.

Check Standard Displays values from check standard injections.

Matrix Displays values from matrix blank injections.

Blank Displays values from blank run injections.

Spiked Displays values from spiked injections.

Unspiked Displays values from unspiked injections.

Custom Conditions Only include injections that match Displays only injections that fulfill certain conditio ns, b a se d o n re port
the following conditions variables.

ALL (Any field from the inje c tio n Restrict the data points shown based on comparing the selected variable
list – including user defined with a user-defined value and using the following logical arguments:
columns) Is equal to (=)
Is not equal to (<>)
Is larger than (>)
Is smaller than (<)
Is larger than or equal to (=>)
Is smaller than or equal to (=<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
AND [Any field from the injection As for the previous parameter.
list – including user defined
columns]
or Allows for matching based on only one comparison in the rule

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Parameter Sub Parameter Description

Link to Injections Allows multiple injections to be included in the array of SmartLink objects
Include Current Selections/Pins In addition to those injections specified by type or by custom con dit ion
(below), the currently selected and pinned injections will be includ ed in
the list of SmartLink injections
and Forces matching based on every rule in the list. The or sub p a ra met er
overrides the requirement to match every comparison in the specific rule
list.

Display By
Defines how the SmartLink objects w ill be ordered.

Parameter Description
Peaks per injection When a single injection is selected, the peak objects for that injection are plotted in horizontal order.
When multiple injections are selected, each injection has its own row and each peak has its own column.
Injections per peak When a single peak is selected, the peak objects for each injection are plotted in horizontal order.
When multiple peaks are selected, each peak has its own row and each injection has its own column.

5.8.14I-t Plot
The follow ing I-t plot display options are available:

5.8.14.1 I-t Plots

Parameter Sub Parameter Description

Currently selected I-t plots N/A Peak and time scans of current I-t plot.
(interactive mode only!)
Peak I-t plots Name Displays the I-t plot for the peak of the selected name.

Greatest height Displays the I-t plot for the peak with the greatest height.
Greatest area Displays the I-t plot for the peak with the greatest area.

Number Displays the I-t plot for the peak with the selected num ber i n
the chromatogram.
Component table number Displays the I-t plot for the peak with the selected num ber i n
the component table.
SLS hit number Displays the I-t plot for the peak with t he se l ecte d S L S h it
number.
Time scans at fixed retent ion t i me N/A Displays the I-t plot at a fixed retention time (or bunched o ver
(or bunched over a range) a time range).

5.8.14.2 Channel
This section defines w hich channel is show n. There are tw o options:
• Currently selected channel (interactive mode only!)

• Fixed Channel (Channel is specified by the user)

5.8.14.3 Scale

Parameter Sub Parameter Description

Apply scaling to all plots N/A Applies scaling to all I-t plots

Waveform Time From Defines the start value of the waveform axis.
To Defines the end value of the waveform axis.
Autoscale When this is selected, the plot is scaled to show the full
waveform range of the I-t plot.

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Chromeleon 7

Parameter Sub Parameter Description

Fixed intervals of tick marks Chromeleon automatically determines t h e i nt erv a l o f t ic k
marks (the small lines that mark values) on the time axis. T o
customize the intervals, select the Fixed intervals of tick marks
check box and then type or select a number in the Majo r t ick
mark and/or Minor tick mark box. A tick mark inte rva l o f 0 . 0
removes the tick marks.
Current From Defines the start value of the response axis.

To Defines the end value of the response axis.

Autoscale When this is selected, the plot is scaled to show the full
response range of the I-t plot.
Fixed intervals of tick marks Chromeleon automatically determines t h e i nt erva l o f t ick
marks (the small lines that mark values) on the time axis. T o
customize the intervals, select the Fixed intervals of tick marks
check box and then type or select a number in the Majo r t ic k
mark and/or Minor tick mark box. A tick mark inte rva l o f 0 . 0
removes the tick marks.

5.8.14.4 Frame & Axes

This section defines settings for the axes, grid and normalization of the I-t plot.

Parameter Sub Parameter Description

Axes Waveform time axis Displays a waveform time axis on the I-t plot.
Current axis Displays a current axis on the I-t plot.

Font Allows the font type and size of the axes to be defined.
Axis to Plot Gap Defines the distance in mm between the axes and the
chromatogram plot.
Frame Displays plot frame when selected
Axis Titles Axis Titles Applies titles to the I-t plot axes.

Units Displays units on the axes of the I-t plot.

Font Allows the font type and size of the axis titles to be defined

Grid Horizontal grid lines Applies horizontal grid lines to the I-t plot.

Vertical grid lines Applies vertical grid lines to the I-t plot.
Orientation Horizontal Displays the chromatogram horizontally with re sp ect t o t h e
waveform time axis.
Vertical Displays the chromatogram vertically with respect to the
waveform time axis.
Normalization None No normalization is performed. Signal response is reported in
mAU.
Absolute Maximum Performs I-t plot normalization relative to the absolute
maximum of the I-t plots.
Relative Maximum Performs I-t plot normalization relative to the relative
maximum of the I-t plots.
Fixed Waveform Time at Performs I-t plot normalization relative to the fixed wa v ef orm
time point selected.

5.8.14.5 Title
This section defines the caption for the I-t plot.

Parameter Sub Parameter Description

Draw titles Shows a title for the I-t plot.

Font Allows the font for the I-t plot title to be defined.
Left title Draw left title Displays the left part of the title.

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Parameter Sub Parameter Description

Use default When checked left part of the title is shown as in Chrome leon
7.2.
When not checked the left part of t he t i tle can b e d e fin ed
based on formulas in the edit field.
Center title Draw center title Displays the middle part of the title.
Use default When checked middle part of the title is shown as in
Chromeleon 7.2.
When not checked the middle part of the title can b e d ef ine d
based on formulas in the edit field.
Right title Draw right title Displays the right part of the title.

Use default When checked right part of the title is shown as in Chromeleon
7.2.
When not checked the right part of the t i tle can b e d ef ine d
based on formulas in the edit field.

5.8.14.6 Peak I-t Plots

This section defines w hich I-t plots are show n.

Parameter Sub Parameter Description

I-t plot Sampling Points Apex I-t plot Displays the I-t plot at the peak apex.
Front 1 (%) Displays the I-t plot at the selected % height of the peak
ascending flank.
Front 2 (%) Displays the I-t plot at the selected % height of the peak
ascending flank.
Tail 1 (%) Displays the I-t plot at the selected % height of the peak tailing
flank.
Tail 2 (%) Displays the I-t plot at the selected % height of the peak tailing
flank.
Reference Overlay None No reference overlay is displayed.

Apex I-t plot of recent calibrat ion The I-t plot of the currently displayed peak is overlaid with the I-
standard t plot of the peak with the same name from the last calibrat ion
standard injection of the sequence.
Apex I-t plot of a fixed injection The I-t plot of the currently displayed peak is overlaid with the I-
t plot of the peak with the same name from the selected
injection.

5.8.14.7 Label
This section defines how labels are show n in the I-t plot.

Parameter Sub Parameter Description

Label Maxima Rotation Defines the angle at which the I-t plot label is shown.

Maxima Count Defines how many maxima should be labeled.

Font Defines the font for the I-t plot label.

Options Show match factor Displays, in the caption for each I-t plot, the match f act or f o r
that I-t plot relative to the corresponding main I-t plot. The main
I-t plot is either the peak I-t plot, or a reference I-t plot (I -t p lo t
comparison).
Show baseline correction info Displays information about baseline correction in the caption of
each I-t plot.

5.8.14.8 Analysis
This section controls how I-t plot analysis is performed.

Parameter Sub Parameter Description

I-t plot Analysis None No analysis is performed.

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Chromeleon 7

Parameter Sub Parameter Description

Difference Forms the difference between the main I-t plot and the
remaining individual I-t plot s o f t he p an e. De p en ding o n
whether normalization is performed (see Frame & Axes),
representation of the difference I-t plots is in percent or in t h e
corresponding dimension (nA).
First derivative Calculates and displays the first derivat ive o f ea ch I -t p lot
displayed.
Second derivative Calculates and displays the second derivative of each I-t p lot
displayed.

5.8.14.9 Comparison
This section defines Arrangement, Offset, Overlay and Mirror settings.

Parameter Sub Parameter Description

Arrangement Stacked All overlaid I-t plots are shown in stacked plots
Overlaid All overlaid I-t plots are shown in one plot

Offset Scan offset Offsets the overlaid I-t plot by the scan value selected

Intensity offset Offsets the overlaid I-t plot by the intensity value selected
Overlay Overlay with right signal axis If selected the overlaid I-t plot is measu re d a g ain st a ri ght
signal axis.
Mirror Mirror signal If selected displays the overlaid I-t plot as a mirror of exist i ng
spectrum.

5.8.14.10 Line & Fill Styles

This section defines the color of each item in the peak I-t plot. The follow ing items can have their color defined:
• Grid Lines • Uncorrected I-t plot • Second Front I-t plot
• Axes • I-t plot 1-8 • First Tail I-t plot
• Reference I-t plot • Apex I-t plot • Second Tail I-t plot
• Background I-t plot • First Front I-t plot
The follow ing items can have their fill color defined:

• Background

5.8.14.11 SmartLink
The follow ing options are available:

Link To Chromatogram

Parameter Sub Parameter Description

Select the chromatogram plot to link None No link is selected

with
Interactive Chromatogram Links with the interactive chromatogram in the data processing
category.
Chromatogram Plot (sheet name) Allows the user to link with a chromatogram plot on any o t he r
sheet within the current report.
Multiple Peak Selection N/A Shows I-t plot for selected components
Zoom Area N/A Shows I-t plot for components whose peak apex is wit h in t he
zoom area.

Link to Injection

Parameter Sub Parameter Description

Link to Injections Allows multiple injections to be included in the array of SmartLink objects

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Include Current Selections/Pins In addition to those injections specified by type or by custom c on dit ion
(below), the currently selected and pinned injections will be includ ed in
the list of SmartLink injections
Include Injection Types Unknown Displays values from unknown injections.
Calibration Standard Displays values from calibration standard injections.

Check Standard Displays values from check standard injections.

Matrix Displays values from matrix blank injections.

Blank Displays values from blank run injections.

Spiked Displays values from spiked injections.

Unspiked Displays values from unspiked injections.

Custom Conditions Only include injections that match Displays only injections that fulfill certain conditio ns, b a se d o n re port
the following conditions variables.

ALL (Any field from the inje ctio n Restrict the data points shown based on comparing the selected variable
list – including user defined with a user-defined value and using the following logical arguments:
columns) Is equal to (=)
Is not equal to (<>)
Is larger than (>)
Is smaller than (<)
Is larger than or equal to (=>)
Is smaller than or equal to (=<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
AND [Any field from the injection As for the previous parameter.
list – including user defined
columns]
or Allows for matching based on only one comparison in the rule

and Forces matching based on every rule in the list. The or sub p a ra met er
overrides the requirement to match every comparison in the specific rule
list.

Display By
Defines how the SmartLink objects w ill be ordered.

Parameter Description
Peaks per injection When a single injection is selected, the peak objects for that injection are plotted in horizontal order.
When multiple injections are selected, each injection has its own row and each peak has its own column.
Injections per peak When a single peak is selected, the peak objects for each injection are plotted in horizontal order.
When multiple peaks are selected, each peak has its own row and each injection has its own column.

5.8.15Chromeleon Report Tables

Chromeleon report tables are designed to show groups of Chromeleon variables (see section 7) e.g. integration tables and
summary tables. The follow ing tables are available.

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Chromeleon 7

5.8.15.1 Grouping Columns

For those tables that support grouping, the follow ing group columns are available:
• Group Sum • Group Standard Deviation • Group Relative Range

• Group Count • Group Relative Standard Deviation • Group Minimum

• Group Average • Group Range • Group Maximum
When row s of the tables are grouped, the group columns display the calculated values for each row group. There are tw o
options w hen creating a group column:
• Group the values in Column number x, w here x is the
number of a column in the table.

• Group the values calculated by a user-defined formula.

5.8.15.2 Results – Integration Table

This table is designed to show results based on the chromatogram e.g. retention time, peak area, etc. An unlimited number
of columns can be created, and each column can show any variable show n in section 7. The details in this table change,
depending on w hich injection is being view ed.
The follow ing properties can be defined for the report:

Table Channels

Parameter Description
Single channel Lists peaks of a single (currently active or specific) channel

Multiple channels Lists peaks of one or more specific channels

Channels of detector Lists peaks of al channels of selected detectors

Filter Peaks

Parameter Sub Parameter Description

Include Peaks Identified Peaks Shows all peaks that have been identified.

Unidentified Peaks Shows all peaks that have not been identified.
Undetected Components Includes rows for components of the Component Ta ble t h at
have not been detected in the current injection.
Custom Conditions Only include peaks that match the Displays only peaks that fulfill certain condit ion s, b a se d o n
following conditions report variables.

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Parameter Sub Parameter Description

ALL (Any field from the sequen ce Restrict the data points shown based on comparing the
table – including user defined selected variable with a user-defined va lu e a nd u sin g t h e
columns) following logical arguments:
Is equal to (=)
Is not equal to (<>)
Is larger than (>)
Is smaller than (<)
Is larger than or equal to (=>)
Is smaller than or equal to (=<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
ANY [Any field from the sequence As for the previous parameter.
table – including user defined
columns]

Grouping Options

Parameter Sub Parameter Description

Sort the report table according to Retention time of peak Sorts the table according to peak retention time.
evaluation of this formula Peaks are grouped by the user-defined formula.

Report only the last row fo r e a ch Reports only the last row of each group.
group

Ignore case when comparing t ext Ignore case when comparing text results.
results
Use Chromeleon 6 Sort Order Uses the sort order used in Chromeleon 6

Evaluate for channel Channel used for sorting.

Group columns for fixed c h ann els Channel Groups report columns by channel.
by
Report Variable Groups report columns by report variable.

Report Column

Parameter Sub Parameter Description

Column Management N/A Manages report columns.

Inserts new report column before selected.

Appends new report column at the end of the table.

Removes selected report column.

Selects previous report column.

Selects next report column.

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Chromeleon 7

Parameter Sub Parameter Description

Column Properties Formula Defines content of report column by selecting a report variable
formula. This formula can be based on report variables f ro m
all categories detailed in section 7.
Header Defines the report column header.

Unit Defines the unit.

Format Defines the number or date format for displaying results.

Channel Defines whether report columns display peak results from
multiple channels. This depends on the corresponding
settings on the Table Channels tab (section
0.0.1959744544.27).
Selected Channel: Displays values of currently selected
channel.
All Channels: Displays values of all ta ble cha nn els i n o ne
column per channel.
Highest Response: Displays values of the detection cha nne l
where a peak shows the highest response.
Highest Response per Detector: Displays values of the
detection channel where a peak shows the highest resp o nse
for each detector in one column per detector.
Quantitation Channel: Displays values of the channel selected
for quantitation of the component, defined in the p rocessi n g
method.
Fixed Channel: Displays values of the detection ch ann el a s
defined here.
Advanced Column Properties N/A Defines content for additional header rows as selected on the
Header Rows tab (section 0.0.1959744544.27).
Channel Row Defines content of Channel header row.

Header Rows

Parameter Description
Channel Displays an additional channel header row.

SmartLink

Parameter Sub Parameter Description

Select the chromatogram plot to link N/A Links integration table to a selected chromatogram plot.
with
Multiple Peak Selection Selected peaks define which peaks are displayed in the table.

Zoom Area Chromatogram zoom area defines which peaks are displayed
in the table.

Multiple Component Assignments

If a peak is assigned to multiple components the result row of this peak is repeated for every assigned component. The
basis peak results as peak area, height, etc… w ill be identical in every row but the component based results as amount or
calibration related results w ill depend on the corresponding component.

5.8.15.3 Results – Peak Summary Table

This table is designed to show a summary of the results from all the chromatograms in the sequence e.g. retention time,
amount, etc. An unlimited number of columns can be created, and each column can show any variable from those sections
detailed in section 7. The details in this table do not change if different chromatograms are selected.
The follow ing properties can be defined for the report:

Filter Injections

Parameter Sub Parameter Description

Include Injection Types Unknown Displays values from unknown injections.
Calibration Standard Displays values from calibration standard injections.

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Parameter Sub Parameter Description

Check Standard Displays values from check standard injections.
Blank Displays values from blank run injections.

Matrix Displays values from matrix blank injections.

Spiked Displays values from spiked injections.

Unspiked Displays values from unspiked injections.

Custom Conditions ALL (Any field from the sequen ce Restrict the data points shown based on comparing the
table – including user defined selected variable with a user-defin ed va lu e a nd u sin g t h e
columns) following logical arguments:
Is equal to (=)
Is not equal to (<>)
Is larger than (>)
Is smaller than (<)
Is larger than or equal to (=>)
Is smaller than or equal to (=<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
Is during previous
Is not during previous

ANY [Any field from the sequence As for the previous parameter.
table – including user defined
columns]

Grouping Options

Parameter Sub Parameter Description

Sort the report table according to default order for injections Sorts the table according to injection number

evaluation of this formula Peaks are grouped by the user-defined formula

Report only the last row fo r e a ch Reports only the last row of each group.
group

Ignore case when comparing t ext Ignore case when comparing text results
results
Use Chromeleon 6 Sort Order Uses the sort order used in Chromeleon 6

Report Column

Parameter Sub Parameter Description

Column Management N/A Manages report columns.

Inserts new report column before selected.

Appends new report column at the end of the table.

Removes selected report column.

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Chromeleon 7

Parameter Sub Parameter Description

Selects previous report column.

Selects next report column.

Column Properties Formula Defines content of report column by selecting a report variable
formula. This formula can be based on report variables f ro m
all categories detailed in section 7.
Header Defines the report column header.
Unit Defines the unit.

Format Defines the number or date format for displaying results.

Channel Defines from which channel the report column displays p e ak

results.
Selected Channel: Displays values of currently selected
channel.
Fixed Channel: Displays values of the detection ch ann el a s
defined here.
Component Defines from which component the report colu mn d isp la ys
peak results.
Selected Component: Displays values of current ly se le cte d
component.
Fixed Component: Displays values of the component as
defined here.
Advanced Column Properties N/A Defines content for additional header rows as selected on the
Header Rows tab (section 0.0.1959744544.27).
Channel Row Defines content of Channel header row.

Component Row Defines content of Component header row.

Header Rows

Parameter Description
Channel Displays an additional channel header row.

Component Displays an additional component header row.

SmartLink

Parameter Sub Parameter Description

Select the chromatogram plot to link N/A Links peak summary table to a selected chromatogram plot.
with
Chromatogram Overlays Chromatogram overlays define which injections are displayed
in the table.
Multiple Peak Selection Selected peaks define which peaks are displayed in the table.

5.8.15.4 Results – Consolidated Table

This table is designed to show results based on the peaks in the chromatograms in row s and the results from injections in
the sequence in columns, e.g. retention time, peak area, etc. An unlimited number of columns can be created, and each
column can show any variable show n in section 7.
The follow ing properties can be defined for the report:

Filter Injections

Parameter Sub Parameter Description

Include Injection Types Unknown Displays values from unknown injections.
Calibration Standard Displays values from calibration standard injections.

Check Standard Displays values from check standard injections.

Matrix Displays values from matrix blank injections.

Blank Displays values from blank run injections.

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Parameter Sub Parameter Description

Spiked Displays values from spiked injections.
Unspiked Displays values from unspiked injections.

Custom Conditions Only include injections that matc h Displays injections that fulfill a certain condition.
the following conditions

ALL (Any field from the sequen ce Restrict the data points shown based on comparing the
table – including user defined selected variable with a user-defin ed va lu e a nd u sin g t h e
columns) following logical arguments:
Is equal to (=)
Is not equal to (<>)
Is larger than (>)
Is smaller than (<)
Is larger than or equal to (=>)
Is smaller than or equal to (=<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty

ANY [Any field from the sequence As for the previous parameter.
table – including user defined
columns]

Table Channels

Parameter Description
Single channel Lists peaks of a single (currently active or specific) channel

Multiple channels Lists peaks of one or more specific channels

Channels of detector Lists peaks of all channels of selected detectors

Filter Peaks

Parameter Sub Parameter Description

Include Peaks Identified Peaks Shows all peaks that have been identified.
Unidentified Peaks Shows all peaks that have not been identified.

Undetected Components Includes rows for components of the Component Ta ble t h at

have not been detected in the current injection.
Custom Conditions Only include peaks that match the Displays only peaks that fulfill certain condit ion s, b a se d o n
following conditions report variables.

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Chromeleon 7

Parameter Sub Parameter Description

ALL (Any field from the sequen ce Restrict the data points shown based on comparing the
table – including user defined selected variable with a user-defined va lu e a nd u sin g t h e
columns) following logical arguments:
Is equal to (=)
Is not equal to (<>)
Is larger than (>)
Is smaller than (<)
Is larger than or equal to (=>)
Is smaller than or equal to (=<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
ANY [Any field from the sequence As for the previous parameter.
table – including user defined
columns]

Grouping Options

Parameter Sub Parameter Description

Sort the report table according to Retention time of peak Sorts the table according to peak retention time.
evaluation of this formula Peaks are grouped by the user-defined formula.

Report only the last row fo r e a ch Reports only the last row of each group.
group

Ignore case when comparing t ext Ignore case when comparing text results.
results
Use Chromeleon 6 Sort Order Uses the sort order used in Chromeleon 6.

Evaluate for channel Channel used for sorting.

Group columns for fixed c h ann els Injection Groups report columns by injection.
by
Report Variable Groups report columns by report variable.

Report Column

Parameter Sub Parameter Description

Column Management N/A Manages report columns.

Inserts new report column before selected.

Appends new report column at the end of the table.

Removes selected report column.

Selects previous report column.

Selects next report column.

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Parameter Sub Parameter Description

Column Properties Formula Defines content of report column by selecting a report variable
formula. This formula can be based on report variables f ro m
all categories detailed in section 7.
Header Defines the report column header.

Unit Defines the unit.

Format Defines the number or date format for displaying results.

Injection Defines whether report columns display peak results from
multiple injections. This depends on corresponding settings on
the Filter injection tab (section 0.0.1959744544.27).
First Injection: Displays values of first injection a result is found
for the respective peak.
All Injections: Displays values of all table i nje ctio ns i n o ne
column per injection.
Channel Defines whether report columns display peak results from
multiple channels. This depends on the corresponding
settings on the Table Channels tab (section
0.0.1959744544.27).
Selected Channel: Displays values of currently selected
channel.
All Channels: Displays values of all ta ble cha nn els i n o ne
column per channel.
Highest Response: Displays values of the detection cha nne l
where a peak shows the highest response.
Highest Response per Detector: Displays values of the
detection channel where a peak shows the highest resp o nse
for each detector in one column per detector.
Quantitation Channel: Displays values of the channel selected
for quantitation of the component, defined in the p rocessi n g
method.
Fixed Channel: Displays values of the detection ch ann el a s
defined here.
Advanced Column Properties N/A Defines content for additional header rows as selected on the
Header Rows tab (section 0.0.1959744544.27).
Injection Row Defines content of Injection header row.

Channel Row Defines content of Channel header row.

Header Rows

Parameter Description
Injection Displays and additional injection header row.

Channel Displays an additional channel header row.

SmartLink

Parameter Sub Parameter Description

Select the chromatogram plot to link N/A Links consolidated table to a selected chromatogram plot.
with
Chromatogram Overlays Chromatogram overlays define which injections are displayed
in the table.
Multiple Peak Selection Selected peaks define which peaks are displayed in the table.
Zoom Area Chromatogram zoom area defines which peaks are displayed
in the table.

5.8.15.5 Results – Test Case Table

This table show s a summary of the system suitability test and Intelligent Run Control results of all injections in the current
sequence. An unlimited number of columns can be created, and each column can show any variable from section 7.
The follow ing properties can be defined for the report:

Filter By Case

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Chromeleon 7

Parameter Sub Parameter Description

Filter By Case Type SST Case Displays only system suitability test cases in the report table.
Unconditional Case Displays only unconditional test cases in the report table.

Both Displays both system suitability test cases and uncondit ion al
test cases in the report table.

Filter Results

Parameter Sub Parameter Description

Filter Test Results Show only executed test cases Limits display to only executed tests.

Include detailed results for p e aks Displays the results of the peaks and aggregated injections i n
and injections used for computing a separate line.
the statistic result

Grouping Options

Parameter Sub Parameter Description

Grouping Options Group by test case Groups the report by test cases.
Group by injection Groups the report by injections.

Report Column

Parameter Sub Parameter Description

Column Management N/A Manages report columns.
Inserts new report column before selected.

Appends new report column at the end of the table.

Removes selected report column.

Selects previous report column.

Selects next report column.

Column Properties Formula Defines content of report column by selecting a report variable
formula. This formula can be based on report variables f ro m
the categories detailed in sections 7.1, 7.2 and 7.7
Header Defines the report column header.

Unit Defines the unit.

Format Defines the number or date format for displaying results.

5.8.15.6 Results – M S Raw Spectra

This report table creates a list of the mass spectral peaks for the indicated chromatographic peak. The table consists of the
absolute and relative abundances for each of the detected mass fragments (m/z).
The follow ing properties can be defined in the report:

Spectra

Parameter Description
Interactive spectrum Displays the data of the currently selected spectrum.

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Parameter Description
Peak spectrum Displays the spectrum data of a selected peak. Click the down arrow to specify the
criterion by which the peak is selected. The following criteria are available:
- by number
- by name
- by component table number
- by group
- ISTD (Internal Standard)
- by reference peak
- by SLS hit
- by condition
- by retention time
- by greatest area
- by greatest height

Spectrum of a fixed Retention Time (or bunched over Displays data for a spectrum with a specific retention t i me o r a re t en tio n t ime
a time range) range. Type the appropriate retention time or time range in the min box.

Spectrum of a fixed Scan Number (or bunched over a Displays data for a spectrum with a specific scan number or a range of n umb ers.
number range) Enter the appropriate number or range in the min box.

MS Filter

Parameter Description
Filter Filter definition to obtain data that match the specified filter settings.

Baseline Correction

Parameter Description
No baseline correction No baseline correction is performed.

Use settings of processing method Baseline correction settings of the current processing method is used.

Noise Reduction

Parameter Description
Use settings of processing method Use noise reduction settings defined in the processing method.

Do not reduce noise Does not exclude mass peaks from the plot based on their intensity values.
Relative Threshold, removes all masses below a Removes mass peaks from the plot that have an intensity below a specified
relative intensity of threshold value entered (in %) in the box.
Fixed Threshold Include only a specified number of mass peaks with the greatest intensities.

5.8.15.7 Results – Frame Table

This table is designed to show results of non-targeted MS processing. A limited number of columns can be created – one
column for each variable listed in section 7.38. The details in this table change, depending on w hich injection is being
view ed.
The follow ing properties can be defined for the report:

Frame Filter
See section 5.5.4.1 for details on use

Sort Options

Parameter Sub Parameter Description

Sort the report table according to the <List of Frame variables> Sorts the report table according to the user-selecte d Fra me
evaluation of this formula variable. If disabled, the frame table is sorted by Frame ID

Report Column

Parameter Sub Parameter Description

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Chromeleon 7

Parameter Sub Parameter Description

Column Management N/A Manages report columns.
Inserts new report column before selected.

Appends new report column at the end of the table.

Removes selected report column.

Selects previous report column.

Selects next report column.

Column Properties Formula Defines content of report column by selecting a report variable
formula. This formula can be based on report variables f ro m
all categories detailed in section 7.38.
Header Defines the report column header.
Unit Defines the unit.

Format Defines the number or date format for displaying results.

5.8.15.8 Results - NTM S Processing Parameters Table

The NTMS Processing Parameters table show s the parameter values that w ere used to process each individual injection.
The entries show n are parameters that w ere defined in the processing method, but w hich w ere subject to change bas ed on
the actual data for that injection.
This is a static table, w ith no customization properties.

5.8.15.9 Results – Tentative Identification Table

This table is designed to show results of tentatively identified peaks.
The follow ing properties can be defined for the report:

Report Column

Parameter Sub Parameter Description

Column Management N/A Manages report columns.

Inserts new report column before selected.

Appends new report column at the end of the table.

Removes selected report column.

Selects previous report column.

Selects next report column.

Column Properties Formula Defines content of report column by selecting a report variable
formula. This formula can be based on report variables f ro m
all categories detailed in section 7.38.
Header Defines the report column header.
Unit Defines the unit.

Format Defines the number or date format for displaying results.

Header Rows

Parameter Description
Channel Displays an additional channel header row.

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SmartLink

Parameter Sub Parameter Description

Select the chromatogram plot to link N/A Links consolidated table to a selected chromatogram plot.
with
Zoom Area Chromatogram zoom area defines which peaks are displayed
in the table.

5.8.15.10 Results - IPD Component Results Table

The Component Results pane displays a nested table of the protein deconvolution results.
The follow ing properties are available:

Filter

Parameter Sub Parameter Description

Display Individual When enabled, a sub-table will be added for each row t o d isp l ay in dividu al i nje ct ion re su lt s
Injections (Multiconsensus results only)
Charges When enabled, a sub-table will be added for each row to display individual charge state results
Components Match XXX of t he ALL is equivalent to the AND logical operator. Finds injections with variable values that match all o f
following rules the criteria specified in the rules that are assigned the AND logical operator.
ANY is equivalent to the OR logical operator. Finds injections with variable values that match any o f
the criteria specified in the rules that are assigned the OR logical operator.
Variable Selects an intact protein deconvolution variable from the list.

Comparison Select the operator to be used for comparing variable values:

operator = (is equal to)
<> (is not equal to)
< (is less than)
<= (is less than or equal to)
> (is greater than)
>= (is greater than or equal to)
is between
is not between
is during previous
is not during previous
is like (use with wildcards) (for Quick Search only)
is not like (use with wildcards) (for Quick Search only)
contains
does not contain
starts with
does not start with
ends with
does not end with
is any
is not any
is empty
is not empty
Value Select the compare value.

Injections Match XXX of t he ALL is equivalent to the AND logical operator. Finds injections with variable values that match all o f
following rules the criteria specified in the rules that are assigned the AND logical operator.
ANY is equivalent to the OR logical operator. Finds injections with variable values that match any o f
the criteria specified in the rules that are assigned the OR logical operator.
Variable Selects an intact protein deconvolution variable from the list.

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Chromeleon 7

Parameter Sub Parameter Description

Comparison Select the operator to be used for comparing variable values:

operator = (is equal to)
<> (is not equal to)
< (is less than)
<= (is less than or equal to)
> (is greater than)
>= (is greater than or equal to)
is between
is not between
is during previous
is not during previous
is like (use with wildcards) (for Quick Search only)
is not like (use with wildcards) (for Quick Search only)
contains
does not contain
starts with
does not start with
ends with
does not end with
is any
is not any
is empty
is not empty
Value Select the compare value.

Charge Match XXX of t he ALL is equivalent to the AND logical operator. Finds injections with variable values that match all o f
States following rules the criteria specified in the rules that are assigned the AND logical operator.
ANY is equivalent to the OR logical operator. Finds injections with variable values that match any o f
the criteria specified in the rules that are assigned the OR logical operator.
Variable Selects an intact protein deconvolution variable from the list.

Comparison Select the operator to be used for comparing variable values:

operator = (is equal to)
<> (is not equal to)
< (is less than)
<= (is less than or equal to)
> (is greater than)
>= (is greater than or equal to)
is between
is not between
is during previous
is not during previous
is like (use with wildcards) (for Quick Search only)
is not like (use with wildcards) (for Quick Search only)
contains
does not contain
starts with
does not start with
ends with
does not end with
is any
is not any
is empty
is not empty
Value Select the compare value.

Sort Options

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Parameter Description

Sort the report table according to the Sorts the table according to the user defined formula (this can be based on any variab le f ro m t he
evaluation of this formula Intact Protein Deconvolution in section 7).
Ignore case when comparing text results.

Report Column

Parameter Sub Parameter Description

Column Management N/A Manages report columns.

Inserts new report column before selected.

Appends new report column at the end of the table.

Removes selected report column.

Selects previous report column.

Selects next report column.

Column Properties Formula Defines content of report column by selecting a report variable
formula. This formula can be based only upon report variables
from the Intact Protein Deconvolution cat eg ory d et aile d i n
section 7.
Header Defines the report column header.

Unit Defines the unit.

Format Defines the number or date format for displaying results.

5.8.15.11 Results - IPD Processing Parameters Table

The IPD Processing Parameters table show s the parameter values that w ere used to process each individual injection. The
entries show n are parameters that w ere defined in the processing method, but w hich were subject to change based on the
actual data for that injection.
This is a static table, w ith no customization properties.

5.8.15.12 Processing M ethod – Component Table

This table show s the component table defined in the processing method. An unlimited number of columns can be created,
and each column can show any variable from section 7. The details in this table can change if different chromatograms are
selected and the appropriate variables are displayed in the table.
The follow ing properties can be defined for the report:

Sort Options

Parameter Description

Sort the report table according to the Sorts the table according to the user defined formula (this can be based on any variable i n se ct io n
evaluation of this formula 7).
Ignore case when comparing text results.

Filter Components

Parameter Description
Show only components with Limits table to only show specific channel for which you want to show the results in the report.
channel

Report Column

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Chromeleon 7

Parameter Sub Parameter Description

Column Management N/A Manages report columns.
Inserts new report column before selected.

Appends new report column at the end of the table.

Removes selected report column.

Selects previous report column.

Selects next report column.

Column Properties Formula Defines content of report column by selecting a report variable
formula. This formula can be based on report variables f ro m
all categories detailed in section 7.
Header Defines the report column header.
Unit Defines the unit.

Format Defines the number or date format for displaying results.

Channel Defines from which channel the report column displays p e ak
results.
Selected Channel: Displays values of currently selected
channel.
Fixed Channel: Displays values of the detection ch ann el a s
defined here.
Advanced Column Properties N/A Defines content for additional header rows as selected on the
Header Rows tab (section 0.0.1959744544.27).
Channel Row Defines content of Channel header row.

Header Rows

Parameter Description
Channel Displays an additional channel header row.

5.8.15.13 Processing method – Peak Group Table

This report table show s the peak groups as defined in the processing method. An unlimited number of columns can be
created, and each column can show any variable from section 7.
The follow ing properties can be defined for the report: The follow ing properties can be defined for the report:

Sort Options

Parameter Description

Sort the report table according to the Sorts the table according to the user defined formula (this can be based on any variable i n se ct io n
evaluation of this formula 7).
Ignore case when comparing text results.

Filter Peak Groups

Parameter Description

Show only peak groups with Limits table to only display the peak groups that are assigned to the specified channel.
channel

Group Type Selection Controls which peak groups should appear in the report table depending on t he ir co rresp o nd ing
group type. Possible values are
Show all groups – all peak groups
Show only timed groups – only peak groups of group type ‘Timed Group’
Show only named groups – only peak groups of group type ‘Named Group’

Report Column

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Parameter Sub Parameter Description

Column Management N/A Manages report columns.
Inserts new report column before selected.

Appends new report column at the end of the table.

Removes selected report column.

Selects previous report column.

Selects next report column.

Column Properties Formula Defines content of report column by selecting a report variable
formula. This formula can be based on report variables f ro m
all categories detailed in section 7.
Header Defines the report column header.
Unit Defines the unit.

Format Defines the number or date format for displaying results.

Channel Defines from which channel the report column displays p e ak
results.
Selected Channel: Displays values of currently selected
channel.
Fixed Channel: Displays values of the detection ch ann el a s
defined here.
Advanced Column Properties N/A Defines content for additional header rows as selected on the
Header Rows tab (section 0.0.1959744544.27).
Channel Row Defines content of Channel header row.

Header Rows

Parameter Description
Channel Displays an additional channel header row.

Peak Group Results using the Peak Results / Calibration Category

The report table can also be used to report peak group evaluation results. For this purpose the formulas of the peak report
and calibration category (see 7.11 and 7.12 for details) are evaluated in a dedicated w ay, e.g. the formula peak.area w ill
return the sum of all areas of all peaks in the currently selected chromatogram belonging to the peak group. Such a group-
evaluation of peak-formulas is only available in this report table! Not all peak formulas provide a reasonable value for the
corresponding peak group. There is also the group evaluation property (Calibration, Reporting, None), w hich limits the
usage of peak-formulas, e.g. for group evaluation ‘None’, there is no peak-formula evaluation at all. Below is a list of valid
peak-formulas and their corresponding evaluations in this context, i.e. as a report column in a peak group result table.

Peak Formula Group Ev aluation ‘Calibration’ Group Ev aluation ‚Reporting‘

peak.amount The area/height of the peak group Sum of all amount values of all peaks wh i ch b elo ng t o t h e
peak.groupAmount is evaluated against the peak peak group are added together.
group calibration. T he re su lt ing
value is multiplied with the Factor-
value of the peak group record.
peak.amount_deviation The deviation of peak.amount vs. Sum of all amount_deviation values of all peaks which belong
the reference peak group amount to the peak group.
peak.area Returns the area of the peak Same as for Group-Evaluation ‘Calibration’.
peak.groupArea group, i.e. the sum of all area
values of all peaks which belong to
the peak group.

peak.calCoefficient and other Specific result of the group N/A

calibration relevant peak formulas calibration as calCoefficient,
calMode, calPointFx, etc.
peak.concentration The peak.amount value for the Similar to peak.amount all peak.concentration values of peaks
peak group (see above) divided by which belong to the peak group are added together.
the injection volume.

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Chromeleon 7

Peak Formula Group Ev aluation ‘Calibration’ Group Ev aluation ‚Reporting‘

peak.height Returns the height of the peak Same as for Group-Evaluation ‘Calibration’.
peak.groupHeight group, i.e. the sum o f a ll h eig ht
values of all peaks which belong to
the peak group.
peak.rel_amount Returns the relative amount where Returns the relative amount where the g roup Amo un t (se e
the groupAmount (see a b ove) i s above) as the nominator relative value.
the nominator of the relative value.
peak.rel_area Returns the relative amount where Same as for Group Evaluation ‘Calibration’.
the groupArea (see above) is t h e
nominator relative value.
peak.rel_height Returns the relative amount where Same as for Group Evaluation ‘Calibration’.
the groupHeight (see above) is the
nominator relative value.

For all “relative value” formulas above the reference value (denominator) depends on the corresponding parameter setting. For ‘All peaks o f
the same group’ the corresponding values (Amount, Area, and Height) of all peaks which belong t o t h e sa m e p eak g ro u p a re a dd ed
together. In 7.2.9 you can also select a fixed group via ‘Fixed component or group’ and the corresponding group n a me. I n t h is c a se t h e
groupAmount of the specified group is the reference value.
peak.name Returns the name of the peak Same as for Group Evaluation ‘Calibration’.
group which is Identical to the
peakGroup.name variable (see
7.30). This formula is also valid for
Group Evaluation ‘None’.
peak.group Returns the list of all assigned Same as for Group Evaluation ‘Calibration’.
named groups to the peak g ro u p
which is Identical to the
peakGroup.group variable (see
7.30). This formula is also valid for
Group Evaluation ‘None’.

Peak group results are also available in other report tables as Integration, Summary and Consolidated Report Tables. The
follow ing peak-formulas return group relevant results:

Peak Formula Function

peak.name If an unidentified peak belongs to a timed group, peak.name returns th e n ame o f
this timed group. If such a peaks belongs to multiple timed group s, t he n ame o f
timed group with the smallest start time value is returned.
peak.group Returns the list of all named groups (possibly separated by list separat or) wh e re
the peak belongs to.
peak.groupAmount Returns the peak.groupAmount value as described in the previous t a b le f o r t h e
peak group where the peak belongs to. If a peak belongs to more tha n o ne p eak
group, the group amount of the first assigned peak group (lexicographic o rde r) i s
returned.
peak.groupArea Returns the peak.groupArea value as described in the previous table for the p ea k
group where the peak belongs to. If a peak belongs to more than one peak grou p,
the group area of the first assigned peak group (lexicographic order) is returned.
peak.groupHeight Returns the peak.groupHeight value as described in the previous table for the peak
group where the peak belongs to. If a peak belongs to more than one peak grou p,
the group height of the first assigned peak group (lexicographic order) is returned.
peak.rel_amount Similar to the “relative” peak formulas in the table above but now using the si n gle
peak.rel_area peak amount, area or height values as the nominator. The reference value
(denominator) for the option ‘All peaks of the same group’ comes always from t he
peak.rel_height first peak group to which the peak is assigned to (lexicographic order).

5.8.15.14 Processing M ethod – Detection Settings Table

This table show s the detection parameters defined in the processing method. This table contains no report columns and
cannot be modified. Note that this table does not show the global Cobra settings. These must be added as individual
variables (see section 7.28).

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5.8.15.15 Processing M ethod – Calibration History Table

This table is designed to show results based on the calibration type i.e. depending on w hich chromatogram the table is
printed out for and w hich calibration mode is selected the results w ill change. For example, if a bracketed calibration mode is
used the values in this table w ill depend on w hether the table is printed for a sample in the first bracket or in the second
bracket. An unlimited number of columns can be created, and each column can show any variable from those detailed in
section 5.9.

Grouping Options

Parameter Sub Parameter Description

Sort the report table according to Default order for injections Sorts the table according to injection number.

Evaluation of this formula Peaks are grouped by the user-defined formula.

Report only the last row fo r e a ch Reports only the last row of each group.
group

Ignore case when comparing t ext Ignore case when comparing text results.
results
Use Chromeleon 6 sort order Uses the sort order used in Chromeleon 6

Report Column

Parameter Sub Parameter Description

Column Management N/A Manages report columns.

Inserts new report column before selected.

Appends new report column at the end of the table.

Removes selected report column.

Selects previous report column.

Selects next report column.

Column Properties Formula Defines content of report column by selecting a report variable
formula. This formula can be based on report variables f ro m
all categories detailed in section 7.
Header Defines the report column header.

Unit Defines the unit.

Format Defines the number or date format for displaying results.

Channel Defines from which channel the report column displays p e ak

results.
Selected Channel: Displays values of currently selected
channel.
Fixed Channel: Displays values of the detection ch ann el a s
defined here.
Component Defines from which component the report colu mn d isp la ys
peak results.
Selected Component: Displays values of current ly se le cte d
component.
Fixed Component: Displays values of the component as
defined here.
Advanced Column Properties N/A Defines content for additional header rows as selected on the
Header Rows tab (section 0.0.1959744544.27).
Channel Row Defines content of Channel header row.

Component Row Defines content of Component header row.

Header Rows

Parameter Description

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Chromeleon 7

Parameter Description
Channel Displays an additional channel header row.
Component Displays an additional component header row.

SmartLink

Parameter Sub Parameter Description

Select the chromatogram plot to link N/A Links calibration history table to a select ed ch ro mat og ram
with plot.
Multiple Peak Selection Selected peaks define which peaks are displayed in the table.

5.8.15.16 Processing M ethod – SST and IRC Table

This table contains the Intelligent Run Control (IRC) configuration of the test cases defined on the SST/IRC tab page of the
Processing Method Editor.
The follow ing properties can be defined for the report:

Filter By Case

Parameter Sub Parameter Description

Filter By Case Type SST Case Displays only system suitability test cases in the report table.

Unconditional Case Displays only unconditional test cases in the report table.
Both Displays both system suitability test cases and uncondit ion al
test cases in the report table.

5.8.15.17 Processing M ethod – M S Detection Settings

This table show s the MS detection parameters defined in the processing method. This table contains no report columns.
The follow ing properties can be defined for the report:

Display Settings

Parameter Sub Parameter Description

Show detection settings of N/A Defines which MS detection settings to show.
All Settings Displays all MS detection settings.

Processing Method Displays MS detection settings of a specific processing

method.
Selected Component Displays MS detection settings of the currently selected
component.
Fixed Component Displays MS detection settings of the component as specified
here.

5.8.15.18 Processing M ethod – Peptide Table

Upon import of a Pinpoint w orkbook, the Peptide Table w ill be populated w hich is primarily read-only. The user has the
ability to delete an isotope of a peptide but cannot re-add deleted peptide isotopes.
The follow ing properties can be defined for the report:

Sort Options

Parameter Description

Sort the report table according to the Sorts the table according to the user defined formula (this can be based on any variable i n se ct io n
evaluation of this formula 7).
Ignore case when comparing text results.

Filter Peptides

Parameter Description

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Parameter Description

Show only components with Limits table to only show specific channel for which you want to show the results in the report.
channel

Report Column

Parameter Sub Parameter Description

Column Management N/A Manages report columns.
Inserts new report column before selected.

Appends new report column at the end of the table.

Removes selected report column.

Selects previous report column.

Selects next report column.

Column Properties Formula Defines content of report column by selecting a report variable
formula. This formula can be based on report variables f ro m
all categories detailed in section 7.
Header Defines the report column header.

Unit Defines the unit.

Format Defines the number or date format for displaying results.

Channel Defines from which channel the report column displays p e ak
results.
Selected Channel: Displays values of currently selected
channel.
Fixed Channel: Displays values of the detection ch ann el a s
defined here.
Advanced Column Properties N/A Defines content for additional header rows as selected on the
Header Rows tab (section 0.0.1959744544.27).
Channel Row Defines content of Channel header row.

Header Rows

Parameter Description
Channel Displays an additional channel header row.

5.8.15.19 Instrument M ethod – Overview

This table contains general information about the instrument method as displayed on the Overview page of the Instrument
Method Editor. This table contains no report columns and cannot be modified.

5.8.15.20 Instrument method – Script

This table show s all the commands from the instrument method used for the injection. This table contains no report columns
and cannot be modified.

5.8.15.21 Instrument M ethod – M S Instrument Method (XRaw)

This table contains all the conditions from the MS Instrument Method used for the injection. This table contains no report
columns and cannot be modified.

5.8.15.22 Instrument M ethod – M S Tune Report

When MS data is acquired, the current Tune data is stored along w ith the dataset. Inserting an MS Tune Report into a report
sheet creates a table of the MS tune parameters used to acquire the data. The raw file data can contain multiple sets of
tunes.
The follow ing properties can be defined for the report:

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Chromeleon 7

Sort Options

Parameter Description
Show all sets Displays the data of all tune sets in the Xcalibur raw file.

Show set number A set number can be entered to display the data of the specified tune data set.

5.8.15.23 Instrument M ethod – Smart Startup / Shutdown / Standby Settings

This table contains the conditions defined for a Smart Startup, Smart Shutdow n or Smart Standby procedure. This table
contains no report columns and cannot be modified.

5.8.15.24 Instrument M ethod – Extended

This table contains miscellaneous method information, such as Inverse Gradient information or embedded third-party
methods (for example, an Agilent ICF or Waters Acquity method). This table contains no report columns and cannot be
modified.

5.8.15.25 Status and Audit – Audit Trail Table

This table show s the audit trail and changes depending on w hich chromatogram is selected / printed. This table contains no
report columns. The follow ing properties can be defined for the report table:

Filter & Day Time

Parameter Sub Parameter Description

Filter Audit Level Defines the level of messages shown in the audit trail:
• Normal
• Advanced
• Expert
• Errors and
Warnings
Show run Displays run audit trail entries.
Show preconditions Displays preconditions audit trail entries.

Day Time Format Defines the date and time formatting.

Show day time Displays day and time information.

Device Show device Displays device information.

5.8.15.26 Status and Audit – Data Audit Trail

This table show s the data audit trail depending on w hich object is defined. The follow ing properties can be defined for the
report table:

Filter

Parameter Sub Parameter Description

Object Type N/A Filters data audit trail table to defined object.

Current sequence Shows data audit trail of current sequence.

Current injection Shows data audit trail of current injection.

Current chromatogram Shows data audit trail of current chromatogram.

Current processing method Shows data audit trail of current processing method.

Current instrument method Shows data audit trail of current instrument method.

Current report template Shows data audit trail of current report template.
Time Restrictions Show all Shows all data audit trail entries.

Show data audit trail of recent Shows audit trail entries from the recent defin ed n umbe r o f
days/weeks/months/years.
Show data audit trail from Shows data audit trail entries from defined dat e t o t he ne xt
defined date.

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Sort Order

Parameter Sub Parameter Description

Sort Order N/A Sorts data audit trail entries by Data/Time.

Ascending Sorts data audit trail entries by ascending data/time.

Descending Sorts data audit trail entries by descending data/time.

Report Column

Parameter Sub Parameter Description

Column Management N/A Manages report columns.
Inserts new report column before selected.

Appends new report column at the end of the table.

Removes selected report column.

Selects previous report column.

Selects next report column.

Column Properties Formula Defines content of report column by selecting a report variable
formula. This formula can be based on report variables f ro m
the categories detailed in sections 7.1, 7.2 and 7.7.
Header Defines the report column header.
Unit Defines the unit.

Format Defines the number or date format for displaying results.

If a Show Details report variable for the Data Audit Trail report category (see section 7.7) is part of the report columns of the
table every detailed record is listed in a separate row . All report columns referring to formulas w hich are not Show Details
ones w ill display their corresponding values only for the first row of this data audit trail record.

5.8.15.27 Status and Audit – Audit Trail Events

This table show s the audit trail events for the current sequence. The follow ing properties can be defined for the report table:

Filter

Parameter Sub Parameter Description

Event Type <All Events> Shows all audit trail events.
Specific event type Shows all audit trail events of the selected event type.

Sort Order

Parameter Sub Parameter Description

Sort Order Sort by date/time of event Sorts the audit trail events based on their corresponding
date/time property.
Sort by event type Sorts the audit trail events based on their corresponding event
type in lexicographical order.

Report Column

Parameter Sub Parameter Description

Column Management N/A Manages report columns.
Inserts new report column before selected.

Appends new report column at the end of the table.

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Chromeleon 7

Parameter Sub Parameter Description

Removes selected report column.

Selects previous report column.

Selects next report column.

Column Properties Formula Defines content of report column by selecting a report variable
formula. This formula can be based on report variables f ro m
the categories detailed in sections 7.1, 7.2, 7.7 and 7.8.
Header Defines the report column header.
Format Defines the number or date format for displaying results.

5.8.15.28 Status and Audit – Audit Trail Event Configuration

This report table show s all audit trail event types w hich are configured and enabled to be observed for a sequence. The
table consists alw ays of tw o columns displaying the event type labelled as ‘Event type’ and the number of occurrences for
every single configured and enabled event labelled as ‘#Occurrences’.
The follow ing properties can be defined for the report table:

Filter Events

Parameter Sub Parameter Description

Filter Audit Trail Events <All Events> Shows all configured and enabled audit trail event types.

Only events that occurred Shows only those event types which are recorded in the
sequence at least once.
Only events that did not occurr Shows only those event types which are not recorde d i n t h e
sequence.

5.8.15.29 Status and Audit – Chromeleon 6 History Table

This table show s the Chromeleon 6 history only. The follow ing properties can be defined for the report table:

History Objects

Parameter Sub Parameter Description

Show Chromeleon 6 History of current injection Displays all modifications regarding the current injection.

current sequence Displays all modifications of all objects that are included in the
current sequence.
Current report template Displays all modifications of the current report defin itio n f ile
(RDF).

current injection including Displays all modifications that may affect the quantification o f
quantification the current injection.

current sequence including Displays all modifications that may affect the quantification o f
quantification the current sequence.

fixed object Displays all modifications of a single o bje ct wh ich ca n b e

chosen. Objects can either be files, injections, sequences, o r
directories.

Show also history of contents option to display modifica tio ns

of subdirectories, injections, or files contained.

Time Restrictions

Parameter Sub Parameter Description

Time Restrictions Show all Shows all entries with no time restriction.

Show Chromeleon 6 history of Shows entries from the recent defined number of
recent days/weeks/months/years.
Show Chromeleon 6 history from Shows entries from defined date to the next defined date.

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Users

Parameter Sub Parameter Description

Show Chromeleon 6 history of All users Shows Chromeleon 6 history of all users.

Selected users Shows Chromeleon 6 history of the selected use rs yo u ca n

select in the Users field.
All but selected users Shows Chromeleon 6 history of all user(s) except those
selected in the Users field.

Operations

Parameter Sub Parameter Description

Operations to show N/A Defines operations to be displayed in the Chromeleon 6
History report.
General Contains general operations to select; Created, Created
(Save As), Changed, Copied, Moved, De le te d, Re nam ed,
Overwrite, Deleted Content.
Chromatogram Contains modifications affecting the chromatogram to sel e ct ;
Save manipulations, Delete manipulations, S a ved m an ua l
peak identification, Deleted all manual peak id ent if ica tio ns,
Saved results, Saved calibration.

Datasource & Directory Contains modifications affecting the datasource and the
Modifications directory; Disabled history mode, Enab led h ist o ry m od e –
comments required, Enabled history mode – no c o mmen ts
required, Locked, Unlocked, Changed user access, S a mp le
GUID column created, Changed datasource protection,
Changed user-defined columns, Changed datasource
availability, Changed availability of sample status “Multiple”.
Batch Contains modifications affecting the bat ch; S ta rt ed b a tch,
Finished batch, Aborted batch, Started diagnostics, Fin ish ed
diagnostics.
Miscellaneous Contains different modifications; Batch report, Export,
Changed sign requirements, Restored from Backup and
Verified, Failed to execute signed program, Saved to Backup,
Restored from Backup, Signed, Removed signature.

Sort Order

Parameter Description
History entry sorting Define how history entries are organized. The following variables are available under Sort by:
• Time
• Operator
• Operation
• Name
• Object Path
• Version
• Comment
Results of Sort by can then be further sorted by Ascending or Descending options.
Two variables can be combined using ‘Then by’: All variables under Sort by, except those previously
selected, can be used. Results can then be further sorted by Ascending or Descending options.
History detail sorting Define how history details are organized. The following variables are available under Sort by:
• Detail Number
• Detail Object
• Detail Column
• Detail Old Value
• Detail New Value
• Detail Comment
Results of Sort by can then be further sorted by Ascending or Descending options.
Two variables can be combined using ‘Then by’.All variables under Sort by, except those previousl y
selected, can be used. Results can then be further sorted by Ascending or Descending options.

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Chromeleon 7

Report Column

Parameter Sub Parameter Description

Column Management N/A Manages report columns.

Inserts new report column before selected.

Appends new report column at the end of the table.

Removes selected report column.

Selects previous report column.

Selects next report column.

Column Properties Formula Defines content of report column by selecting a report variable
formula. This formula can be based on report variables f ro m
the categories detailed in sections 7.1, 7.2 and 7.7.
Header Defines the report column header.

Format Defines the number or date format for displaying results.

5.8.15.30 Status and Audit – M S Device Information

This table show s device-specific information about the mass spectrometer used for data acquisition, such as device name,
hardw are and firmw are version used. This table contains no report columns and cannot be modified.

5.8.15.31 Status and Audit – M S Status Log

When MS data is acquired, the current MS instrument status information is stored along w ith the dataset. Inserting an MS
Status Log into a report sheet creates a table of the MS instrument status parameters during the injection.
The follow ing properties can be defined for the report:

Status Log Of

Parameter Description
Status Log Number Displays information for a definable status log number.

Retention Time Displays the status log for a definable retention time.
Component Displays the status information from the scan at apex for a specific component using either Selected
Component or a Fixed Component.

5.8.15.32 Fractionation – Fraction Table

This table show s the fractions collected during the selected injection. An unlimited number of columns can be created, and
each column can show any variable from section 7.
The follow ing properties can be defined for the report:

Filter Fractions

Parameter Description
Show fractions of Shows fractions of the selected channel, all channels or a specific channel.

Report Column

Parameter Sub Parameter Description

Column Management N/A Manages report columns.

Inserts new report column before selected.

Appends new report column at the end of the table.

Removes selected report column.

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Parameter Sub Parameter Description

Selects previous report column.

Selects next report column.

Column Properties Formula Defines content of report column by selecting a report variable
formula. This formula can be based on report variables f ro m
all categories detailed in section 7.
Header Defines the report column header.
Unit Defines the unit.

Format Defines the number or date format for displaying results.

Channel Defines from which channel the report column displays p e ak

results.
Selected Channel: Displays values of currently selected
channel.
Fixed Channel: Displays values of the detection ch ann el a s
defined here.
Advanced Column Properties N/A Defines content for additional header rows as selected on the
Header Rows tab (section 0.0.1959744544.27).
Channel Row Defines content of Channel header row.

Header Rows

Parameter Description
Channel Displays an additional channel header row.

SmartLink

Parameter Sub Parameter Description

Select the chromatogram plot to link N/A Links fraction table to a selected chromatogram plot.
with
Chromatogram Overlays Chromatogram overlays define which injections are displayed
in the table.
Multiple Peak Selection Selected peaks define which peaks are displayed in the table.
Zoom Area Chromatogram zoom area defines which peaks are displayed
in the table.

5.8.15.33 Fractionation – Tube Table

This table show s the tubes of the currently selected injection. An unlimited number of columns can be created, and each
column can show any variable from section 7.
The follow ing properties can be defined for the report:

Filter Tubes

Parameter Description
Show tubes outside of fractions Includes any tubes collected outside of fractions in the table.

Report Column

Parameter Sub Parameter Description

Column Management N/A Manages report columns.

Inserts new report column before selected.

Appends new report column at the end of the table.

Removes selected report column.

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Chromeleon 7

Parameter Sub Parameter Description

Selects previous report column.

Selects next report column.

Column Properties Formula Defines content of report column by selecting a report variable
formula. This formula can be based on report variables f ro m
all categories detailed in section 7.
Header Defines the report column header.
Unit Defines the unit.

Format Defines the number or date format for displaying results.

Channel Defines from which channel the report column displays p e ak

results.
Selected Channel: Displays values of currently selected
channel.
Fixed Channel: Displays values of the detection ch ann el a s
defined here.
Advanced Column Properties N/A Defines content for additional header rows as selected on the
Header Rows tab (section 0.0.1959744544.27).
Channel Row Defines content of Channel header row.

Header Rows

Parameter Description
Channel Displays an additional channel header row.

SmartLink

Parameter Sub Parameter Description

Select the chromatogram plot to link N/A Links fraction table to a selected chromatogram plot.
with
Chromatogram Overlays Chromatogram overlays define which injections are displayed
in the table.
Multiple Peak Selection Selected peaks define which peaks are displayed in the table.
Zoom Area Chromatogram zoom area defines which peaks are displayed
in the table.

5.8.16 Composite Scoring Parameters Table

The Composite Scoring Parameters Table show s the settings from the processing method used to perform composite
scoring. It includes te follow ing:

Section Parameter Description

General Scoring Result Criteria The requirements for passing and failing scores:
Pass score if at least ... criteria passed: A passing
score is received if the number of passing criteria
is equal to or greater than the value e n te red in
this box.
Fail score if less than ... criteria passed: A failing
score is received if the number of passing criteria
is less than the value entered in this box.
2D Criteria Amount based peak identity verification Reports if Chromeleon compares the peak
amounts of the components obtaine d f ro m t wo
detector channels

Reference Channel Reports the detector/channel that will provide th e

reference data.

Reports the detector/channel that will provide th e

Confirmation Channel
confirmation data.

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Section Parameter Description

The acceptable variation between peak amounts.

Tolerance If the peak amount ratio is within this ra n ge , t h e
identity of the compound is confirmed
MS Criteria Reports the specific MS criteria used to evaluat e
composite scoring.

5.8.17IPD Processing Parameters Table

The Processing Parameters pane show s the parameter values that w ere used to process the selected injection. These are
the values for parameters that w ere defined in the processing method, but w ere subject to change based on the actual data
for that injection.

Parameter Sub - Parameter Shown Description

Chromatogram Parameters End Scan Number This is the ending scan number of the data use d
by the deconvolution algorithm. It i s co m put ed
based on the actual End Time (see belo w) a nd
the actual injection data.
End Time This is the actual ending reten tio n t ime o f t h e
data that is supplied to the deconvolution
algorithm. It is the lesser of (a) the time specifie d
in the processing method and (b) the end time o f
the injection data.
Mass Range High This is the actual maximum mass of the data
used by the deconvolution al gorit hm . I t i s t h e
greater of (a) the high mass specified in the
processing method and (b) the actual max imu m
mass of the injection data.
Mass Range Low This is the actual minimum mass of the data used
by the deconvolution algorithm. It is the greater of
(a) the low mass specified in the processing
method and (b) the actual minimum mass of t h e
injection data.
Start Scan Number This is the starting scan number of the data used
by the deconvolution algorithm. It i s c o m put ed
based on the actual Start Time (see belo w) a nd
the actual injection data.
Start Time This is the actual starting retention t i me o f t he
data that is supplied to the deconvolution
algorithm. It is the greater of (a) the time specified
in the processing method and (b) the start time of
the injection data.
ReSpect Parameters End Time When the option to use the ReSpect algorithm i s
specified in the processing method , t h is i s t h e
actual Ending retention time used for
deconvolution. It is the lesser of (a) the time
specified in the processing method a nd (b ) t h e
end time of the injection data.
Start Time When the option to use the ReSpect algorithm i s
specified in the processing method , t h is i s t h e
actual Starting retention time used for
deconvolution. It is the greate r o f (a ) t he t ime
specified in the processing method a nd (b ) t h e
start time of the injection data.
Sliding Window Parameters Start Time When the option to use the Sliding Window
algorithm is specified in the processing met ho d,
this is the actual Starting retention time use d f o r
deconvolution. It is the greate r o f (a ) t he t ime
specified in the processing method a nd (b ) t h e
start time of the injection data.
Stop Time When the option to use the Sliding Window
algorithm is specified in the processing met ho d,
this is the actual Ending retention time u se d f o r
deconvolution. It is the lesser of (a) the time
specified in the processing method a nd (b ) t h e
end time of the injection data.

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Chromeleon 7

Parameter Sub - Parameter Shown Description

Xtract Parameters End Time When the option to use the Xtract Window
algorithm is specified in the processing met ho d,
this is the actual Ending retention time u se d f o r
deconvolution. It is the lesser of (a) the time
specified in the processing method a nd (b ) t h e
end time of the injection data.
Start Time When the option to use the Xtract a lg orit hm i s
specified in the processing method , t h is i s t h e
actual Starting retention time used for
deconvolution. It is the greate r o f (a ) t he t ime
specified in the processing method a nd (b ) t h e
start time of the injection data.

5.8.18IPD Component Results Table

The IPD Component Results Table show s the results of protein deconvolution.

5.8.18.1 Table Columns

Parameter Description

Result Component Shows “Result Component 1” for the first component, “Result Component 2” for the second, and so on.
Monoisotopic Mass Displays a weighted average of the monoisotopic masses of each charge state
Sum Intensity Displays the sum of the intensities of the isotopic clusters in a charge state.
Relative Abundance Displays the relative abundance of the peaks in the sample that are above the threshold set by the Rel.
Abundance Threshold (%) (for Xtract) or Rel. Abundance Threshold (%) (for ReSpect) parameter.
Fractional Abundance Displays the fractional abundance of a component, which is the abundance for that peak relative to the
total abundance of all peaks in the spectrum, expressed as a percentage.
Score Displays the quality score of the deconvolved component.
Number of Charge States Displays the number of detected isotopic clusters for a given deconvolved mass.
This is the same number as the number of rows at the charge state level below the component level.
Charge State Distribution Displays the range of charge states detected for the component, from the lowest to the highest charge
state.
Mass Std. Dev. Displays the standard deviation, in Daltons, of the delta masses for all the charge states of a
component (for example, the standard deviation of Delta Mass (Da)).
Delta Mass Displays the difference between the mass of a specific component a nd t he ma ss o f t h e h igh est -
intensity component.
Start Time (min) Displays the start of the retention time range for of the Results Component in the selected injection
Stop Time (min) Displays the end of the retention time range for of the Results Component in the selected injection

RT Range Displays the range of the Results Component in the selected injection
Apex RT Displays the Apex RT of the Results Component in the selected injection

Number of Detected Intervals Displays the number of sliding windows within the specified tolerances where the application found the
component of interest
Scan Range (Visible only for sliding windows deconvolution experiments.) Displays t h e S t art Time (m in) f o r a
specific raw data file.
Protein Name The Protein Name variable returns the name of the target sequence that mat ch es t h i s co mp one nt
within a given tolerance.
Modification Modification of the target sequence that best matches a specific component within a given tolerance.

Matched Mass Error (ppm) Error associated with the best target sequence that matches this component.

Theoretical Mass (Da) Theoretical mass of a component.

Drug Load Drug load of a component.

Average Charge The weighted average charge, based on abundance of each charge state

Monoisotopic Mass CV CV (coefficient of variation) of the monoisotopic masses for each charge state
Apex RT %CV CV (coefficient of variation) percentage of the apex retention time of a component.

Sum Intensity %CV CV (coefficient of variation) percentage of the apex intensities of a component.

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 Chromeleon 7

Number of Files Observed Number of raw data files in which the component was detected.

Score %CV CV (coefficient of variation) percentage of the score of a component.

Condition Condition of a component.

The follow ing Property tabs are available for the Component Results Table:

5.8.18.2 Filter

Parameter Sub Parameter Description

Display Individual Injections When reporting multi-consensus results, tick the box to enable
reporting of all the individual contributing injections.
Charges Tick the box to enable reporting of all the individual contributing
charge states.
Match Match XXX of the following rules ALL is equivalent to the AND logical operat or. Fi nds re p o rt
(Separate sections for Components, rows with variable values that match all of the criteria specified
Injections and Charge States) in the rules that are assigned the AND logical operator.
ANY is equivalent to the OR logical operator. Finds report rows
with variable values that match any of the criteria specifie d i n
the rules that are assigned the OR logical operator.
Variable Selects a variable from the list.

Comparison operator Select the operator to be used for comparing variable values:
= (is equal to)
<> (is not equal to)
< (is less than)
<= (is less than or equal to)
> (is greater than)
>= (is greater than or equal to)
is between
is not between
is during previous
is not during previous
is like (use with wildcards) (for Quick Search only)
is not like (use with wildcards) (for Quick Search only)
contains
does not contain
starts with
does not start with
ends with
does not end with
is any
is not any
is empty
is not empty
Value Select the compare value.

5.8.18.3 Sort Options

Parameter Sub Parameter Description

Sort the report table according to the <List of report variables> Sorts the report table according to the user-se l ecte d re p ort
evaluation of this formula variable. If disabled, the table is sorted by Component
Number

5.8.18.4 Report Column

Parameter Sub Parameter Description

Column Management N/A Manages report columns.

Inserts new report column before selected.

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Chromeleon 7

Parameter Sub Parameter Description

Appends new report column at the end of the table.

Removes selected report column.

Selects previous report column.

Selects next report column.

Column Properties Formula Defines content of report column by selecting a report variable
formula. This formula can be based on report variables f ro m
all categories detailed in section 7.38.
Header Defines the report column header.

Unit Defines the unit.

Format Defines the number or date format for displaying results.

5.8.19SIEVE Processing Parameters Table

The SIEVE Processing Parameters table show s the parameter values that w ere used to process the selected injection w hen
the SIEVE Algorithm is used.. These are the values for parameters that w ere defined in the processing method, but w ere
subject to change based on the actual data for that injection

Parameter Sub - Parameter Shown Description

Global Setting Description Actual description of the experiment, which m ay
be updated form the processing method default.
Max Threads Minimum of (the Maximum number of logical CPU
cores which the algorithm is allowed t o ru n o n )
and (the number of logical CPU cores available)
Relative Reference Injection Path to reference injection if refere nce m o de i s
set to Fixed.
Alignment Parameters Alignment Bypass Whether the alignment step is bypassed or not
Alignment Min Intensity Maximum of (Minimum signal intensity spec ifie d
by the processing method) and (minimum va lue
of the data)
Correlation Bin Width Maximum, in Daltons, of (Width specified in t he
processing method for the MS segment to
correlate reference TIC to unknown TIC data
point) and (minimum of the data being processed)
Max RT Shift Minimum of (Maximum allowable retentio n t ime
shift of a datapoint when align ing a n u nkn o wn
against a reference TIC specified in the
processing method) and (maximu m RT o f t h e
data)
RT Limits for Alignment Maximum of (the Maximum allowed retention time
transformation of unknown TIC datapoin t wh e n
aligning to reference TIC) and (the RT limit o f t e
data)
Tile Size Initial size (in number of scans) of a tile that
correlates base peak alignment across the
reference and unknown injections
Frame Parameters Frame Time Width [min] The effective retention time widt h, i n m in, o f a
frame that is created to evaluate whether si g n al
meets or exceeds the peak intensity t h resh o ld,
based on the processing method and the data
m/z Max Minimum of (the start of the m/z range in wh ic h
the algorithm is permitted to cre at e a f ra me a s
specified in the processing method) and (the m/ z
max of the data)

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Parameter Sub - Parameter Shown Description

m/z Min Maximum of (the end of the m/z range i n wh ich
the algorithm is permitted to create a f ra me, a s
specified in the method) and (the minimum m/z of
the data)
m/z Width [ppm] The effective m/z width, in ppm, of a frame that is
created to evaluate whether signal meets or
exceeds the peak intensity threshold, b ase d on
the processing method and the data
Maximum Number of Frames Minimum of (the maximum number of frames th e
algorithm will detect before stopping, as specified
in the processing method) and (the limit of
possible frames in the data)
Peak Intensity Threshold The minimum signal intensity in a frame in o rde r
to designate a frame as valid based on a selected
value, as auto computed or defined in the
processing method
Peak Threshold Pct The percent of the reference peak used for
filtering frames
Peak Threshold Peak Type The source of the rreference peak used for
filtering frames (TIC, BPC, or N/A if not auto-
computed)
Peak Threshold Type How the threshold level is computed (fixed or
auto-computed)

Retention Time Start [min] Maximum of (the start time of the range in wh ich
the algorithm is permitted to create a f ra me, a s
defined in the processing method) and (the
starting RT of the data)
Retention Time Stop [min] Minimum of (the end time of the range i n wh ich
the algorithm is permitted to create a f ra me, a s
defined in the processing method) and (the
ending RT of the data)
Scan Filter(s) The MS TIC filter the algorithm uses to eva lua te
and create frames.

5.8.20 BioPharma Finder Processing Parameters Table

The BioPharma Finder Processing Parameters table show s the parameter values that w ere used to process the selected
injection w hen the BioPharma Finder Algorithm is used.. These are the values for parameters that w ere defined in the
processing method, but w ere subject to change based on the actual data for that injection

Section Parameter Description

General Displays the number and the name o f in jectio n

Control Injection #, Name that was used in the processing run as the
reference injection.

Corresponds to the type of processing t h at wa s

selected in the Processing Method pane using the
Select Task to be Performed drop-down list. This
parameter can have one of the following two
values:
Processing Type
Find All Ions in the Run: Result are presented a s
each ion representing a separate en try. Th is i s
the default.
Find All Masses in the Run: Combines m u lt iple
charge states into a single entry

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Chromeleon 7

Section Parameter Description

Basic Auto-Compute Basic Parameters Corresponds to the selection made in t he A ut o-

Populate check box of the Processi n g Me th od
pane:
True: The check box was checked and the
parameter values were filled automatically, based
on the specific injection data.
False: The check box was cleared checke d a nd
the parameters values were selected
Corresponds to the Absolute MS Signal
Absolute MS Signal Threshold
Threshold parameter.

This parameter represents the noise level i n t h e

MS data, in terms of absolute intensities.
It is one of the two factors affecting the va lu e o f
MS Noise Level the Absolute MS Signal Threshold used for
distinguishing signals from noise. The fact or, b y
which the noise level has to be surpassed to
recognize an absolute intensity value as a signal,
is specified by the S/N Threshold.
This parameters represents the signal-t o-n oise
threshold used when interpreting the raw MS
data, to distinguish a signal from noise.
The value specifies the factor by which a value of
S/N Threshold the MS absolute intensity has to surpass the M S
Noise Level, in order to be considere d a si g na l
and not noise. This parameter is one of t h e t wo
factors affecting the value of t h e A b so lut e M S
Signal Threshold.

This parameter represents the typical wi dt h o f

peaks near the beginning of the chromatographic
run. It complements the Typical
Beginning Peak Width (min) Chromatographic Peak Width to take into
account the tendency of chromatographic p ea ks
to broaden during the course of a
chromatographic run.
This parameter represents the typical wi dt h o f
chromatographic peaks in the analyze d L C/ MS
run.
Note: When the Auto-populate check box is
selected in the Processing Method pane, the
value of Typical Chromatographic Peak Wid th is
set to the width of the highest peak in the
Typical Chromatographic Pk Width (min)
chromatogram.
To take into account the tendency of
chromatographic peaks to broa d en d uring t he
course of a chromatographic run, the Typical
Chromatographic Peak Width is compl emen te d
with the Beginning Peak Width and t he E nd ing
Peak Width.
This parameter represents the typical wi dt h o f
peaks near the end of the chromatographic run. It
complements the Typical Chromatographic
Ending Peak Width (min)
Peak Width to take into account the tendency o f
chromatographic peaks to broa d en d uring t he
course of a chromatographic run.

This parameter represents the maximum width of

chromatographic peaks in the LC/ MS ru n . A n y
peak wider than this value will be consi de red t o
be part of the background and will not be includ e
it in the results.
Max Chromatographic Pk Width (min)
Note: When the Auto-populate check box is
selected in the Processing Method pane, the
value of Maximum Chromatographic Peak Wid t h
is set to the geometric mean of the wi dth o f t h e
highest peak and the range of the chromatogram.

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 Chromeleon 7

Section Parameter Description

This parameter specifies the start retention t i me

of a truncated chromatogram time ran ge t h at is
Time Limit Start (min)
used to reduce the NTMS processing to an
appropriate area.

This parameter specifies the end retention time of

a truncated chromatogram time range that is used
Time Limit End (min)
to reduce the NTMS processing to an appropriate
area.

This parameter represents the maximum allowed

mass difference of the same ion in different
scans. Depending on the resolut ion o f t h e M S
Mass Tolerance
data, the value is reported in ppm (for high-
resolution data) or in daltons (for low-re so lu tio n
data).

This parameter represents the maximum allowed

mass deviation when comparing the theo ret ical
Mass Accuracy
mass to the calculated mass of a particular ion t o
determine identification.

This parameter specifies the maximum

considered retention time shift when co mp arin g
Maximum RT Shift (min) two or more LC/MS runs. It is one of the basic Ion
Alignment parameters of the BioPharma Fin de r
NTMS Processing Method pane
Advanced This parameter represents the lowest relative
abundance of a component in the MS signal, as a
percentage of the base peak, required to d et ect
an ion at a given point in the chromatogram.
Unlike the Absolute MS Signal Threshold, wh ic h
sets the minimum MS signal for detection of a ny
Relative MS Signal Threshold
ion in the MS data, the Relative MS Signal
Threshold defines the minimum relative
abundance for detection o f a comp on ent t ha t
coelutes with a larger compone nt in t he sa m e
LC/MS run.

This parameter represents the lowest signal

Relative Analog Threshold value, relative to the highest peak in the
chromatogram, that the application can detect.

This parameter represents the factor used to

divide the Typical Chromatographic Peak Wi d t h
value to obtain the width of the G au ssi a n f ilt er
used to average nearby full MS scans. For
example, a value of 4 means the filter width is one
fourth of the typical chromatographic peak width.
Filtering improves the signal-to-noise ratio (S / N)
Width of Gaussian Filter of each scan by reducing noise, but this may
decrease chromatographic resolution. Lower th is
parameter value to improve sensitivity by
suppressing noise and increase th e n umb er t o
improve chromatographic resolution. A value of 1
represents maximum noise suppression using the
Gaussian filter width equal to t he t ypical p e ak
width.

This parameter represents the minimum size of a

valley between a pair of peaks, as a perce n t ag e
Minimum Chromatography Valley (%)
value, for considering the pair as t wo se p a ra te
peaks.

This parameters represents the minimum width of

Minimum MS Peak Width (Da) MS peaks used to generate a range for the
isotopic envelope of the ion

This parameters represents the maxmum width of

Maximum MS Peak Width (Da) MS peaks used to generate a range for the
isotopic envelope of the ion

This parameter represents the maximum mass to

Maximum Mass (Da) change the calculation of the average mass of an
ion.

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Chromeleon 7

Section Parameter Description

This parameter represents a percen ta ge va lue

Mass Centroid Cutoff (% from base) cutoff to change the calculation of t h e a ve rage
mass of an ion.

5.8.21 BioPharma Finder Component Results Table

The BioPharma Finder Component Results Table show s the results of new peak detection using the BioPharma Finder
Algorithm. The results can be filtered to remove know n/expected peaks.
The table has the follow ing columns:

Column Description
Component Number Component number of the nth result component.

Control RT (min) Retention time of the peak corresponding to the nth result component from the control injection.

Control RT Start (min) Retention time of the start of the peak corresponding to the nth result component f rom t he co n tro l
injection.
Control RT Stop (min) Retention time of the end of the peak corresponding to nth result component from the control injection.

Retention time of the peak corresponding to the nth result component from th e t arg et i nject ion . I t
RT (min)
displays the retention time for the component from the first raw data file.

RT Start (min) Retention time of the start of the peak corresponding to the nth result comp one nt f rom t he t a rg et
injection. It displays the retention time for the component from the first raw data file.

RT Stop (min) Retention time of the end of the peak corresponding to the nth result co mpo nen t f ro m t h e t a rge t
injection.
Control M/Z Mass-to-charge ratio of the nth result component from the control injection.
M/Z Mass-to-charge ratio of the nth result component from the target injection.

Control Charge State Charge state of the nth result component from the control injection.

Charge State Charge state of the nth result component from the target injection.
Control Mono Mass Exp Experimental (observed) monoisotopic mass of the nth result component from the control injection.

Mono Mass Exp Experimental (observed) monoisotopic mass of the nth result component from the target injection.

Control Avg Mass Exp Average experimental (observed) mass of the nth result component from the control injection.
Average Mass Exp Average experimental (observed) mass of the nth result component from the target injection.

Max MS Area Maximum MS area of the nth result component from the target injection.
Control MS Area MS area of the nth result component from the control injection.

MS area of the nth result component from the target injection. It displays the area for the component ,
MS Area
specific to each individual raw data file.
MS Area Ratio MS ratio of the target vs. control injection of the nth result component from the target injection.

The follow ing display options are available for the Component Results Table:

5.8.21.1 Result Components Filter

Parameter Sub Parameter Description

Filter target components which (Checkbox) Tick the box to enable filter the results using items in the it em
match within the following MS Components table. In order to be filtered, the RT and Mass
tolerances of an entry in the Component Results Table must ma tch t h at
MS Components table within the limits specified below.
Retention Time (min or %) Select either a maximum RT differen ce o r a m aximum RT
percent difference in order for a component to be considered a
match
M/Z (amu or %) Select either a maximum amu difference or a maximum am ua
percent difference in order for a component to be considered a
match

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Match Match XXX of the following rules ALL is equivalent to the AND logical operator. Finds table rows
with variable values that match all of the criteria specified in the
rules that are assigned the AND logical operator.
ANY is equivalent to the OR logical operator. Finds table ro ws
with variable values that match any of the criteria specifie d i n
the rules that are assigned the OR logical operator.
Variable Selects a variable from the list.

Comparison operator Select the operator to be used for comparing variable values:
= (is equal to)
<> (is not equal to)
< (is less than)
<= (is less than or equal to)
> (is greater than)
>= (is greater than or equal to)
is between
is not between
is during previous
is not during previous
is like (use with wildcards) (for Quick Search only)
is not like (use with wildcards) (for Quick Search only)
contains
does not contain
starts with
does not start with
ends with
does not end with
is any
is not any
is empty
is not empty
Value Select the compare value.

5.8.21.2 Sort Options

Parameter Sub Parameter Description

Sort the report table according to the <List of report variables> Sorts the report table according to the user-se l ecte d re p ort
evaluation of this formula variable. If disabled, the table is sorted by Component
Number

5.8.21.3 Report Column

Parameter Sub Parameter Description

Column Management N/A Manages report columns.

Inserts new report column before selected.

Appends new report column at the end of the table.

Removes selected report column.

Selects previous report column.

Selects next report column.

Column Properties Formula Defines content of report column by selecting a report variable
formula. This formula can be based on report variables f ro m
all categories detailed in section 7.38.
Header Defines the report column header.

Unit Defines the unit.

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Chromeleon 7

Parameter Sub Parameter Description

Format Defines the number or date format for displaying results.

5.8.22Result/Scatter Charts
The follow ing display options are available for result charts:

5.8.22.1 Data Settings

Parameter Sub Parameter Description

Horizontal Axis Variable n.a. Displays horizontal axis variable that can be user defined
based on all report formulas from all t he are as d e t ai led i n
section 7.
Note: This option is only available for scatter charts.
Variables Chart Type Defines chart type. All chart types from section 5 . 8. 22. 2 a re
available.
Chart Variable Defines chart variable that can be based on all report formulas
from all the areas detailed in section 7.
Style Defines color, line style and symbol type for the chart.

Notes:
For the bubble chart type an additional Circle Diameter parameter is displayed, to define the bubble diameter.
For the High Low chart type, tw o additional lines are displayed, to define formulas used for start and end values.
For each selected Control Chart option (5.8.22.2) a line is displayed to define the formula.

5.8.22.2 Chart Type

The follow ing chart types are available:

Scatter

• Scatter w ith only points • Scatter w ith points & lines • Scatter w ith points & splines
• Scatter w ith lines • Scatter w ith splines

Line
• Line • Line w ith points • Spline w ith points

• Spline

Column
• Column • Stacked column (100%) • Stacked column 3D
• Stacked column • Column 3D • Stacked column (100%) 3D

Area
• Area • Stacked area (100%) • Stacked area 3D
• Stacked area • Area 3D • Stacked area (100%) 3D

Pie & Doughnut

• Pie • Pie 3D • Doughnut 3D
• Doughnut

Miscellaneous

• Bubble • Range Area • Column range 3D

• High Low • High Low 3D • Range area (100%) 3D

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 Chromeleon 7

• Column Range

5.8.22.3 Filter Options – Injection Charts

Parameter Sub Parameter Description

Include Injection Types Unknown Displays values from unknown injections.
Calibration Standard Displays values from calibration standard injections.

Check Standard Displays values from check standard injections.

Matrix Displays values from matrix blank injections.

Blank Displays values from blank run injections.

Spiked Displays values from spiked injections.

Unspiked Displays values from unspiked injections.

Custom Conditions Only include injections that match Displays only injections that fulfill certain conditions, b a se d o n
the following conditions report variables.

ALL (Any field from the injectio n Restrict the data points shown based on comparing the selected
list – including user defined variable with a user-defined value and using the following logical
columns) arguments:
Is equal to (=)
Is not equal to (<>)
Is larger than (>)
Is smaller than (<)
Is larger than or equal to (=>)
Is smaller than or equal to (=<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty

AND [Any field from the injection As for the previous parameter.
list – including user defined
columns]
or Allows for matching based on only one comparison in the rule

and Forces matching based on every rule in the l ist . T he o r su b

parameter overrides the requirement to match every
comparison in the specific rule list.

5.8.22.4 Filter Options –Peak Charts

Parameter Sub Parameter Description

Identified Peaks Include Unidentified Peaks Shows all peaks that have not been identified.

Unidentified Peaks Include not identified peaks of t h e Shows all components of the component table that h ave n ot
component table been detected in the current injection.
Undetected components Reject peaks with a smaller Shows all components of the component table that h ave n ot
relative area than n % been detected in the chromatogram.
Custom Conditions Only include peaks that match the Displays only peaks that fulfill certain co ndit ion s, b a se d o n
following conditions report variables.

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Chromeleon 7

Parameter Sub Parameter Description

ALL (Any field from the i nje ctio n Restrict the data points shown based on comparing the
list – including user defined selected variable with a user-defin ed va lu e a nd u sin g t h e
columns) following logical arguments:
Is equal to (=)
Is not equal to (<>)
Is larger than (>)
Is smaller than (<)
Is larger than or equal to (=>)
Is smaller than or equal to (=<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
AND [Any field from the inje ct ion As for the previous parameter.
list – including user defined
columns]
or Allows for matching based on only one comparison in the rule

and Forces matching based on every rule in the list . T he o r su b

parameter overrides the requirement to match every
comparison in the specific rule list.

5.8.22.5 Grouping Options – Injection Charts

Parameter Sub Parameter Description

Sort the injections according to injection Number Sorts the injections according to injection number.

evaluation of this formula Injections are grouped by the user-defined formula base d o n
all report formulas from all the areas detailed in section 7.
Ignore case comparing text results Ignore case when comparing text results.
Use Chromeleon 6 Sort Order Uses the sort order used in Chromeleon 6.

Group Labels Displays group labels in interactive charts.

5.8.22.6 Grouping Options – Peak Charts

Parameter Sub Parameter Description

Sort the peaks according to Peak Number Sorts the peaks according to peak number.

Evaluation of this formula Injections are grouped by the user-defined formula base d o n
all report formulas from all the areas detailed in section 7.
Ignore case comparing text results Ignore case when comparing text results.

Use Chromeleon 6 Sort Order Uses the sort order used in Chromeleon 6.
Group Labels Displays group labels in interactive charts.

5.8.22.7 Title

Parameter Sub Parameter Description

Draw titles Displays results chart titles.

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 Chromeleon 7

Parameter Sub Parameter Description

Font Allows the font type and size of the titles to be defined.
Left title Draw left title Displays the left part of the title.
When checked the middle part of t h e t i tle can b e d ef ine d
based on all report formulas from all t he are as d e t ai led i n
section 7.
Middle title Draw middle title Displays the middle part of the title.
When checked the middle part of t h e t i tle can b e d ef ine d
based on all report formulas from all t he are as d e t ai led i n
section 7.
Right title Draw right title Displays the right part of the title.
When checked the middle part of t h e t i tle can b e d ef ine d
based on all report formulas from all t he are as d e t ai led i n
section 7.

5.8.22.8 Frame & Axes

Parameter Sub Parameter Description

Axes Horizontal Axis Displays a horizontal axis on the results chart.
Vertical Axis Displays a vertical axis on the results chart.

Axes Description Draw Axes Title Applies titles to the results chart axes.

Units Displays units on the axes of the results chart.

Group labels Displays the group labels.

Horizontal Axis Label Formula Labels horizontal axis with details g e n erat ed b y t he use r-
defined formula based on all report formulas from all the areas
detailed in section 7.
Font Allows the font type and size of the axes to be defined.
Grid Horizontal grid lines Applies horizontal grid lines to the results chart.

Vertical grid lines Applies vertical grid lines to the results chart.

5.8.22.9 Horizontal Axis

Parameter Sub Parameter Description

Range From Defines the start value of the horizontal axis. Either Auto or a
specific value can be selected.
To Defines the end value of the horizontal axis. Either Auto or a
specific value can be selected.

5.8.22.10 Vertical Axis

Parameter Sub Parameter Description

Settings for axis Determines the vertical axis for which to define the settings. T o b e
able to select between different vertical axes, you have to h ave at
least two chart variables.
Range From Defines the start value of the vertical axis. Either Auto or a specific
time can be selected.
To Defines the end value of the vertical axis. Either Auto or a sp e cif ic
time can be selected.

5.8.22.11 Data Labels

This section defines how peaks should be labeled. The follow ing options are available:

Parameter Sub Parameter Description

Data Point Labels Draw Data Point Labels Labels all data points with details generated by the user-defined formula.

Font Defines the font for data point labels.

Chart variable name Displays the (short) name of chart variable in the label.

Functional Specifications, 7.3.1, Rev. 1.0 Page 295

Chromeleon 7

Parameter Sub Parameter Description

X value Displays x value of the data point (for scatter charts only).
Y value Displays y value of the data point.

Report Formula The formula can be based on variables from all the areas detailed in section 7.

Legend Show Legend Displays legend in the upper right corner of the chart. Options:
• Inside
plot area
• Outside
plot area

5.8.22.12 Statistics

Function Description
Mean Displays a horizontal line at the average value of the data set.

Linear trend line Displays a linear trend line of the data set.
Show trend line formula includes the linear formula for the trend line in its data label
1s (Mean +/- 1 Std. Deviation) Displays two horizontal lines at the 1s level of significance value of the data set.

2s (Mean +/- 2 Std. Deviation) Displays two horizontal lines at the 2s level of significance value of the data set.

3s (Mean +/- 3 Std. Deviation) Displays two horizontal lines at the 3s level of significance value of the data set.
Font Defines the font for the labels.

5.8.22.13 Control Chart

Function Description
Upper Limit Displays the line of the defined upper limit value or report formula.
Target Displays the line of the defined target value or report formula.

Lower Limit Displays the line of the defined lower limit value or report formula.
Font Defines the font for control chart labels.

Note: The Upper Limit, Target, and Low er Limit values or report formulas have to be defined on the Data Setting
properties page (4.7.4.1).

5.8.22.14 Appearance
This section allow s a consistent color scheme for the objects in the results chart to be defined. The follow ing items can hav e
their line color defined:
• Mean • 3s • Gridlines
• Linear Trend • Upper Limit • Minor Gridlines
• 1s • Target

• 2s • Low er Limit
The follow ing items can have their fill color defined:
• Back Interior • Chart Interior

Parameter Sub Parameter Description

Border Style n.a. Defines the border style for the results chart:
None
Emboss
Arrangement Overlaid All charts are shown overlaid.
Stacked All charts are shown stacked (above each other).

3D Mode n.a. Shows chart as 3-dimensional chart.

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 Chromeleon 7

5.8.22.15 SmartLink
The follow ing options are available:

Parameter Sub Parameter Description

Select the chromatogram plot to link None No link is selected

with
Interactive Chromatogram Links with the interactive chromatogram in the data processing
category.
Chromatogram Plot (sheet name) Links with a chromatogram plot on any other sheet within t he
current report.
Multiple Peak Selection N/A Shows I-t plot for selected components
Zoom Area N/A Shows I-t plot for components whose peak apex is wit h in t he
zoom area.

5.8.23General Charts
It is possible to insert user-defined charts that display the data selected by the user. The follow ing chart types are supported:

5.8.23.1 Scatter
• Scatter w ith only points • Scatter w ith points & lines • Scatter w ith points & splines
• Scatter w ith lines • Scatter w ith splines •

5.8.23.2 Line
• Line • Line w ith points
• Spline • Spline w ith points

5.8.23.3 Column
• Column • Stacked Column (100%) • Stacked Column 3D
• Stacked Column • Column 3D • Stacked Column (100%) 3D

5.8.23.4 Area
• Area • Stacked Area (100%) • Stacked Area 3D
• Stacked Area • Area 3D • Stacked Area (100%) 3D

5.8.23.5 Pie & Doughnut

• Pie • Pie 3D
• Doughnut • Doughnut 3D

5.8.23.6 M iscellaneous
• Bubble • Range Area • Range Area 3D
• High Low • High Low 3D
• Column range • Column Range 3D

5.8.24Illustrations
It is possible to insert pictures from a file into a w orksheet, or shapes can be used. The follow ing illustration types are
supported:

5.8.24.1 Picture
Inserts a picture from a file.

Functional Specifications, 7.3.1, Rev. 1.0 Page 297

Chromeleon 7

5.8.24.2 Shapes
• Line • Rectangle • Oval

5.8.25Chromeleon Report Variables

Chromeleon report variables can be inserted into any cell of the report sheet. See section 7 for details of variables available.

5.8.25.1 M athematical Operators

The follow ing mathematical operators can be used in any numeric report variable or report table column:
• + (Add) • * (multiply) • / (divide)
• - (Minus) • ^n (exponentiation) • - a (unary minus (negative value))
Report variables can be multiplied, etc. by numbers or by other numeric report variables.

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 Chromeleon 7

5.8.26Spreadsheet Formulas
It is possible to enter Spreadsheet formulas directly into Chromeleon report definition files. The follow ing formulae are
supported:
• ABS • EXACT • MATCH • SIGN

• ACOS • EXP • MAX • SIN

• ACOSH • FACT • MID • SINH
• ADDRESS • FALSE • MIDB • SLOPE
• AND • FIND • MIN • SQRT
• ASC • FINDB • MINUTE • STDEV
• ASIN • FIXED • MOD • STDEVP
• ASINH • FLOOR • MONTH • SUBSTITUTE
• ATAN • HLOOKUP • N • SUM
• ATAN2 • HOUR • NA • SUMIF
• ATANH • IF • NOT • SUMSQ

• AVERAGE • INDEX • NOW • T

• CEILING • INDIRECT • ODD • TAN
• CHAR • INT • OFFSET • TANH
• CHOOSE • INTERCEPT • OR • TEXT
• CLEAN • ISBLANK • PI • TIME
• CODE • ISERR • PRODUCT • TIMEVALUE
• COLUMN • ISERROR • PROPER • TODAY
• COLUMNS • ISLOGICAL • RAND • TRIM
• CONCATENATE • ISNA • REPLACE • TRUE
• CORREL • ISNONTEXT • REPLACEB • TRUNC
• COS • ISNUMBER • REPT • TYPE

• COSH • ISREF • RIGHT • UPPER

• COUNT • ISTEXT • RIGHTB • VALUE
• COUNTA • LEFT • ROUND • VAR
• COUNTIF • LEFTB • ROUNDDOWN • VARP
• DATE • LEN • ROUNDUP • VLOOKUP

• DATEVALUE • LENB • ROW • WEEKDAY

• DAY • LN • ROWS • YEAR
• DAYS360 • LOG • SEARCH
• DBCS • LOG10 • SEARCHB
• ERRORTY PE • LOOKUP • SECOND

• EVEN • LOWER
• Print & Export Settings
The Print & Export settings define w hich pages of the report w ill be printed for w hich samples. It also defines the export
options for the report. These options can be modified by the user w hen batch reporting the sequence. The f ollow ing options
are available:

5.8.26.1 Print Settings

The Print Settings Dialog box is divided in tw o sections:

• Printer: select printer to print this report

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Chromeleon 7

• Select Sheets to be printed: Select w hich sheets w ill be printed w hen. For each sheet of the report the follow ing print
options are available:

Parameter Sub Parameter Description

Print N/A When tagged the sheet is printed under the
conditions set in the conditions column.
Condition Each Injection The sheet is printed for each injection.

Blank The sheet is printed for all blank injections.

Matrix The sheet is printed for all matrix injections.

Spiked The sheet is printed for all spiked injections.

Unspiked The sheet is printed for all unspiked injections.

Calibration Standard The sheet is printed for all calibration sta n dard
injections.
Check Standard The sheet is printed for all check standard
injections.
Unknown The sheet is printed for all unknown injections.

First Injection Prints the sheet for the first injection in the
sequence.
Last Injection Prints the sheet for the last injection in the
sequence.
Last Injection in a list of cal. standards Prints the sheet for the last injection in a l ist o f
standards.
More Conditions Prints the sheet under user defined conditio ns.
For details see table below.
Create an electronic report option generates an electronic report that contains the results of the current sequence.
The More condition options are:

More conditions Any field from the sequence table – Restricts when the sheet is printed based on
including user defined columns comparing the selected variable wi t h a u se r-
defined value and using the followin g l ogic a l
arguments:
Is equal to (=)
Is not equal to (<>)
Is larger than (>)
Is smaller than (<)
Is larger than or equal to (=>)
Is smaller than or equal to (=<)
Is like
Is not like
Starts with
Doesn’t start with
Ends with
Doesn’t end with
Contains
Doesn’t contain
Is empty
Is not empty
Is any
Is not any
Multiple conditions can be added.

5.8.26.2 Export Settings

Parameter Sub Parameter Description

Destination Path Parent Folder The location for the export file. Can either be a fixed text value
or based on a Chromeleon report variable. All t h e va ria bles
listed in section 7 can be used.

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 Chromeleon 7

Parameter Sub Parameter Description

Sub Folder The formula for the directory for the export file. Can either be a
fixed text value or based on a Chromeleon report variable. All
the variables listed in section 7 can be used.
Export Formats & Filenames Text format (Results) (.txt) Exports the results as an ASCII file.

Text format (Raw Data) (.txt) Exports the raw data as an ASCII file.

Excel file format (.xls) Exports the sequence as an Excel file.

PDF file format (.pdf) Exports the sequence as an Acrobat file.

GAML file format (*. gaml) Exports the sequence to Generalized Analytical Markup
Language file format.
AnDI/NetCDF file format (*.cdf) Exports the sequence to Analytical Data Interchange file
format.
Raw file format (.raw) Exports MS raw data to the raw data file format, which can be
opened in applications such as Xcalibur.

Chromeleon data file format Exports the sequence to a Chromeleon data file format.
(*.cmbx)
Allotrope Data File Format (*.adf) Exports the sequence to an Allotrope XML file

External Program Call external program If activated, launches an external program during t he b atch
report/export.
Notifications Enable Notifications If activated, email notifications (as configured in t he E xp ort
Notifications Settings window) will be sent duri ng t h e b a tch
export.

For all export formats chosen it is possible to define a file name. This can either be a fixed text value or based on a
Chromeleon report variable. All the variables listed in section 7 can be used. Choices for w hich sheets are exported ar e the
same as for the print settings (see 5.8.26.1).

External Program
This section allow s the conditions under w hich external program w ill be run, to be defined. The follow ing options are
available:

Parameter Sub Parameter Description

Program N/A Name and location of file to be opened.

Arguments N/A User defined formula based on Chro mele on v aria ble s. A ll
variables detailed in section 7 can be used).
Execution Options Offline Batch If activated allows the external program to be run if the batch is
processed offline.
Online Batch If activated allows the external program to be run if the batch is
processed online.
Do Not Execute The external program is not run.

Execute after each injection The external program is executed after each sample.
Execute under certain conditions The external program is executed under cert ain co n dit ions.
The conditions available are the same as for the print
conditions (see section 5.8.26.1).

Wait until External Program N/A The next client action is started only after the external program
Terminates stops running.
Wait up to x minutes N/A The start of the next client action is delayed for at least x
minutes. Enter the desired maximum delay time in t he e nt ry
field. If the external program stops running bef ore t he d ela y
time has elapsed, the next client action will automatically st a rt
immediately.

Do not wait for external progra m t o N/A With this option, the execution of the next client action does not
terminate wait for the external program to stop running.

Export Notification Settings

This w indow allows the conditions under w hich email notifications w ill be sent during exporting to be defined. The follow ing
options are available:

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Chromeleon 7

Parameter Sub Parameter Description

Send notification email when Mail recipient Email address(es) of person(s) to receive ema il n ot ificat ion
sequence finishes exporting when the export is produced.

Include the user who created the N/A If enabled, the user who created the sequence will be notified ,
sequence in addition to the other recipients specified above

Include the user who last m odif ied N/A If enabled, the user who last modified the se q u en ce wi ll b e
the sequence notified, in addition to the other recipients specified above

5.8.27Page Setup
The follow ing options are available for the page setup:

5.8.27.1 Page

Option Sub Option Description

Orientation Portrait Prints the sheet with portrait orientation.
Landscape Prints the sheet with landscape orientation.

Scaling Scale to: The scale of the printout (fixed %).

Fit to If activated this option ensures that the printout is fitted t o t h e

selected number of pages (wide and tall). Note: This option will
shrink the size of the text and graphics to the selected number
of pages but will not expand the size.

5.8.27.2 M argins

Option Sub Option Description

Margins N/A Defines the Top, Bottom, Left and Right margins as well as the
margins for the Header and Footer.
Center on page Horizontally Centers the printout horizontally
Vertically Centers the printout vertically.

5.8.27.3 Header/Footer
Headers and footers can contain text and specific format codes. The syntax is compatible w ith Microsoft Excel. Observe the
order of the single entries.
Codes can be entered into the Left, Center, and Right areas of the header and footer.
The default font is Arial 10. A different font can only be defined after the header and/or footer alignment has been defined.
The new font can be defined as follow s:
• &B: Bold • &U: Underline • &"fontnam e": Uses the specified font
• &I: Italic • &S: Strikeout • &nn: Uses the specified font size
Finally, the follow ing parameters can be defined:

• &A Prints the current sheet name

• &D Prints the current date
• &T Prints the current time
• &F Prints the Report Template file name
• &P Prints the page number
• &P+Num ber Prints the follow ing page number: current page + entered number. For example: &P+4 prints
page 16 if the current page is page 12.
• && Prints an ampersand
• &N Prints the total number of pages in the document
In addition to the pre-defined variables above, you can enter variables pertaining to Chromeleon. These variables must be
enclosed in braces. Example:

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Operator: {gen.loggedOnUser} , Instrument: {seq.instrument} , Sequence:{seq.name} Page &P of &N &D

This example produces the follow ing header or footer:
Operator: cm admin, Instrument: HPLC, Sequence: Calibration Page 1 of 12 4/6/2011

5.8.27.4 Sheet

Option Sub Option Description

Print Gridlines Prints grid lines between the cells

Row Headings Prints the row headings.

Column Headings Prints the column headings

Black and White Prints any colored objects in black and white.

Page Order Top to Bottom Defines the order in which the information is p ri n te d i f t h e
printout required more than 1 page.
Left to Right

5.8.27.5 Print Area

When the report contains more data than required to print, the print area can be set. The print area defines the area of the
report sheet that w ill be printed. After setting a print area it is possible to release it again.

5.8.27.6 Print Titles

When a table is large it can extend on multiple pages (horizontally or vertically). In these cases, it is useful to repeat specif ic
row s or columns as titles at the top or on the left of every printed page. This option is available in the Page Setup group on
the Page Layout ribbon tab. The follow ing options are available:

Parameter Description
Set Print Titles Set the selected rows or columns as print titles.

Release Print Titles Releases the set print titles.

5.8.28Autorepeat Areas
It is often useful to repeat the output of reports for other channels, injections, components, and peaks, other than the
currently selected. In Chromeleon, you can automatically repeat the output of reports for:

• Each injection of a sequence or selection

• Each component in a component table or the current chromatogram
• Each peak of an injection
• Each channel of an injection
Up to two object types may be specified for autopreating. If two object types are specified, then autorepeat occurs in a nested fash i on. Fo r
example, if one specifies autorepeat by injection and then by component, the order of the reported data will be:
The data from all injections for the first component
The data from all injections for the second component
And so on

Note: Only one autorepeat area can be defined on each sheet in a report definition file.

5.8.28.1 General Settings

Option Sub Option Description

(Level 1) None Do not autorepeat the selected area.
Repeat the report objects inside th e Channels Autorepeat the selected area for certain channels.
autorepeat are for:
Injections Autorepeat the selected area for certain injections.

Components Autorepeat the selected area for certain components.

Peaks Autorepeat the selected area for certain peaks.

Grouping Items per group Limits the number of items shown in one object.

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Chromeleon 7

Option Sub Option Description

Sort by Can define a report variable to sort the objects. All the
variables listed in section 7 can be used.
(Level 2) None Do not autorepeat the selected area.
Repeat the report objects inside th e Channels * Autorepeat the selected area for certain channels.
autorepeat are for:
Injections * Autorepeat the selected area for certain injections.

Components * Autorepeat the selected area for certain components.

Peaks * Autorepeat the selected area for certain peaks.

Grouping Items per group Limits the number of items shown in one object.

Sort by Can define a report variable to sort the objects. All the
variables listed in section 7 can be used.
Insert x line(s) after each channel N/A Select this check box to add x empty lines after each chann el
(where x can be set).

Insert page break after each N/A Select this check box to output the selecte d a re a f o r e ach
channel channel on a separate sheet of paper.

Don’t split report tables across N/A The content of an auto-repeated table is printed on one p age
multiple pages unless the content of the table is too large to fit completely o n
one page, in which case a page break is i n se rt ed , a n d t h e
content is continued on subsequent pages.

* If an object type is specified for Level 1 autorepeat, then it will be excluded as a sub-option for Level 2

5.8.28.2 Channel Settings

Parameter Description
All Evaluation Channels The entire page will be reported for the first Evaluation Channel. The selected area
will be repeated for all other evaluation channels.
These Channels Lists all channels. The entire page will be reported for the first channel enable d i n
the list. The selected area will be repeated for all other channels enabled in the list.
Channel(s) of same detector as the current channel The entire page will be reported for the first channel of the current d e te ct or. T he
selected area will be repeated for all other channels of this detector.
Channel(s) of detector Lists all detectors. The entire page will be reported for t h e f irst ch a nn el o f t he
detectors enabled in the list. The selected area wi ll b e re p ea te d f o r a ll o th er
channels of these detectors.

5.8.28.3 Component Settings

Parameter Sub Parameter Description

All Components N/A The entire page will be reported for the first component in t h e
component table of the Processing Method. The selected area
will be repeated for all other components in t h e co mp one nt
table.
These Components N/A Lists all components. The entire page will be reported for t h e
first component in the list. The selected area will be repe ate d
for all other components enabled in the list.

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Parameter Sub Parameter Description

Components that match the ALL (Any field from the sequen ce Restrict the data points shown based on comparing the
following conditions table – including user defined selected variable with a user-defined v a lu e a nd u sin g t h e
columns) following logical arguments:
Is equal to (=)
Is not equal to (<>)
Is larger than (>)
Is smaller than (<)
Is larger than or equal to (=>)
Is smaller than or equal to (=<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
Is during previous
Is not during previous

ANY [Any field from the sequence As for the previous parameter.
table – including user defined
columns]

5.8.28.4 Injection Settings

Parameter Sub Parameter Description

Include Injection Types Unknown Displays values from unknown injections.
Calibration Standard Displays values from calibration standard injections.

Check Standard Displays values from check standard injections.

Matrix Displays values from matrix blank injections.

Blank Displays values from blank run injections.

Spiked Displays values from spiked injections.

Unspiked Displays values from unspiked injections.

Custom Conditions Only include injections that match Displays injections that fulfill a certain condition.
the following conditions

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Chromeleon 7

Parameter Sub Parameter Description

ALL (Any field from the sequen ce Restrict the data points shown based on comparing the
table – including user defined selected variable with a user-defin ed va lu e a nd u sin g t h e
columns) following logical arguments:
Is equal to (=)
Is not equal to (<>)
Is larger than (>)
Is smaller than (<)
Is larger than or equal to (=>)
Is smaller than or equal to (=<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
Is during previous
Is not during previous

ANY [Any field from the sequence As for the previous parameter.
table – including user defined
columns]
Stop repeat after each x injections N/A Select check box to stop the auto-repeated report ing a ft er a
certain number of injections (where x is the number of
injections).

5.8.28.5 Peak Settings

Parameter Sub Parameter Description

Repeat Peaks Identified Peaks Shows all peaks that have been identified.
Unidentified Peaks Shows all peaks that have not been identified.

Custom Conditions Only include peaks that match the Displays only peaks that fulfill certain co ndit ion s, b a se d o n
following conditions report variables.

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ALL (Any field from the sequen ce Restrict the data points shown based on comparing the
table – including user defined selected variable with a user-defin ed va lu e a nd u sin g t h e
columns) following logical arguments:
Is equal to (=)
Is not equal to (<>)
Is larger than (>)
Is smaller than (<)
Is larger than or equal to (=>)
Is smaller than or equal to (=<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
Is during previous
Is not during previous
ANY [Any field from the sequence As for the previous parameter.
table – including user defined
columns]

5.8.29Protection
Sheets can be protected in Chromeleon 7. Once the protection is enabled it is possible to lock/unlock specific cells and
graphics (see Figure 57).

Figure 57: Sheet Protection Options

5.8.30Check for Errors

The entire report can be checked for errors, using the check for errors button in the Home ribbon tab of the report designer .
The follow ing results are available:

Parameter Description
Errors in report Lists all error types that were found during the error check, as well as the number of errors for e a ch
error type.
Check Again Re-runs the error check.

Location Shows the location (sheet name and cell number) of the selected error.
Formula Shows the formula that contains the error.

Error Details Gives details on the error.

5.8.31Custom Formulas
The Custom Formulas Manager can be opened using the button in the Home ribbon tab of the report designer. The
follow ing actions and information are available:

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Chromeleon 7

Parameter Description
Add Opens custom formulas editor (see section 3.1.4)

Remove Deletes the custom formula from the sequence

Edit Opens custom formulas editor (see section 3.1.4)

Used in Shows which objects within the sequence use the custom formula

Location Shows the location (sheet name and cell number) of the selected error.
Formula Shows the details of the custom formula

Description Shows the description of the custom formula

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5.9 Electronic Reports

Electronic reports are a snapshot of the sequence results that are captured electronically and stored in the sequence.
Figure 58 show s a typical electronic report.

Figure 58: Report Template in the Chromatography Studio

5.9.1 Creation Settings

The settings are divided into tw o sections:
Choose a report template and channel: select report template and channel
Choose the sheets and define the conditions: Select w hich sheets w ill be printed w hen. For each sheet of the report the
follow ing options are available:

Parameter Sub Parameter Description

Include N/A When tagged the sheet is printed under the
conditions set in the conditions column.
Condition Each Injection The sheet is printed for each injection.

Blank The sheet is printed for all blank injections.

Matrix The sheet is printed for all matrix injections.

Spiked The sheet is printed for all spiked injections.

Unspiked The sheet is printed for all unspiked injections.

Calibration Standard The sheet is printed for all calibration sta n dard
injections.
Check Standard The sheet is printed for all check standard

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Chromeleon 7

injections.
Unknown The sheet is printed for all unknown injections.

First Injection Prints the sheet for the first injection in the
sequence.
Last Injection Prints the sheet for the last injection in the
sequence.
Last Injection in a list of cal. standards Prints the sheet for the last injection in a l ist o f
standards.
More Conditions Prints the sheet under user defined conditio ns.
For details see table below.
The More condition options are:

More conditions Any field from the sequence table – Restricts when the sheet is printed based on
including user defined columns comparing the selected variable wi t h a u se r-
defined value and using the followin g l ogic a l
arguments:
Is equal to (=)
Is not equal to (<>)
Is larger than (>)
Is smaller than (<)
Is larger than or equal to (=>)
Is smaller than or equal to (=<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
Is during previous
Is not during previous
Multiple conditions can be added.

5.10 Spectral Library

Spectral libraries serve for identifying unknow n substances. Spectra can be saved in spectra libraries and later compared to
the spectrum of the unknow n substance.
Apart from absorption values, each spectrum in a library contains various ID data fields that are freely editable by the user
and that facilitate spectra searches. The follow ing fields are available:

Field Description
Spectrum Thumbnail image of the spectrum.

Name Shows the name under which the substance is included in the spectra library.
ID Shows the short ID that is assigned to the spectrum. Use this column to save several
spectra under the same substance name in a spectra library. The Ids, such as
consecutive numbers, then distinguish the spectra ID.
#Extrema Shows the number of extreme values in the spectrum determin ed b y t h e syst e m .
Select a column entry to change the number.
Solvents Shows the solvent in which the spectrum was recorded. Select a column entry to edit.

Comment Use this column to document details on the saved spectrum.

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Field Description
WL-Range Indicates the wavelength range of the recorded spectrum.
WL-Resolution Shows the Bandwidth with which the spectrum was recorded.

Ret.Time [min] Indicates the retention time at which the spectrum was extracted from a peak.

Ret. Index Indicates the Retention Index of the substance.

Acq.Step Indicates the Step with which the underlying 3D Field was recorded.

Detector Indicates the detector with which the spectrum was recorded. The name is taken from
the Server Configuration.
Detector Serial No. Indicates the serial number of the detector from the Server Configuration.

Instrument Indicates the name of the instrument with which the spectrum was recorded.
Sequence Indicates the name of the sequence in which the spectrum was recorded.

Injection Shows the name of the sample from which the extracted spectrum is taken.

Acq. Date/Time Shows the date and time at which the spectrum o r t he u nde rlying 3 D f ield wa s
originally acquired.
Instrument Method Shows the name of the instrument method, which wa s u se d f o r g e ne rat ing t h e
underlying chromatogram.
Extract Date/Time Shows the data and time at which the spectrum was extracted and saved.
Extract Operator Shows the name of the user who extracted the spectrum and saved it to the sp e ct ra
library.
Spectra can be copied into the library via options provided in the ribbon. All data associated w ith the spectrum (e.g.
Retention time, Detector, etc.) is copied along w ith the spectrum.

5.11 MS Spectral Library

Spectral libraries serve for identifying unknow n substances. Mass spectra can be saved in custom NIST format mass
spectral libraries and later compared to the spectrum of the unknow n substances. Apart from spectra, each entry is
identified by chemical name or peak number and retention time.

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Chromeleon 7

5.12 Data Audit Trail

A data audit trail records all changes made to any data object in a Chromeleon Data Vault w ith versioning enabled. Each
object has a separate data audit trail. The audit trail is recorded automatically and cannot be disabled by users (including
system administrators).
Any data audit trail record of a sequence can be linked to one or more so-called audit trail events. The recording of these
audit trail events need to be enabled in the Administration Console in the Global Policy section and in the Data Vault
Properties (see 4.1.1 and 11.4.17 for more details).
The context menu for every data object (Data Vault, Folder, Sequence, etc…) offers the command „Show Data Audit Trail
…” to show the corresponding Data Audit Trail in a dedicated w indow.

Figure 59: Data Audit Trail Window

Figure 59 above show s the data audit trail w indow of a sequence.
The data audit trail w indow offers the following top-level functions:

Function Description
Reload Reloads the data audit trail from the Data Vault.

Report Creates a report of the data audit trail.

Show Changes Opens a new window showing the changes between any two selected versi ons o f
an item, or changes made in one version if only one entry is selected.
Restore Restores the selected version of an object. The new version will not overwrit e t h e
current version but is a version on its own and is only persisted when saved by t he
user.
Studio Opens a read-only Chromatography Studio window of the currently selected object
and the corresponding version. If the object (e.g. Processing Method) is located in a
sequence the corresponding sequence version is opened in the read-only window.
From <date> to <date> Allows to filter the list to changes made in the given time range.
Filtering Provides a filtering option for each of the columns in the data audit trail.

Grouping Allows the data audit trail to be grouped by any of the columns available.
Search Box Allows entry of text for search purposes.

Find Next Finds the next data audit trail entry that meets the search criteria.

Find Previous Finds the previous data audit trail entry that meets the search criteria.

The data audit trail offers some functionality that can be accessed by right clicking on any one of the data audit trail entries:

Function Description
Show Changes Opens a new window showing the changes between any two selected versions o f
an item, or changes made in one version if only one entry is selected.

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 Chromeleon 7

Function Description
Restore Restores the selected version of an object. The new version will not overwrit e t h e
current version but is a version on its own and is only persisted when saved by the
user.
Studio Opens a read-only Chromatography Studio window of the currently selected object
and the corresponding version. If the object (e.g. Processing Method) is located i n
a sequence the corresponding sequence version is opened in the read-only
window.
Show Data Audit Trail… Shows the data audit trail of the selected data object in a n ew d at a a u dit t rail
window.

For data audit trail records w ith linked audit trail events a yellow flash icon ( ) is show n in the corresponding column. If
such an audit trail record is selected the low er part of the data audit trail w indow show s the corresponding list of audit trail
events.

Figure 60: Data Audit Trail Window incl. Audit Trail Events
If a data audit trail event is selected some additional functionality can be accessed by right clicking on the audit trail event
record. The additional functionality depends on the type of the audit trail event.

Ev ent Type (s) Function Description

Manual Command Interference Open Injection Audit Trail ... Opens the corresponding injection audit trail in a se p ara te win dow
Instrument Error Occured where the corresponding event has been observed during the injectio n
run.
Ext. Report Template Changed Show Data Audit Trail … Shows the data audit trail of the external report t e mpla te / sp e c tra l
Ext. Spectral Library Changed library which caused this event.

Ext. Report Template Changed Studio Opens a Chromatography Studio window of the external report
Ext. Spectral Library Changed template / spectral library which caused this event.

Figure 61: Data Audit Trail Query

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Chromeleon 7

5.13 Injection Audit Trail

The audit trail records a log of all information that w as recorded in the Instrument Audit Trail for a specific injection. The audit
trail is recorded automatically and cannot be disabled by users (including system administrators).
Figure 62 above show s some of the details commonly recorded in the audit trail.

Figure 62: Injection Audit Trail

The injection audit trail offers the following top-level functions:

Function Description
Copy Copies selected audit trail entries to the clipboard.

Print Prints the audit trail.

Filtering Provides a filtering option for each of the columns in the audit trail.

Grouping Allows the audit trail to be grouped by any of the columns available.
Display Offers 4 options:
All: Shows all audit trail entries
Run Only: Shows audit trail entries related t o e ven ts t h a t o ccu r wh ile a
sequence is running
Preconditions only: Shows audit trail entries related to system status prior t o
an injection
Errors and Warnings: Shows only errors and warnings
Level Offers 3 options:
Normal: Only shows audit trail entries for normal user level.
Advanced: Shows audit trail entries for normal and advanced user level.
Expert: Shows audit trail entries up to expert user level.
Next Injection Shows audit trail entries for the next injection.

Previous Injection Shows audit trail entries for the previous injection.

Search Box Allows entry of text for search purposes.

Find Next Finds the next audit trail entry that meets the search criteria.

Find Previous Finds the previous audit trail entry that meets the search criteria.

The audit trail also offers some functionality that can be accessed by right clicking on any one of the column headers:

Function Description
Table Columns Allows definition of which columns should be displayed and in which order.
Fill Last Column Ensures that the last column is extended to fill an empty space.

Show Group Area Activates the grouping option.

Show Tool Strip Shows/hides the tool strip.

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Finally, the audit trail offers some functionality that can be accessed by right clicking on any one of the audit trail entries:

Function Description
Select All Selects all audit trail entries.

Scale Columns to Fit Page Ensures that the audit trail columns are sized to fit the screen view.

Print Preview Offers a print preview.

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6 Versioning
Chromeleon 7 supports full versioning of the follow ing objects:
• Data Vaults
• Folders

• Injections
• Injection Queries
• Instrument Audit Trails
• Chromatogram
• Sequences

• Instrument Method
• Processing Method
• Report Template
• Electronic Reports
• Spectral Libraries
• View Settings
Full copies of each object are retained w hen modifications or deletions are performed, allow ing for prior version to be
restored. In addition, each time an object is modified or deleted, details on the creation, modification, and deletion of files is
recorded in the data audit trail. The follow ing information is recorded:

Information Description
Number Master version number. For example, if changes are made to 4 separate objects within a se q ue nce t h e
master version number will be increased by 4, even though the version number for the associated object s
is only increased by 1.
Name Name of the object

Type Object type

Version Version number of the object

Date/Time Date/time of the action

Operator User id of the operator performing the action

Operation Type of operation performed

Comment User entered comment

Any tw o versions of an object can also be compared, and the comparison tool show s all changes from one version to
another. As all versions are stored, it is also possible to restore a previous version of an object.

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7 Chromeleon Variables
This section details all the variables that Chromeleon can report.

7.1 Global Functions

Variable Description
Absolute Value Returns the absolute value of a given number. The number can be defin ed b y a Ch ro mele on re p ort
variable.
Convert to Text Converts the variable to text.
Create Time The Create Time function constructs an object for representing the given date and (optional ) t ime. Th is
function is required for formulas where a date is used as a constant.
Exponential Function Returns the exponential function of a given value.
Find Position of Text The Find Position of Text function returns the starting position of the text to be found wi t hin t h e t e xt t o
search in, starting at the defined start position.
If Allows use of an If command that reports different values based on the following criteria: if(< cond itio n> ,
<truevalue>,<falsevalue>).
IsError Reports a value of False if the entered variable does not return an error, and a value o f Tru e i f it d oes
report an error.
Logarithm Returns the logarithm function of a given value. The base can be defined as a parameter.
Natural Logarithm Returns the natural logarithm function of a given value.

Round Value Rounds a given number to the specified number of digits. The number can be defined by a Ch ro mele on
report variable.
Select Left Text Selects text from a text variable based on the defined number of characters from the right of the text.

Select Middle Text Selects text from a text variable based on the starting character and a defined length.
Select Right Text Selects text from a text variable based on the defined number of characters from the left of the text.

7.2 General

Variable Sub Function Description

Computer Name N/A The PC name.
Current Printer N/A Printer used for printing the report.

Current Time N/A The current date and time.

Logged On User Full Name Full name of the logged-on user.

Job Title Job title of the logged-on user.

User Name User id of the logged-on user.

My Documents Folder N/A Returns the path of the "My Documents" folder in Windows. If you expo rt
a report, the "My Documents" folder will be the default location.
Report Mode N/A Indicates whether the report was generated automatically or manually
Serial Number N/A The installation serial number (taken from the Chromeleon l icense ke y,
locally or from the Chromeleon Domain Controller).
Version Number N/A The Chromeleon version installed on the PC.

7.3 Sequence

Variable Sub Function Description

Approve Comment N/A Comment that was added in the Approve Signature dialog box during the
Electronic Signature process.

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Chromeleon 7

Variable Sub Function Description

Approve Date & Time Format date/time as text The date and time when the sequence results were approved during t he
Electronic Signature process can have the following formats:
• Default date/time format

• ISO 8601 date/time

• Localized long date
• Localized short date
• Time offset only
• Time w ith seconds and time offset

• Time w ith time offset

Time in universal The time in coordinated universal time standard format.

coordinated time
Time offset in hours The time offset from your local time based on the Windo ws se t t in gs o f
your local computer (including any daylight-savings time adjustments that
apply)
Time using local time zone The conversion of date and time to your local time zone with the following
formats:
Format date/time as text
Default date/time format
ISO 8601 date/time
Localized long date
Localized short date
Time offset only
Time with seconds and time offset
Time with time offset
Time offset in hours
Approve Operator Full Name Full name of the user who approved the sequence re su lts d u ri ng t he
Electronic Signature process.
Job Title Job title of the user who approved the sequence results during the
Electronic Signature process.
User Name User id of the user who approved the sequence results during the
Electronic Signature process.
Comment N/A Sequence comment.
Created by qualification N/A

Creation Date & Time Format date/time as text The date and time the sequence was created ca n h a ve t he f ollo wing
formats:
• Default date/time format
• ISO 8601 date/time
• Localized long date
• Localized short date
• Time offset only

• Time w ith seconds and time offset

• Time w ith time offset

Time in universal The time in coordinated universal time standard format.

coordinated time
Time offset in hours The time offset from your local time based on the Windo ws se t t in gs o f
your local computer (including any daylight savings time adjustments that
apply)

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Variable Sub Function Description

Time using local time zone The conversion of date and time to your local time zone with the following
formats:
• Format date/time as text

• Default date/time format

• ISO 8601 date/time
• Localized long date
• Localized short date
• Time offset only

• Time w ith seconds and time offset

• Time w ith time offset
• Time offset in hours

Creation Operator Full Name Full name of the operator who created the sequence.
Job Title Job title of the operator who created the sequence.

User Name User id of the operator who created the sequence.

Custom Variable N/A The value entered for a custom variable.

Data Vault N/A Name of the corresponding data vault.

Default Channel N/A The default channel

Default Report Template N/A The default report template.

Default View Settings N/A The default view settings.

Directory N/A Directory in which the sequence is stored.

Displaying Imported Results N/A Indicates whether the results were imported or not.

eWorkflow Name N/A The name of the eWorkflow that was used to create the sequence.

Imported Data N/A Indicates whether the data was imported or not
Instrument N/A Assigned instrument for the sequence.

Last Update Date & Time Format date/time as text The date and time the last changes made to the sequence we re sa ve d
can have the following formats:
•Default date/time format
•ISO 8601 date/time
•Localized long date
•Localized short date
•Time offset only
•Time with seconds and time offset
•Time with time offset

Time in universal The time in coordinated universal time standard format.

coordinated time
Time offset in hours The time offset from your local time based on the Windo ws se t t in gs o f
your local computer (including any daylight savings time adjustments that
apply)

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Chromeleon 7

Variable Sub Function Description

Time using local time zone The conversion of date and time to your local time zone with the following
formats:
• Format date/time as text

• Default date/time format

• ISO 8601 date/time
• Localized long date
• Localized short date
• Time offset only

• Time w ith seconds and time offset

• Time w ith time offset
• Time offset in hours

Last Update Operator Full Name Full name of the user who last saved changes to the sequence.
Job Title Job title of the user who last saved changes to the sequence.

User Name User id of the user who last saved changes to the sequence.

Name N/A Sequence name.

Number of Injections N/A Number of injections in the sequence.

Review Comment N/A Comment that was added in the Review Signature dialog box during t h e
Electronic Signature process.
Review Date & Time Format date/time as text The date and time when the sequence results were reviewed durin g t h e
Electronic Signature process can have the following formats:
• Default date/time format

• ISO 8601 date/time

• Localized long date
• Localized short date
• Time offset only
• Time w ith seconds and time offset
• Time w ith time offset

Time in universal The time in coordinated universal time standard format.

coordinated time
Time offset in hours The time offset from your local time based on the Windo ws se t t in gs o f
your local computer (including any daylight savings time adjustments that
apply)
Time using local time zone The conversion of date and time to your local time zone with the following
formats:
• Format date/time as text
• Default date/time format
• ISO 8601 date/time
• Localized long date
• Localized short date

• Time offset only

• Time w ith seconds and time offset
• Time w ith time offset
• Time offset in hours

Review Operator Full Name Full name of the user who reviewed the sequen ce re su lt s d u ring t he
Electronic Signature process.

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Variable Sub Function Description

Job Title Job title of the user who reviewed the sequence results during the
Electronic Signature process.
User Name User id of the user who reviewed the sequence results during the
Electronic Signature process.
Select Injection Select by number Selects a given injection for which to display a chosen result. All variables
from section 7.4 Injection can be chosen.
Select by name
Signature Status N/A The current Electronic Signature status of the sequence.

Signature Steps N/A The Electronic Signature steps (Submit, Review o r A p pro ve ) t ha t a re
defined for the sequence.
Submit Comment N/A Comment that was added in the Submit Signature dialog box during t he
Electronic Signature process.
Submit Date & Time Format date/time as text The date and time when the sequence results were submitted during t h e
Electronic Signature process can have the following formats:
• Default date/time format
• ISO 8601 date/time
• Localized long date
• Localized short date

• Time offset only

• Time w ith seconds and time offset
• Time w ith time offset

Time in universal The time in coordinated universal time standard format.

coordinated time
Time offset in hours The time offset from your local time based on the Windo ws se t t in gs o f
your local computer (including any daylight savings time adjustments that
apply)
Time using local time zone The conversion of date and time to your local time zone with the following
formats:
• Format date/time as text
• Default date/time format
• ISO 8601 date/time

• Localized long date

• Localized short date
• Time offset only
• Time w ith seconds and time offset
• Time w ith time offset

• Time offset in hours

Submit Operator Full Name Full name of the user who submitted the sequence re su lt s d u rin g t h e
Electronic Signature process.
Job Title Job title of the user who submitted the sequence results during the
Electronic Signature process.
User Name User id of the user who submitted the sequence results during the
Electronic Signature process.
Version Comment Comment for this version.
Computer Name Name of the computer on which this version was created.

Data Vault Name of the data vault.

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Chromeleon 7

Variable Sub Function Description

Date & Time Date and time when the version was created. The same sub functions a s
for other date & time variables are available
Format date/time as text
Time in universal coordinated time
Time offset in hours
Time using local time zone
Format date/time as text
Default date/time format
ISO 8601 date/time
Localized long date
Localized short date
Time offset only
Time with seconds and time offset
Time with time offset
Time offset in hours
Number Version number.

Operator Information about the user who created the version. The same sub
functions as for other operator variables are available. These are
Full Name, Job Title and User Name.

7.4 Injection

Variable Sub Function Description

Adducts N/A Displays the positive and negative adducts defined for the injection. T his
can be in a single line or in multi-line format
Adduct Masses N/A Displays the target masses adjusted for the positive and negative adducts
defined for the injection. This can be in a single line or in multi-line format
Auto Dilution Ratio N/A Returns the value of dilution ratio which is how much the sample amoun t
will be reduced in the re-injection.
Calculated Mass Custom Variable Selects an injection custom variable to calculate a mass from

Fixed Formula User-defined molecular formula or peptide sequence to calculat e m a ss

from
Peptide Defines formula source as a peptide sequence – no post -t ran sl ati ona l
modifications are allowed
Chemical Formula Defines formula source as a molecular formula

Positive Defines the molecule as positively charged

Negative Defines the molecule as negatively charged

Charge Defines the charge state of the molecule

Adduct Selects the adduct gain or loss

Chemical Formula and Adducts N/A Displays the chemical formula for the target masses, including the positive
and negative adducts defined for the injection. This can be in a single line
or in multi-line format

Chemical Formula and Adduc t N/A Displays the masses of the positive and negative adducts defined for t h e
Masses injection. This can be in a single line or in multi-line format
Comment N/A The injection comment

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Variable Sub Function Description

Custom Variable N/A The value entered for a custom variable.
Dilution N/A The injection dilution factor.

Evaluate Context The location context of the custom variable (Injection, Sequence,
Component, or Unidentified Peak Group).
Custom Variable List of variables from the selected context only.

GUID N/A Displays globally unique identifier assigned to given injection.

Inject Time Format date/time as text The date and time the injection data acquisition st a rt e d ca n h ave t he
following formats:
Default date/time format
ISO 8601 date/time
Localized long date
Localized short date
Time offset only
Time with seconds and time offset
Time with time offset

Time in universal The time in coordinated universal time standard format.

coordinated time
Time offset in hours The time offset from your local time based on the Windo ws se t t in gs o f
your local computer (including any daylight savings time adjustments that
apply)
Time using local time zone The conversion of date and time to your local time zone with the following
formats:
Format date/time as text
• Default date/time format
• ISO 8601 date/time
• Localized long date
• Localized short date

• Time offset only

• Time w ith seconds and time offset
• Time w ith time offset
• Time offset in hours

Instrument Method N/A The instrument method used for the injection.

IntStd N/A The injection Internal Standard amount.

Level N/A The calibration leve

Level Check N/A The result of level tolerance checks for all applicable co mp on ent s i n a
single injection.
Lock Status N/A Lock status of the injection.

Lock Version Comment Comment for this version.

Computer Name Name of the computer on which this version was created.

Data Vault Name of the data vault.

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Chromeleon 7

Variable Sub Function Description

Date & Time Date and time when the version was created. The same sub functions a s
for other date & time variables are available
Format date/time as text
Time in universal coordinated time
Time offset in hours
Time using local time zone
Format date/time as text
Default date/time format
ISO 8601 date/time
Localized long date
Localized short date
Time offset only
Time with seconds and time offset
Time with time offset
Time offset in hours
Number Version number.

Operator Information about the user who created the version. The same sub
functions as for other operator variables are available. These are
Full Name, Job Title and User Name.
Name N/A The injection name

Number N/A The injection number

Number of re-injections N/A Displays number of re-injections for injection in injection list.

Position N/A The injection position

ProcessingMethod N/A The processing method used for the injection.

Reference Retention Time N/A The injection number and injection name of the retention time st a n dard
Standard referenced by the current injection.
Relative Position N/A Specifies a value for the Relative Position (in the range -9999 to 9999)

Replicate ID N/A The injection Replicate ID.

Retention Time Standard Error N/A The returned error if the injection is an invalid retention time standard.

Retention Time Standard N/A The status (Valid, Invalid, or n.a.) of a retention time standard.
Status
Select Chromatogram N/A Parameter from the selected chromatogra m. S ome va ria ble s i n t h is
category depend on the type of detectors con n ect ed d u ring t he d ata
acquisition.
The options for select chromatogram are:
Use preferred channel of sequence
Use fixed channel
All parameters from section Chromatogram (7.8) can be chosen.
Spike group N/A The spike group for the injection.

Status N/A Displays status of injection

Test Case Overall Result N/A The result of all test cases for the current injection (system suitability t e st
(SST) cases only).
Test Case Specific Result Select by number Selects a given test case either by name or number and the resu lt s o f a
specific test case can be reported by selecting a variable f ro m t he Test
Select by name Case Result category.
Type N/A The injection type

Version Comment Comment for this version.

Computer Name Name of the computer on which this version was created.

Data Vault Name of the data vault.

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Variable Sub Function Description

Date & Time Date and time when the version was created. The same sub functions a s
for other date & time variables are available
• Format date/time as text

• Time in universal coordinated time

• Time offset in hours
• Time using local time zone
• Format date/time as text
• Default date/time format

• ISO 8601 date/time

• Localized long date
• Localized short date
• Time offset only
• Time w ith seconds and time offset

• Time w ith time offset

• Time offset in hours

Number Version number.

Operator Information about the user who created the version. The same sub
functions as for other operator variables are available. These are
Full Name, Job Title and User Name.
Volume N/A The injection volume.
Weight N/A The injection weight

7.5 Audit Trail

The audit trail records all actions executed to an instrument. Depending on the connected instrumentation, hundreds of
Audit Trail variables are available. The lists below show only those variables that are applicable to an UltiMate 3000 HPG-
3200RS pump or a Ultimate 3000 DAD-3000(RS) detector.

7.5.1 HPG-3200RS Pump Audit Trail Variables

Variable Description
Maximum Flow Ramp Down The maximum flow ramp down.

Maximum Flow Ramp Down The maximum flow ramp-up.

Lower Limit The lower pressure limit

Upper Limit The upper pressure limit

Equate (%A, %B) Name of eluent component A, B.

Type (%A, %B) Type of eluent component A, B.

Flow The pump flow rate.

%A, %B The percentage of the respective component in the eluent.

Curve The curve of the gradient.

7.5.2 DAD-3000(RS)
Variable Description
Max. Wavelength (3DFIELD) The maximum wavelength of the 3D Field.

Min. Wavelength (3DFIELD) The minimum wavelength of the 3D Field.

Bunch Width The bunch width of the diode group.

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Chromeleon 7

Variable Description
Response Time The response time of the detector.
Data Collection Rate The data collection rate.

Demo File Name The demo file name used when running in evaluation mode.

Wavelength The wavelength setting of a single acquisition channel.

Bandwidth The bandwidth setting of a single acquisition channel.

Ref Wavelength (UV) The reference wavelength of a single acquisition channel.

Ref Bandwidth (UV) Reference Bandwidth of a single acquisition channel.

Ref Wavelength (3D Field) The reference wavelength of the 3D Field.

Ref Bandwidth (3D Field) Reference Bandwidth of the 3D Field.

7.6 Preconditions
Depending on the connected instrumentation, thousands of Preconditions variables exist. They allow you to display in the
Audit Trails the device settings existing immediately before a sample run. (For more information about the Audit Trails see
section 4.4).

7.7 Data Audit Trail

Variable Sub Function Description

Additional Information N/A Displays additional information regardin g t h e d at a a u dit t rail
record.
Comment N/A Displays the data audit trail comment which the user has put in.

Date/Time N/A Date and time stamp of modification.

Number of Events N/A Displays the number of audit trail events associated with the data
audit trail record.
Object Name N/A Name of the modified object.
Object Version N/A Version of the modified object.

Operation N/A Modification to the object.

Operator Full Name Full name of the user who performed the modification.

Job Title Job Title of the user who the modification.

User Name User id of the user who the modification.

Select Event Select by number Selects the audit trail event record by this number. All v a riable s
from section 7.8 Audit Trail Event can be chosen.
Show Details New Value Displays the new value of the detailed record.

Number The number of the detailed record.

Object Path Display the Object Path. Together with Property this identified the
data object field which has been modified.
Old Value Displays the old value of the detailed record.
Operation Displays the operation of the detailed record.

Property Displays the property or field name o f t he d a ta o bjec t o f t h e

detailed record.
Type N/A Type of the modified object.

7.8 Audit Trail Event

Variable Sub Function Description

Date/Time N/A Date and time stamp of audit trail event.
Description N/A A detailed description of the audit trail event.

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Variable Sub Function Description

Event Type N/A The event type of the audit trail event.
Object Name N/A The name of the data object for which the audit trail e v e nt h as
been recorded.

7.9 Chromatogram
Some variables in this category depend on the type of detectors connected during the data acquisition. The tables below
show the standard variables that are alw ays available and the variables that are available w hen a UVD 340 is used for data
acquisition.

7.9.1 Standard Variables

Variable Sub Function Description
Auto Noise (Cobra) Actual noise Indicates the noise level at a given retention time if the auto noise
option is selected.
Noise level used to search Indicates the noise level used for searching the baseline segment

Noise level of rank Indicates the noise level at a given rank in p e rcent (e . g. 5 0%
returns the median noise level)
Baseline Threshold (Cobra) N/A Indicates the threshold for automatic detection of baseline
segments in the Cobra peak detection at the st a rt -t ime o f t h e
chromatogram or at a given retention time.
Channel N/A User defined name of the data channel.
Count Peaks If… N/A Counts peaks based on a user-defined condition.

Curvature (Cobra) N/A Indicates the value of the 2nd derivative of the chromatogram for
a given retention time.
Curvature Noise (Cobra) N/A The noise in the 2nd derivative at the start-time of the
chromatogram or a given retention time.

Delay Time N/A The delay time between two detectors.

Detection Algorithm N/A The name of the detection algorithm (Ch rome leon 6 , Co b ra,
Genesis, or ICIS) that is currently used for the current
chromatogram.
Detection Reference XIC? N/A Indicates whether the selected XIC is a detection reference X I C
for the selected component / peptide or not.
Detector N/A Name of the detector used to acquire the channel.
Effective Min. Peak Area (Cobra) N/A Indicates the minimum peak area that is applied b y t he Co bra
peak detection at the start-time of the chromatogram or a g ive n
retention time.
Effective Min. Peak Height (Cobra) N/A Indicates the minimum peak area that is applied b y t he Co bra
peak detection at the start-time of the chromatogram or a g ive n
retention time.
Effective Smoothing Width (Cobra) N/A Indicates the smoothing width value the Cobra peak detection is
applying at a given retention time of the chromatogram.
End Time (relative to Inject Time) N/A Chromatogram end time [min].
Evaluate Context The location context of the custom variable (Injection, Sequence,
Component, or Unidentified Peak Group).
Custom Variable List of variables from the selected context only.

Fluorescence Spectrum Retention Time Information about a fluorescence spectrum at a certain retent ion
time from the FL Spectrum category (see section 7.14).
Filter Information about a fluorescence spectrum, filtered for scan type,
photomultiplier or other options (see section 5.8.13.6) from the FL
Spectrum category (see section 7.14).
Import Type N/A Import format type.

Injection Specific XIC Detection Full Name Full name of the user who last modified the injection specific XIC
Operator detection parameter for the chromatogram.

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Chromeleon 7

Variable Sub Function Description

Job Title Job Title of the user who last modified the injection specif ic X IC
detection parameter for the chromatogram.
User Name User id of the user who last modified the injection sp e c if ic X IC
detection parameter for the chromatogram..

Injection Specific XIC Detection Format date/time as text The date and time of the last modification of the injection specific
Time XIC detection parameter for the chromatog ram can h ave t h e
following formats:
Default date/time format
ISO 8601 date/time
Localized long date
Localized short date
Time offset only
Time with seconds and time offset
Time with time offset
Time in universal coordina te d The time in coordinated universal time standard format.
time
Time offset in hours The time offset from your local time based on the Windows
settings of your local computer (including any daylight sa vi ngs
time adjustments that apply)
Time using local time zone The conversion of date and time to your local time zone with t h e
following formats:
Format date/time as text
Default date/time format
ISO 8601 date/time
Localized long date
Localized short date
Time offset only
Time with seconds and time offset
Time with time offset
Time offset in hours
Injection Specific XIC Detection? N/A Indicated if the chromatogram has been processing with enabled
injection specific XIC detection parameters.
Manipulated? N/A Indicates if the chromatogram has been manually manipulated or
not.
Mass Detected N/A Indicates if the target mass specified for the injection (adjusted for
adducts) was detected in the specified filter
Mass Spectrum Spectrum Selection Spectrums selected based upon spectrum of a fixed Re t ent ion
Time (or bunched over a time range) or spectrum of a fixed Scan
Number (or bunched over a number range)
Spectrum Filter Specifies the acquisition filter from which the ch roma to gra m is
extracted.
Baseline Correction Information about a mass spectrum, with o r wi th out b ase lin e
correction.
Noise Reduction Information about a mass spectrum with or without noise
reduction. When applying noise reduction, a Relative Threshold,
removes all masses below a relative intensity of base peak o r a
Fixed Threshold, which limits spectra to only a number of largest
mass intensities for a peak.
Metadata Compute value of metadata Returns additional signal information, such as the polarity, source
voltage, or filter number of a mass channel.
Modification Operator Full Name Full name of the user who last modified the chromatogram.
Job Title Job Title of the user who last modified the chromatogram.

User Name User id of the user who last modified the chromatogram.

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Variable Sub Function Description

Modification Time Format date/time as text The date and time of the last modification can have the following
formats:
• Default date/time format

• ISO 8601 date/time

• Localized long date
• Localized short date
• Time offset only
• Time w ith seconds and time offset

• Time w ith time offset

Time in universal coordina te d The time in coordinated universal time standard format.
time
Time offset in hours The time offset from your local time based on the Windows
settings of your local computer (including any daylight sa vi ngs
time adjustments that apply)
Time using local time zone The conversion of date and time to your local time zone with t h e
following formats:
• Format date/time as text
• Default date/time format
• ISO 8601 date/time
• Localized long date
• Localized short date

• Time offset only

• Time w ith seconds and time offset
• Time w ith time offset
• Time offset in hours

MS Signal Extraction Parameter N/A All variables in section 7.10 become available.

Noise Determination Range End N/A Indicates the end time of the time range that is u se d b y Co b ra
Time (Cobra) peak detection to compute the peak and baseline thresholds.
Noise Determination Range Start N/A Indicates the start time of the time range that is use d b y Co bra
Time (Cobra) peak detection to compute the peak and baseline thresholds.
Number of Peaks N/A Total number of peaks in the chromatogram.
Peak Threshold (Cobra) N/A Indicates the minimum curvature for peaks that is used for p ea k
detection with Cobra at the start-time of the chromatogram o r a
given retention time.
Sample Rate Minimum rate Minimum sample rate at which raw data points were recorded.

Maximum Rate Maximum sample rate at which raw data points were recorded.
Average rate Average sample rate at which raw data points were recorded.

Sample Step Minimum Step Minimum step.

Maximum Step Maximum step.

Average Step. Average step.

Select Peak By name Selects peak by peak name.

By number Selects peak by peak number in the chromatogram.

By component table number Selects peak by peak number in the peak table.

By group Selects peak by peak group.

ISTD (Internal Standard) Selects the internal standard peak.

Reference peak Selects the reference peak.

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Chromeleon 7

Variable Sub Function Description

By SLS-hit Selects peak by hits in the spectra library.
By condition Selects peak based on a user-defined condition.

By retention time Selects peaks based on retention time settings e.g. retention time
and window.
By greatest area Selects peak by area.

By greatest height Selects peak by height.

Signal Description N/A Key parameters for the recorded signal.

Signal Drift N/A The signal drift for the noise determination range that is used f o r
peak determination or over a user defined time segment.
Signal Noise N/A The signal noise for the noise determination range that is used for
peak determination or over a user defined time segment.
Signal Statistic Computed statistic The type of statistical value computed from signal data which can
be either minimum signal value, maximum signal value or
average signal value.
Time range The time range for computing the statistical value ei the r o f t he
entire chromatogram or over a user defined time segment.
Signal Unit N/A The units the signal is reported in e.g. mAU*min.

Signal Value N/A The signal value of the chromatogram at a given retention time.
Slope (Cobra) N/A The slope i.e. the value of the 1st derivative of the chromatogram
for a given retention time.
Start Time (relative to Inject Time) N/A Chromatogram start time [min].

Sum Peak Results If… N/A Adds together user defined peak results based on a user-defined
variable or condition.
UV Spectrum Retention Time Information about a UV spectrum at a certain retention time fro m
the UV Spectrum category (see section 7.18).
Baseline Correction Information about a UV spectrum, with or without baseline
correction, from the UV Spectrum category (see section 7.18).
Version Comment Comment for this version.

Computer Name Name of the computer on which this version was created.

Data Vault Name of the data vault.

Date & Time Date and time when the version was cre a t ed. T he sa m e su b
functions as for other date & time variables are available
• Format date/time as text
• Time in universal coordinated time
• Time offset in hours
• Time using local time zone

• Format date/time as text

• Default date/time format
• ISO 8601 date/time
• Localized long date
• Localized short date
• Time offset only
• Time w ith seconds and time offset
• Time w ith time offset
• Time offset in hours

Number Version number.

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Variable Sub Function Description

Operator Information about the user who created the version. Th e sa m e
sub functions as for other operator variables are available. These
are
Full Name, Job Title and User Name.

7.10 MS Signal Extraction Parameters

Variable Description
Auto Filter The text definition of the scan filter.
End Time The ending retention time of the extraction.

Evaluation Type The type of extracted ion chromatogram in MS data (quantitation peak or confirm ing
peak).
Mass Ranges Mass ranges used for extraction.

Number of Smoothing Points The number of points used for smoothing, if smoothing is enabled.
Simulated Mass The theoretical isotopic mass used in the isotopic dot product calculations for the n t h
isotope in the peptide list.
Simulated Abundance The theoretical abundance of the isotopic distribution used in the isotopic dot product
calculations for the nth isotope in the peptide list.
Smoothing Algorithm The localized name of the smoothing algorithm.
Start Time The starting retention time of the extraction.

Trace Type The localized name of the extracted ion chromatogram type.

7.11 Peak Results

In order to show results for these variables a peak from the component table must be selected. Also, the variable can be
configured to show the data from the current channel selected by the user or from a specified channel.

Variable Sub Function Description

Amount N/A The calculated peak amount

Calibration curve for amount When using the Standard Addition calibration mode , yo u ca n
calibration (Standard Addition choose whether the amount is calculated by using the
only) calibration curve with or without offset.

Amount correction for spiked When using the Standard Addition calibration mode , yo u ca n
samples (Standard Addition only) choose whether the amount is calculated with or without
subtracting the reference amount.
Amount Deviation Absolute in amount units The difference between the calculated amount and the
expected amount.

Relative in % of the expected The relative difference (%) between the calculated amount and
amount the expected amount.
Area Full Time Range of Peak The peak area ([signal]*min) of the peak.

Custom Time Range from x min to The peak area ([signal]*min) for a sp e cif ied re t en tio n t im e
y min range.

Asymmetry (EP, AIA, Statistical N/A The asymmetry of the peak, based on EP/USP, AIA or
Moments) Statistical Moments
Baseline Value at Peak End N/A The baseline signal value at the peak end.
Baseline Value at Peak retention N/A The baseline signal value at the peak retention time.

Baseline Value at Peak Start N/A The baseline signal value at the peak start.

CE Area N/A The CE peak area (area/retention time)

Concentration N/A The peak concentration i.e. the peak amount d ivided b y t he
injection volume of the sample.

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Chromeleon 7

Variable Sub Function Description

Calibration curve for amount When using the Standard Addition calibration mode , yo u ca n
calibration (Standard Addition choose whether the amount is calculated by using the
only) calibration curve with or without offset.
Amount correction for spiked When using the Standard Addition calibration mode , yo u ca n
samples (Standard Addition only) choose whether the amount is calculated with or without
subtracting the reference amount.
Detection Code at Peak End N/A The detection code at peak end.

Detection Code at Peak Start N/A The detection code at peak start.
Evaluate Context The location context of the custom variable (Injection,
Sequence, Component, or Unidentified Peak Group).
Custom Variable List of variables from the selected context only.

Group N/A The name(s) of the named peak group(s) the peak belongs to.

Group Amount N/A The calculated amount of the respective peak group.

Calibration curve for amount When using the Standard Addition calibration mode , yo u c a n
calibration (Standard Addition choose whether the amount is calculated by using the
only) calibration curve with or without offset.

Amount correction for spiked When using the Standard Addition calibration mode , yo u ca n
samples (Standard Addition only) choose whether the amount is calculated with or without
subtracting the reference amount.
Group Area N/A The total area of all peaks in the respective peak group.
Group Height N/A The total height of all peaks in the respective peak group.

Height N/A The peak height ([signal]) of the peak.

Is Excluded N/A Reports if the peak was excluded due to Composi t e S co ring
thresholding criteria (See 5.3.9)
K’ N/A The K’ value of the peak. Can be comput ed a gain st a f ixe d
dead time, or the dead time defined in the processing method.
Left Width The baseline level The left width of the peak at the baseline.
5 % height over the baseline The left width of the peak at 5 % height over the baseline.

10 % height over the baseline The left width of the peak at 10 % height over the baseline.

50 % height over the baseline The left width of the peak at 50 % height over the baseline.
Custom The left width at a user defined % height over the baseline.

Level Check N/A The pass or fail result for components at levels where the
tolerance % is defined.
Level Tolerance High Amount N/A The maximum allowable concentration fo r t he p eak t o p a ss
tolerance test.
Level Tolerance High Response N/A The maximum allowable signal for the peak to pass to l era nc e
test.
Level Tolerance Low Amount N/A The minimum allowable concentration f o r t h e p ea k t o p ass
tolerance test.
Level Tolerance Low Response N/A The minimum allowable signal for the peak to pass t o l era nce
test.
Manipulated? N/A Indicates whether the peak has been manually modified or not.

Manually Assigned N/A Indicates whether the peak name has been manually assigne d
or not.
Name N/A The peak name.

Number N/A The peak number.

Peak Start Time N/A The time at which the peak integration starts.
Peak Stop Time N/A The time at which the peak integration ends.

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 Chromeleon 7

Variable Sub Function Description

Peak to Valley Ratio N/A The ratio for a peak in an unresolved peak group, which is a n
indicator of the quality of peak separation.
The ratios are calculated based on USP (= United States
Pharmacopeia) and PharmEU standards:

Relative Amount All Identified Peaks The amount portion of the peak relative to all identified peaks in
the chromatogram.
All peaks of the same group The amount portion of the peak relative t o a ll p e aks i n t h e
respective group.
The corresponding ISTD The amount portion of the peak relative to the corre sp on ding
component ISTD component.

The corresponding reference The amount portion of the peak relative to the corre sp on ding
component Reference component.
Fixed component The amount portion of the peak relative to the u se r se l e ct ed
component.
Relative Area All detected peaks The relative area of the peak as a percentage of all peaks in the
chromatogram.
All identified peaks The relative area of the peak as a percentage of all i den tif ied
peaks in the chromatogram.
All peaks of the same group The relative area of the peak as a percentage of all peaks in the
respective peak group.
The corresponding ISTD The relative area of the peak as a percentage of the
component corresponding ISTD component.

The corresponding reference The relative area of the peak as a percentage of the
component corresponding reference component.
Fixed component The relative area of the peak as a percentage of the user
selected component.
Multiply values before comput ing Multiply the peak area values with the re tu rne d va lue s o f a
the relative result with formula before the results are calculated
Relative CE Area All detected peaks The relative CE area of the peak as a percentage of all peaks in
the chromatogram.
All identified peaks The relative CE area of the peak as a percentage of all
identified peaks in the chromatogram.
All peaks of the same group The relative CE area of the peak as a percentage of all peaks in
the respective peak group.

The corresponding ISTD The relative CE area of the peak as a percentage of the
component corresponding ISTD component.

The corresponding reference The relative CE area of the peak as a percentage of the
component corresponding reference component.
Fixed component The relative CE area of the peak as a percentage o f t h e u se r
selected component.

Multiply values before comput ing Multiply the peak CE area values with the returned values o f a
the relative result with formula before the results are calculated
Relative Height All detected Peaks The relative height of the peak as a percentage of all pea ks i n
the chromatogram.
All identified Peaks The relative height of the peak as a percentage of all identif ied
peaks in the chromatogram.
All peaks of the same group The relative height of the peak as a percentage of all pea ks i n
the respective peak group.

The corresponding ISTD The relative height of the peak as a percentage of the
component corresponding ISTD component.

The corresponding reference The relative height of the peak as a percentage of the
component corresponding reference component.

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Chromeleon 7

Variable Sub Function Description

Fixed component The relative height of the peak as a perce n tag e o f t he u se r
selected component.

Multiply values before comput ing Multiply the peak height values with the returned va lues o f a
the relative result with formula before the results are calculated
Relative Retention Time First or used reference component The relative retention time of the peak relative to the refere nce
component or a selected component.
Fixed component
The relative retention time can be reported a s a p e rce nt ag e
Reference component (CM6 value (%). This may be expressed with the following formula:
compatibility mode)
Convert to percentage

Resolution (EP, USP, Statistical Next main peak Resolution between the peak and the next m ain p ea k i n t h e
Moments) chromatogram.
Previous main peak Resolution between the peak and the previous main peak in the
chromatogram.
Next identified peak Resolution between the peak and the next identified peak in the
chromatogram.
Previous identified peak Resolution between the peak and the previous identifie d p e ak
in the chromatogram.

Corresponding reference Resolution between the peak and the corresponding reference
component peak.

Corresponding internal st a n da rd Resolution between the peak and the corre sp o ndin g I S TD
component peak.
Fixed component Resolution between the peak and a selecte d p ea k f ro m t h e
component table in the quantification method.
Retention Deviation Absolute in minutes The deviation (in minutes) between the actual re t en tio n t im e
and the expected retention time.
Relative in % of the expected The relative deviation (%) between the actual re te nt ion t ime
retention time and the expected retention time.
Retention Index Interpolation function type Determines the type of function used to calculate interpolat ion
(linear, quadratic, cubic, logarithmic). By default, Ch rome leon
calculates the following linear retention index:

Wherein:
RI = Retention index (usually RI = 100, 200, 300 is entered)
S = Substance
Z = number of the marker
The following is true:

If the peak occurs before the first or behind the last marker
peak, and the Extrapolate check box is selected, the formula i s
calculated for the first two and last two peaks, respectively.
Use detected retention times of Specifies which retention times Chromeleon uses for
calculating the retention index.
“Current injection” uses the retention times of the current
injection.
“Most recent injection with condition” uses the retention times of
the most recent injection that meets a certain condition.
If the “Include expected retention times for not detected
components” check box is activated, the exp ecte d re t en tio n
times of peaks that were not detected are excluded from
calculation.
The “Subtract dead time (Kovats Index)” check b o x p ro vide s
the Kovats Index if activated.

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 Chromeleon 7

Variable Sub Function Description

Extrapolate If the option “Extrapolate if the peak's retention time is o u t si de
the retention time reference range” is deactivated, Chromeleon
excludes the retention times outside the specified retention time
reference range from extrapolation.
Retention Time Detected value The retention time (in minutes) of the peak.

Expected value The expected retention time (as defined in the q ua nt ificat ion
method) of the peak.
At a given peak area % The retention time when the specified re la tive p eak a re a i s
reached.
Retention Window Width N/A The width of the retention window (as defined in the component
table of the processing method).
Right Width the baseline level (base width, The right width of the peak at the baseline.
default)
5 % height over the baseline The right width of the peak at 5 % height over the baseline.

10 % height over the baseline The right width of the peak at 10 % height over the baseline.
50 % height over the baseline The right width of the peak at 50 % height over the baseline.

Custom The right width at a user defined % height over the baseline.

Signal to Noise Ratio Injection for noise calculation Calculates noise from:
• Current injection
• Blank run injection of the corresponding
processing method

• Recent blank run in sequence

• Fixed injection

Method of noise calculation Calculates noise using:

Peak to peak (ASTM)
RMS
Time range for noise calculation - Use x times the “variable y” equally around the peak
boundaries.
Options for variable y:
• Peak w idth at 50% height
• Base peak w idth
- Use a fixed time interval from x to y min
- Use n datapoints from retention time x
- Find the lowest noise range consisting of n datapoints
Signal Value at Peak End N/A The signal value at the peak end.
Signal value at Peak Retention N/A The signal value at the peak retention time.

Signal Value at Peak Start N/A The signal value at the peak start.

Skewness N/A The skewness of the peak.

SN Intermediate Results Injection for noise calculation Calculates noise from:
• Current injection

• Blank run injection of the corresponding

processing method
• Recent blank run in sequence
• Fixed injection

Method of noise calculation Calculates noise using:

Peak to peak (ASTM)
RMS

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Chromeleon 7

Variable Sub Function Description

Time range for noise calculation - Use x times the “variable y” equally around the peak
boundaries.
Options for variable y:
• Peak w idth at 50% height
• Base peak w idth
- Use a fixed time interval from x to y min
- Use n datapoints from retention time x
- Find the lowest noise range consisting of n datapoints
Statistical Moments Zeroth moment The zero moment (peak area).
First moment The first moment (averaged retention time).

Second Moment The second moment (retention time variance).

Theoretical Plates (EP , US P , J P , N/A The number of theoretical plates for the peak.
Statistical Moments)
Type N/A Peak Type.
Note: If a peak has been manually integrated the “*” sym b ol i s
appended to the peak type.
Width the baseline level (base width, The peak width at the baseline.
default)
5 % height over the baseline The peak width at 5 % height over the baseline.

10 % height over the baseline The peak width at 10 % height over the baseline.
50 % height over the baseline The peak width at 50 % height over the baseline.

Custom The peak width at a user defined % height over the baseline.

7.12 Peak Calibration

In order to show results for these variables a peak from component table must be selected. Also, the variable can be
configured to show the data from the current channel selected by the user or from a specified channel.

Variable Sub Function Description

Calibration Coefficient N/A Shows the relevant calibration coefficient for a use r-d ef ine d
exponent e.g. 0 (zero) provides the intercept, 1 sup p lies t h e
slope, etc.
Calibration Mode N/A The calibration mode used.
Calibration Point Status Current injection Returns the calibration point status for the curren t i nje ct ion
(default). If the current injection is not involved in the
calibration, the entry reads n.a.
Minimum x-value Returns the calibration point status for the ca libra tio n p oin t
with the minimum x-coordinate.
Maximum x-value Returns the calibration point status for the ca libra tio n p oin t
with the maximum x-coordinate.
Minimum y-value Returns the calibration point status for the ca libra tio n p oin t
with the minimum y-coordinate.
Maximum y-value Returns the calibration point status for the ca libra tio n p oin t
with the maximum y-coordinate.
Number of calibration point Returns the calibration point status for a cert a in ca libra t ion
standard. The number is considered as consecutive n umb er
regarding the list of all calibration standard injections.
Calibration Point Weight Current injection Returns the weight factor for the current injection (default ). I f
the current injection is not involved in the calibration, the entry
reads n.a.
Minimum x-value Returns the weight factor for the calibra tio n p o int wit h t h e
minimum x-coordinate.
Maximum x-value Returns the weight factor for the calibra tio n p o int wit h t h e
maximum x-coordinate.

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 Chromeleon 7

Variable Sub Function Description

Minimum y-value Returns the weight factor for the calibra tio n p o int wit h t h e
minimum y-coordinate.
Maximum y-value Returns the weight factor for the calibra tio n p o int wit h t h e
maximum y-coordinate.
Number of calibration point Returns the weight factor for a certain calibrat ion st a nd ard .
The number is considered as consecutive number regard ing
the list of all calibration standard injections.
Calibration Point X/Y Current injection Returns the calibration point x/y value for the current injectio n
(default). If the current injection is not involved in the
calibration, the entry reads n.a.
Minimum x-value Returns the calibration point x/y value for the calibration point
with the minimum x-coordinate.
Maximum x-value Returns the calibration point x/y value for the calibration point
with the maximum x-coordinate.
Minimum y-value Returns the calibration point x/y value for the calibration point
with the minimum y-coordinate.
Maximum y-value Returns the calibration point x/y value for the calibration point
with the maximum y-coordinate.
Number of calibration point Returns the calibration point x/y value for a certain calibration
standard. The number is considered as consecutive n umb er
regarding the list of all calibration standard injections.
Calibration Type N/A The calibration type of the peak.

Coeff. of Determination N/A The coefficient of determination (R-square) value for the
calibration curve associated with the peak.
Correlation Coefficient N/A The linear correlation coefficient.

DOF-Adjusted Coeff. of N/A The coefficient of determination corrected by t he d eg ree o f

Determination freedom.
Evaluation of Cal. Function for X Current injection Returns the value of the calibration function for the x-value o f
the calibration point. If the current injection is not invo lve d i n
the calibration, the entry reads n.a.
Minimum x-value Returns the value of the calibration function for the x-value o f
the calibration point with the minimum x-coordinate.
Maximum x-value Returns the value of the calibration function for the x-value o f
the calibration point with the maximum x-coordinate.
Minimum y-value Returns the value of the calibration function for the x-value o f
the calibration point with the minimum y-coordinate.
Maximum y-value Returns the value of the calibration function for the x-value o f
the calibration point with the maximum y-coordinate.
Number of calibration point Returns the value of the calibration function for the x-value o f
a certain calibration standard. The number is con sid ere d a s
consecutive number regarding the list of all calibration
standard injections.
Hubaux Vos Limit of Detection Upper prediction limit Select a probability of a true positive detection (equal t o 1 -α,
where α is the probability of a false positive d e te ct ion ). Fo r
example, an upper prediction interval of 99% correspo nds t o
an α value of 1%.
Lower prediction limit Select a probability of a true negative detection (equal to 1 -β,
where β is the probability of a false negative detect ion ). Fo r
example, a lower prediction interval of 95% corresponds t o a
β value of 5%.
Lower Confidence Limit (From Smallest calibration level The lower confidence limit of the ca libra t ion cu rve a t t h e
Processing Method, 95, 97.5, 99, smallest calibration level.
99.5, 99.9, 99.95 or 99.995)
Greatest calibration level The lower confidence limit of the ca libra t ion cu rve a t t h e
greatest calibration level.
Average of all calibration levels The lower confidence limit of the ca libra t ion cu rve a t t h e
average of all calibration levels.

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Chromeleon 7

Variable Sub Function Description

Reference amount (calibration and The lower confidence limit of the ca libra t ion cu rve a t t h e
check standards \ QC Sample reference amount level.
only)
Computed amount The lower confidence limit of the ca libra t ion cu rve a t t h e
computed amount.
Any fixed value: x The lower confidence limit of the ca libra t ion cu rve a t t h e
specified amount (x)
Probability The probability (confidence level) that the specified values are
correct: 95%, 97.5%, 99%, 99.5%, 99.9%, 99.95%, and
99.995% or can be set to be read from processi n g m et hod
selected in the Low. Conf. Prob or Up. Conf. Prob colu mn o f
the component table.

Lower Prediction Limit (From Smallest calibration level The lower prediction limit of the calibration curve at the
Processing Method, 95, 97.5, 99, smallest calibration level.
99.5, 99.9, 99.95 or 99.995)
Greatest calibration level The lower prediction limit of the calibration curve at the
greatest calibration level.
Average of all calibration levels The lower prediction limit of the calibration curve at the
average of all calibration levels.

Reference amount (calibration and The lower prediction limit of the calibration curve at the
check standards \ QC Sample reference amount level.
only)
Computed amount The lower prediction limit of the calibration curve at the
computed amount.
Any fixed value: x The lower prediction limit of the calibration curve at the
specified amount (x).
Probability The probability (confidence level) that the specified values are
correct: 95%, 97.5%, 99%, 99.5%, 99.9%, 99.95%, and
99.995% or can be set to be read from processi n g m et hod
selected in the Low. Conf. Prob or Up. Conf. Prob colu mn o f
the component table.
Number of Calibr. Points N/A The number of calibration point s i n t he ca libra tio n cu rve
associated with the peak.
Number of disabled Calibr. Points N/A The number of disabled calibration points in t h e ca libra tio n
curve associated with the peak.
Reference Inject Volume N/A The reference inject volume selected.

Relative Standard Deviation N/A The relative standard deviation value for the calibration cu rve
associated with the peak.
Relative Standard Error N/A The relative standard error value for t h e ca libra tio n cu rve
associated with the peak.
Residual of Calibr. Point X Current injection The difference between the expected Y value for the
calibration point and the actual Y value. If the current injection
is not involved in the calibration, the entry reads n.a.
Minimum x-value The difference between the expected Y value for the
calibration point with the minimum x-coordinate and the actual
Y value.
Maximum x-value The difference between the expected Y value for the
calibration point with the maxim um x -co ord inat e a n d t h e
actual Y value.
Minimum y-value The difference between the expected Y value for the
calibration point with the minimum y-coordinate and the actual
Y value.
Maximum y-value The difference between the expected Y value for the
calibration point with the maxim um y -co ord inat e a n d t h e
actual Y value.
Number of calibration point The difference between the expected Y value f or a ce rt ain
calibration point with the minimum x-coordinate and the actual
Y value.
RF-Value (Amount/Area) N/A The reciprocal of the slope (c1) value i.e. the peak
amount/peak area.

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 Chromeleon 7

Variable Sub Function Description

Standard Deviation N/A The standard deviation value for the calibration curve
associated with the peak.

Upper Confidence Limit (From Smallest calibration level The upper confidence limit of the ca libra tio n cu rve a t t he
Processing Method, 95, 97.5, 99, smallest calibration level.
99.5, 99.9, 99.95 or 99.995)
Greatest calibration level The upper confidence limit of the ca libra tio n cu rve a t t he
greatest calibration level.
Average of all calibration levels The upper confidence limit of the ca libra tio n cu rve a t t he
average of all calibration levels.

Reference amount (calibration and The upper confidence limit of the ca libra tio n cu rv e a t t he
check standards \ QC Sample reference amount level.
only)
Computed amount The upper confidence limit of the ca libra tio n cu rve a t t he
computed amount.
Any fixed value: x The upper confidence limit of the ca libra tio n cu rve a t t he
specified amount (x).
Probability The probability (confidence level) that the specified values are
correct: 95%, 97.5%, 99%, 99.5%, 99.9%, 99.95%, and
99.995% or can be set to be read from processi n g m et hod
selected in the Low. Conf. Prob or Up. Conf. Prob colu mn o f
the component table.

Upper Prediction Limit (From Smallest calibration level The upper prediction limit of the calibration curve at the
Processing Method, 95, 97.5, 99, smallest calibration level.
99.5, 99.9, 99.95 or 99.995)
Greatest calibration level The upper prediction limit of the calibration curve at the
greatest calibration level.
Average of all calibration levels The upper prediction limit of the calibration curve at the
average of all calibration levels.

Reference amount (calibration and The upper prediction limit of the calibration curve at the
check standards \ QC Sample reference amount level.
only)
Computed amount The upper prediction limit of the calibration curve at the
computed amount.
Any fixed value: x The upper prediction limit of the calibration curve at the
specified amount (x)
Probability The probability (confidence level) that the specified values are
correct: 95%, 97.5%, 99%, 99.5%, 99.9%, 99.95%, and
99.995% or can be set to be read from processi n g m et hod
selected in the Low. Conf. Prob or Up. Conf. Prob colu mn o f
the component table.
Variance N/A The variance value for the calibration curve associ at ed wi t h
the peak.
Variance Coefficient N/A The variance coefficient value for the calibration curve
associated with the peak.
Weights N/A The Weights variable returns a text identifying the we igh tin g
method that is defined in processing method.

7.13 Peak Purity and Identification

In order to show values for these variables a peak from the component table must be selected. Also, the variable can be
configured to show the data from the current channel selected by the user or from a specified channel.

Variable Description
Composite Scoring All variables in section 7.14 become available.

Confirmation Chromatogram Chromatogram of corresponding confirmation ion. A ll va ria ble s i n se ct i on 7 . 9. 1

become available.
Confirmation Peak The number of the corresponding confirming peak. Al l v a riable s i n se c t ion 7 .1 1
become available.
Fluorescence Spectrum All variables in section Error! Reference source not found. become available.

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Chromeleon 7

Variable Description
ISTD Chromatogram Chromatogram of the corresponding ISTD peak. All variables in section 7.9.1 become
available.
ISTD Peak ISTD peak. All variables in section 7.11 become available.

MSLS Hit Information about the matching mass spectra (hits) found
during MS library screening. All variables in section 7.16 become available.
Number of MSLS Hit The matching mass spectra (hits) found during MS library screening

Number of SLS hits The number of hits in the spectral library.

Peak Confirmation Ratio The peak confirmation ratio of a user definable number of component traces.
Peak Confirmation Result The peak confirmation result. Can be computed against all componen t t ra ces, o r a
user definable number of component traces.
Peak Mass Spectrum Information about the mass spectrum. All variables in section 7.17 become available.

Peak Purity Index The peak purity index of the peak.

Peak Purity Match Average peak purity match.

Peak Ratio Mean Value The mean value of the quotients of all (baseline-corrected) signal data point values (of
a peak) from the current and the first channel (in alphabetic order) of the same
detector that is not the current channel (for example, if UV _V IS _2 is t h e cu rren t
channel of a UV detector, UV_VIS_1 is used for the calculation).
Peak UV Spectrum All variables in section 7.18 become available.

Reference Spectrum Match The match factor with the reference spectra.

RSD Peak Purity Index The relative standard deviation of the peak purity index.
RSD Peak Purity Match The relative standard deviation of the peak purity match.

RSD Peak Ratio The relative standard deviation of the peak ratio mean value.

SLS Hit The rank of the match can be defined and all vari able s i n se ct ion 7 .19 b ecom e
available.
Noise
Summed Charge State Confirming Peak Area The sum of the areas of the isotopes (confirming ions) across all charge states
Sub-parameters are available to specify the isotope and to opt iona lly e xclu de l ow
abundance Isotopes as defined by Composite Scoring (see 5.3.9)
Summed Confirming Peak Area The sum of the areas of all the isotopes (confirming ions) for the selected compo nen t
(charge state)
A Sub-parameter is available to optionally exclude low abundance isotopes as defined
by Composite Scoring (see 5.3.9)
Tentative Identification All variables in section 7.20 become available.

7.14 Composite Scoring (Peak Purity and Identification)

Variable Parameter Description

Amount Difference <Parameterless> Returns the difference as a percentage (%) in peak a m ou nt b et ween
data obtained from 2 discrete detectors as defined by t he p rocessi n g
method.
<Channel Name> Returns the difference as a percentage (%) in peak a m ou nt b et ween
data obtained from 2 discrete detectors wit h t he re fe ren ce ch ann el
defined by the processing method and confirmation channel defined b y
the parameter selection.
Composite Score Processing Method Overall composite scoring result based on results evaluated defined b y
the processing method.
Amount ratio Composite scoring result based on evaluation of amount ratio
confirmation as defined by the processing method.
Isotopic Dot Product <Parameterless> Composite scoring result based on evaluation of isotop ic d ot p rodu ct
between theoretical and observed isotope distributions of peptides.

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 Chromeleon 7

Variable Parameter Description

Mass Accuracy <Peak Number> Composite scoring result of mass accuracy against an exact mass. The
parameterless report variable returns a result for the quantitation p eak.
Otherwise, the variable returns mass accuracy for the designated
confirmation peak.
Peak Apex Alignment <Peak Number> Composite scoring result of peak apex alignment against the
quantitation peak.

7.15 FL Spectrum

Variable Sub Function Description

Baseline Corrected N/A Returns whether Baseline Correction is enabled in the
Processing Method.
Baseline Correction Bunch Side Returns the baseline correction left/right bunch width for peak-
dependent baseline correction on the UV S pe ctra S et tin gs
dialog box of the Processing Method Editor
Noise N/A The noise for the whole wavelength range of the spectrum.
Number of relative Extrema N/A The number of relative extrema of the spectrum.

Property Unit N/A Unit of meta data property of the spectrum.

Property Name Defines the property.

Property Value N/A Value of meta data property of the spectrum.

Property Name Defines the property.

Restrict Wavelength Range Use sub range from x nm to y nm Restricts wavelength range of spectrum considered for
calculations to entered values.
Retention Time N/A The retention time of the spectrum.
Scan Index N/A The peak purity index of the spectrum.

Scan Maximum N/A Indicates the upper limit of the wavelength range of the
reference spectra.
Scan Minimum N/A Indicates the lower limit of the wavelength range of the
reference spectra.
Scan Resolution N/A Indicates the optical resolution of the reference spectra.

Scan Unit N/A Indicates the unit of the scan axis.

Scan Value Compute wavelength of the The scan value (usually the wavelength) o f a n a bso l ut e o r
relative signal extremum.
Options are:
absolute minimum
absolute maximum
greatest relative maximum
second greatest relative maximum
third greatest relative maximum
fourth greatest relative maximum
fifth greatest relative maximum
Signal Maximum N/A The maximum value on the signal axis.
Signal Minimum N/A The minimum value on the signal axis.

Signal Unit N/A Indicates the unit of the signal axis.

Signal Value Compute at wavelength The signal value for a selected scan value of the spectrum.

Statistical Moment N/A The first statistical moment for the spectrum.

7.16 Hit Mass Spectrum

Variable Sub Function Description

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Chromeleon 7

Variable Sub Function Description

CAS Number N/A Chemical Abstracts Service (CAS) registry number of the chemical
associated with the mass spectrum found during MS library screening.
Chemical Formula N/A The chemical formula of a mass spectrum found during MS library
screening.
Library Name N/A The name of the MS library in which the mass spectrum found du ring M S
library screening is stored.
Match Factor N/A The Match Factor for the hit mass spectrum and the mass spectrum
submitted for MS library screening.
Molecular Weight N/A The molecular weight of a mass spectrum found during MS library
screening.
Name N/A The chemical name of the mass spectrum found during MS library
screening.
Probability N/A The probability (in %) that a mass spectrum found during MS library
screening matches the spectrum submitted for screening.
Reverse Match Factor N/A The Reverse Match Factor of the hit mass spectrum and the mass
spectrum submitted for MS library screening.
Spectrum Data N/A It returns the mass or intensity of a peak in the mass spectrum found during
MS library screening. By default, the mass or intensity o f t he ma ss p e a k
with the greatest mass in the spectrum is reported.

7.17 Mass Spectrum

Variable Sub Function Description

Baseline Corrected N/A When True, the spectrum has been baseline corrected. Whe n
False, the spectrum has not been baseline corrected.
Baseline N/A Returns the MS baseline value for the specified m/z
(N) Index value (see below)

Greatest Criterion for the index (Intensity or M/Z)

Baseline Correction N/A Returns information about the baseline correction a p plied t o
the selected spectrum. The displayed results are formatted a s
follows:
start time - end time (spectra count), where:
start time is the retention time at the start of the bunch region
end time is the retention time at the end of the bunch region
spectra count is the total number of sp e ct ra i n t h e b un ch
region
.Left Returns details about spectra in the left region bunch
.Right Returns details about spectra in the right region bunch

Detected Mass Accuracies N/A Returns a list of mass differences between the actual detected
masses found in the spectrum and the targ et m asse s. T h e
mass detection method uses mass tolerance from processi n g
method MS settings.
Adducts Select either ‘Use injection adducts’ or ‘Select an adduct’. If
‘Select an adduct’ is chosen, select a specific adduct from the
drop-down lists. The lists are populated with only a d duct s o f
the corresponding charge state.
If the injection has an absolute target mass entered, t he n t h e
adduct value is not used.
Output Format Select either ‘Single line list’ or ‘Multi-line list’. The multi-line
list displays one item per line, which is useful when the
returned value is a long list.
Detected Masses N/A Returns a list of actual masses found in the spectrum that
match the injection target masses within the allowed tolerance.
The mass detection method uses the mass tolerance from th e
processing method MS settings.
To define the adducts to be reported, click Parameters:

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Variable Sub Function Description

Select either ‘Use injection adducts’ or ‘Select a n a ddu c t’. I f

‘Select an adduct’ is chosen, select a specific adduct from t he
drop-down lists. The lists are populated with only a d duct s o f
Adducts the corresponding charge state.
If an absolute target mass is entered for the injection, the
adduct value is not used.

Select either ‘Single line list’ or ‘Multi-line list’. The multi-line list
Output Format displays one item per line, which is useful when the re t urn ed
value is a long list.
FT_Resolution N/A Returns the resolution of the selected spectrum, based on t he
instrument method settings used to acquire te data.
Intensity N/A The intensity of a peak in a mass spectrum. B y d ef ault , t he
intensity is reported for the mass peak with the greatest m a ss
in the spectrum.

Compute Intensity for the mass The intensity of the mass peak according to its relative rank i n
peak with the ... the mass spectrum, based on either the peak's mass or its
intensity.

Compute Intensity for the mass Reports the intensity of a mass peak at a specific mass to
peak at ... charge ratio.
Mass N/A The mass of a peak in the mass spectrum fo un d d uri ng M S
library screening according to its relative rank in the mass
spectrum, based on either the peak's mass or its intensity.
Mass Detected N/A returns True or False, depending on whether the target
mass(es) are detected in the spectrum. If at least one of the
target masses is detected, the variable returns True.

Select either ‘Use injection adducts’ or ‘Select a n a ddu c t’. I f

‘Select an adduct’ is chosen, select a specific adduct from t he
drop-down lists. The lists are populated with only a d duct s o f
Adducts the corresponding charge state.
If an absolute target mass is entered for the injection, the
adduct value is not used.
Mass Detected Formulas N/A Returns a list of target [chemical formula + adduct] and
[chemical formula - adduct] that are detected in the spectrum.
The mass detection method uses mass t o l era nce f ro m t h e
processing method MS settings.

Select either ‘Use injection adducts’ or ‘Select a n a ddu c t’. I f

‘Select an adduct’ is chosen, select a specific adduct from t he
drop-down lists. The lists are populated with only a d duct s o f
Adducts the corresponding charge state.
If an absolute target mass is entered for the injection, the
adduct value is not used.
Select either ‘Single line list’ or ‘Multi-line list’. The multi-line list
Output Format displays one item per line, which is useful when the re t urn ed
value is a long list.
Mass Range N/A Reports the extracted mass range.

Maximal Mass N/A Maximal mass of the spectrum mass range.

Minimal Mass N/A Minimal mass of the spectrum mass range.

Noise N/A Returns the MS noise for the specified m/z

(N) Index value (see below)

Greatest Criterion for the index (Intensity or M/Z)

Number of Data Points N/A Number of mass data points in the mass spectrum.

Relative Intensity N/A Relative intensity of a peak in the mass spectrum.

Resolution N/A Returns an internally compute value. Not o f in te rest t o e nd
users.
Saturated N/A Returns ‘True’ when the MS photomultiplier response is
saturated (outside the linear range).
Signal To Noise N/A Returns the MS signal to noise for the specified m/z

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Chromeleon 7

Variable Sub Function Description

(N) Index value (see below)
Greatest Criterion for the index (Intensity or M/Z)

Spectrum Type N/A Spectrum type of the mass

spectrum.
TIC N/A Total of intensities of the single peaks in the mass spectrum.

7.18 UV Spectrum

Variable Sub Function Description

Baseline Corrected N/A Returns whether Baseline Correction is enabled in the
Processing Method.
Baseline Correction Bunch Side Returns the baseline correction left/right bunch width for peak-
dependent baseline correction on the UV S pe ctra S et tin gs
dialog box of the Processing Method Editor
Noise N/A The noise for the whole wavelength range of the spectrum.

Number of relative Extrema N/A The number of relative extrema of the spectrum.

Restrict Wavelength Range Use sub range from x nm to y nm Restricts wavelength range of spectrum considered for
calculations to entered values.
Retention Time N/A The retention time of the spectrum.
Scan Index N/A The peak purity index of the spectrum.

Scan Maximum N/A Indicates the upper limit of the wavelength range of the
reference spectra.
Scan Minimum N/A Indicates the lower limit of the wavelength range of the
reference spectra.
Scan Resolution N/A Indicates the optical resolution of the reference spectra.

Scan Unit N/A Indicates the unit of the scan axis.

Scan Value Compute wavelength of the The scan value (usually the wavelength) o f a n a bso l ut e o r
relative signal extremum.
Options are:
absolute minimum
absolute maximum
greatest relative maximum
second greatest relative maximum
third greatest relative maximum
fourth greatest relative maximum
fifth greatest relative maximum
Signal Maximum N/A The maximum value on the signal axis.
Signal Minimum N/A The minimum value on the signal axis.

Signal Unit N/A Indicates the unit of the signal axis.

Signal Value Compute at wavelength The signal value for a selected scan value of the spectrum.

Statistical Moment N/A The first statistical moment for the spectrum.

7.19 Hit Spectrum

Variable Sub Function Description

Acquisition Step N/A The sample rate that was used to record the spectrum.
Comment N/A Comment of the hit spectrum.

Component Name N/A The peak name of the hit spectrum.

Data Acquisition Date/Time N/A Date and time the injection used to obtain the hit spectrum was acquired.

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Variable Sub Function Description

Detector Name N/A The name of the detector used to acquire the hit spectrum.
Detector Serial Number N/A The serial number of the detector used to acquire the hit spectrum.

Extract Date/Time Format date/time a s The date and time when the spectrum was extracted can have the following
text formats:
• Default date/time format
• ISO 8601 date/time
• Localized long date
• Localized short date
• Time offset only

• Time w ith seconds and time offset

• Time w ith time offset

Time in universal The time in coordinated universal time standard format.

coordinated time
Time offset in hours The time offset from your local time based on the Windows settings of yo u r
local computer (including any daylight savings time adjustments that apply)

Time using local time The conversion of date and time to your local time zone with the f ol lowing
zone formats:
Format date/time as text
Default date/time format
ISO 8601 date/time
Localized long date
Localized short date
Time offset only
Time with seconds and time offset
Time with time offset
Time offset in hours
Extract User Name N/A The user id of the operator who extracted the hit spectrum.

ID N/A The unique identifier (ID) of the spectrum.

Injection N/A Provides details of the injection used to extract the hit spectra. Allows use of
any variable from the Injections category (see 0).
Injection Name N/A The name of the injection from which the spectrum was extracted.
Injection URL N/A Provides the URL of the injection used to extract the hit spectrum.

Instrument N/A The instrument used to obtain the hit spectrum.

Instrument Method N/A The name of the instrument method used to run the injection that was use d
to obtain the hit spectrum.
Library Name N/A The name of the spectral library containing the hit spectrum.
Library Record N/A Opens the Library Record category.

Match Factor N/A The match factor with the hit spectrum.
Number of relative Extrema N/A The number of extrema in the hit spectrum.

Retention Index N/A The retention index of the hit spectrum.

Retention Time N/A The retention time at which the spectrum was extracted.
Sequence Header Record N/A Returns the selected information about the sequence from which the
spectrum was extracted. All variables in section 7.3 become available.
Sequence Name N/A The name of the sequence from which the spectrum was extracted.

Solvent Composition N/A Solvents used when measuring the hit spectrum.

Spectrum Data N/A Provides details of the hit spectrum. Allows use of any variable from the UV
Spectrum category (see 7.18).
Version Comment Comment for this version.
Computer Name Name of the computer on which this version was created.

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Chromeleon 7

Variable Sub Function Description

Data Vault Name of the data vault.
Date & Time Date and time when the version was created. The same sub f un ct ion s a s
for other date & time variables are available
• Format date/time as text
• Time in universal coordinated time
• Time offset in hours

• Time using local time zone

• Format date/time as text
• Default date/time format
• ISO 8601 date/time
• Localized long date

• Localized short date

• Time offset only
• Time w ith seconds and time offset
• Time w ith time offset
• Time offset in hours

Number Version number.

Operator Information about the user who created the version. The same sub
functions as for other operator variables are available. These are
Full Name, Job Title and User Name.

7.20 Peak Tentative Identification

Variable Description
Amount Estimated amount of the peak.

CAS Number The CAS number of the tentatively identified component.

Int. Std. The internal standard peak used for calculating the estimated amount value.

Library Name Name of the MS library in which the hit spectrum was found.

Match Factor Match factor (SI) for the hit spectrum and the apex spectrum of the peak.
Name Tentative name of the peak.

Probability Probability that the hit spectrum and the apex spectrum of the peak are identical.

Reverse Match Factor Reverse Match Factor (RSI) for the hit spectrum and the apex spectrum of the peak.

7.21 Processing Method

Variable Sub Function Description

Available algorithm version N/A Available version of the preferred algorithm type.

Detection Algorithm Select the algorithm to be reported.

Blank Run injection Record N/A Selected information about the injection that is sp e c i fie d a s
fixed blank injection for chromatogram subtraction. All
variables in section 0 become available.
Calibration Level Name N/A Name of the amount column. The name can be se l ect ed a s
follows:
• Current injection (default)
• Calibration level number

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Variable Sub Function Description

Calibration Mode N/A Returns a text identifying the calibration mode as d e f ine d i n
the Global Calibration Settings of the processing method , f o r
example, Total or Bracketed.
Comment N/A Processing method comment.

Composite Scoring N/A All variables in section 7.22 become available

Creation Date and Time Format date/time as text The processing method creation date and time can have t he
following formats:
Default date/time format
ISO 8601 date/time
Localized long date
Localized short date
Time offset only
Time with seconds and time offset
Time with time offset
Time in universal coordinated time The time in coordinated universal time standard format.
Time offset in hours The time offset from your local time based on t he Win do ws
settings of your local computer (including any daylight savings
time adjustments that apply)
Time using local time zone The conversion of date and time to your local time zone wi t h
the following formats:
Format date/time as text
Default date/time format
ISO 8601 date/time
Localized long date
Localized short date
Time offset only
Time with seconds and time offset
Time with time offset
Time offset in hours
Creation Operator Full Name Full user name of the user who created the Processing
method.
Job Title Job title of the user who created the Processing method.

User Name User id of the user who created the Processing method.

Curve Fitting N/A Displays the curve fitting model selected in t he p rocessi n g
method.
Data Vault N/A Name of the corresponding data Vault.
Dead Time N/A The method dead time.

Delay Time N/A The delay time of the (2 nd, 3 rd) detector.

Delay Time Detector N/A The (2 nd, 3 rd) detector device name.
Detection Algorithm N/A Displays the detection algorithm used.

Directory N/A Directory where the processing method is saved.

Effective algorithm version N/A The version of the corresponding detection algorith m t ha t i s
stored in the processing method.
Detection Algorithm Select the algorithm to be reported.
Is latest algorithm version N/A Reports whether the effective algorithm version is equal to the
currently available algorithm version in this Chromeleon
release.
Detection Algorithm Select the algorithm to be reported.

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Chromeleon 7

Variable Sub Function Description

Last Fixed Calibration Update Da t e Format date/time as text The date and time of when the last update of the fixed
and Time calibration standards of a processing method was performe d
can have the following formats:
• Default date/time format
• ISO 8601 date/time
• Localized long date
• Localized short date

• Time offset only

• Time w ith seconds and time offset
• Time w ith time offset

Time in universal coordinated time The time in coordinated universal time standard format.
Time offset in hours The time offset from your local time based on t he Win do ws
settings of your local computer (including any daylight savings
time adjustments that apply)
Time using local time zone The conversion of date and time to your local time zone wi t h
the following formats:
• Format date/time as text
• Default date/time format
• ISO 8601 date/time
• Localized long date
• Localized short date

• Time offset only

• Time w ith seconds and time offset
• Time w ith time offset
• Time offset in hours

Last Fixed Calibration Update Full Name Full user name of the user who last modified the fixed
Operator calibration standards of the Processing method.
Job Title Job title of the user who last modified th e f ix e d c a libra tio n
standards of the Processing method.
User Name User id of the user who last modified t he f ixed calib rat ion
standards of the Processing method.
Last Update Date and Time Format date/time as text The date and time of when the last update o f a p rocessi n g
method was performed can have the following formats:
• Default date/time format
• ISO 8601 date/time
• Localized long date
• Localized short date

• Time offset only

• Time w ith seconds and time offset
• Time w ith time offset

Time in universal coordinated time The time in coordinated universal time standard format.
Time offset in hours The time offset from your local time based on t he Win do ws
settings of your local computer (including any daylight savings
time adjustments that apply)

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Variable Sub Function Description

Time using local time zone The conversion of date and time to your local time zone wi t h
the following formats:
Format date/time as text
Default date/time format
ISO 8601 date/time
Localized long date
Localized short date
Time offset only
Time with seconds and time offset
Time with time offset
Time offset in hours
Last Update Operator Full Name Full user name of the user who last modified the Proce ssi n g
method.
Job Title Job title of the user who last modified the Processing method.

User Name User id of the user who last modified the Processing method.

Matrix Correction Enabled N/A Displays if matrix correction is enabled or not.

MS Detection Algorithm N/A The name of the detection algorithm used for mass
spectrometry.
MS Library Screening Parameters N/A Returns the selected information about the library scre e n ing
parameters for mass spectrometry. All variab les i n se ct io n
7.23 become available.
MS Settings N/A Returns the selected information about the settings f o r m a ss
spectrometry. All variables in section 7.24 become available.
Name N/A Processing method name.

Number of Calibration Levels N/A Number of calibration levels in the Processing method.
Number of Components N/A The number of components in the component table.

Number of Detection Parameters N/A The number of detection parameters used.

Number of Test Cases N/A The number of the single test cases.
Number of Peak Groups N/A The number of peak groups.

Origin of Fixed Calibration N/A Original location of calibration standards in Fixed mode.
Standards
Parent Sequence Header Record N/A Returns the selected information about the sequence in which
the processing method is currently used. All variables in
section 7.3 become available.
Parent Sequence Name N/A The name of the sequence in which the processing method is
stored.
Reference Inject Volume N/A Reference injection volume setting for amount interpretation.
Retention Time Determination N/A Displays Retention Time Determination selected in the
processing method.
Select Component in the Select component in co mpo nen t Details about the components in the component table.
Component Table table Components can be selected as follows:
by Name
by Number
by Group
ISTD (Internal Standard)
Reference Component
N/A All variables in section 7.29 become available.
Select Test Case Test Case Selection Returns the results of a system suitability test case. T he t e st
case is selected using the following options:
Select by number
Select by name
N/A All variables in section 7.25 become available.

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Chromeleon 7

Variable Sub Function Description

Select Peak Group Select Peak Group Returns a specific peak group. The peak group record is
selected using the following options:
by Name – the name of the peak group
by Number – the number of the peak group if so rt e d b y t h e
retention time
by Group – the Peak Group(s) property of the peak group
record (see 5.3.4 for details)
N/A All variables in section 7.30 become available.

Separate Calibration N/A Displays if dual column separate calibration mode is activated.

Spectra Library Screening N/A Displays spectra library screening settings.

Parameters
N/A All variables in section 7.26 become available.

Subtraction Mode N/A Displays the type of blank run subtraction used.

UV Spectra Settings N/A Displays the settings for UV spectra comparison and baseline
correction. All variables in section 7.27 become available.
Version Comment Comment for this version.
Computer Name Name of the computer on which this version was created.

Data Vault Name of the data vault.

Date & Time Date and time when the version was created. The sam e su b
functions as for other date & time variables are available
• Format date/time as text
• Time in universal coordinated time

• Time offset in hours

• Time using local time zone
• Format date/time as text
• Default date/time format
• ISO 8601 date/time
• Localized long date
• Localized short date
• Time offset only
• Time w ith seconds and time offset
• Time w ith time offset
• Time offset in hours

Number Version number.

Operator Information about the user who created the version. The same
sub functions as for other operator variables a re a vaila ble .
These are
Full Name, Job Title and User Name.

7.22 Composite Scoring (Processing Method)

Variable Description
Amount Ratio Confirmation Channel Returns the confirmation channel used for amount ratio confirmation scoring as d e f ine d i n
the processing method.

Amount Ratio Reference Channel Returns the reference channel used for amount ratio confirmation scoring as defined i n t h e
processing method.
Amount Ratio Tolerance % Returns the pass/fail tolerance percentage (%) used fo r a mou nt ra tio co nfi rmat ion a s
defined in the processing method.

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Variable Description
Fail Threshold Returns the overall composite scoring failure threshold.
Is Filter Isotopes Used Returns whether or not filtering of low abundance isotopes is enabled

Filter Isotopes Reference Percent Returns an absolute height value or the percent of the height o f t he TI C o r B PC, wh ich
defines the low isotope threshold level. Returns n.a. when ‘Is Filter Isotopes Used’ I false o r
the reference type is height.
Filter Isotopes Reference Type Returns ‘%TIC’, ‘%BPC’ or ‘Height’, which when combined with the Filter Isotopes
Reference Percent, determines the value of the isotope abundance threshold
Filter Isotopes Reference Value Returns the effective value of the low abundance threshold. Isotopes below t his l e vel a re
excluded from calculations
Is Amount Ratio Used Returns whether or not amount ratio confirmation scoring is enabled

Is Confirming Ion Ratio Used Returns whether or not confirmation ion ratios and ion coelution is used for scoring.
Is Isotopic Dot Product Used Returns whether or not isotopic dot product is used for scoring.

Is Mass Accuracy Used Returns whether or not mass accuracy is used for scoring.
Is Peak Apex Alignment Used Returns whether or not peak apex alignment is used for scoring.

Isotopic Dot Product Threshold Returns the pass/fail threshold for isotopic dot product scoring.

Mass Accuracy Calculation Returns the method used for calculating mass accuracy
Mass Accuracy Threshold Returns the numerical value for mass accuracy scoring.

Mass Accuracy Unit Returns the mass accuracy threshold unit (PPM, MMU, or AMU) for mass accuracy scoring.

Pass Threshold Returns the overall composite scoring pass threshold.

Peak Apex Alignment Threshold Returns the pass/fail threshold for peak apex alignment scoring.

Peak Apex Alignment Type Returns the method used for calculating peak apex alignment

7.23 MS Library Screening

Variable Description
Is MS Library Used Returns whether a selected library is searched during MS library screening. Th e M S
library is selected using the following options:
Select by number
Select by name
Match Threshold The threshold value set for Match Factor (SI).

Mol. Weight The molecular weight entered in the Search with Mol. Weight box.
MS Library The name of the selected MS library available for library screening. The MS libra ry i s
selected using the following options:
Select by number
Number of MS Libraries The number of MS libraries in the MS libraries to be searched.
Probability Threshold The threshold value (in %) set for Probability

Reverse Match Threshold The threshold value set for Reverse Match Factor (RSI).

Reverse Search Reports whether or not Reverse Search is selected.

Search Type The MS Library search type.

Search with Mol. Weight Reports whether or not Search with Mol. Weight is selected.

7.24 MS Settings

Variable Description
Baseline Correction The selected baseline correction method

Fixed Noise Reduction Threshold Reports a specified number of mass peaks with the greatest intensities included in the
spectrum.

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Chromeleon 7

Variable Description
Inhibit Integration for TIC Allows disabling integration for TIC. Especially useful for timed SIM an d t ime d S RM
experiments.
Left Region Bunch The number of single spectra which are bunched (averaged) b ef ore t he st a rt o f a
peak.
Manually Defined Mass Tolerance Reports whether a default mass tolerance has been manually defined.

Mass Tolerance The specified mass tolerance value which defines how many mass units be f o re a nd
after a specified mass are included in an extracted ion chromatogram (XIC).
Mass Tolerance Unit The specified unit of a manually defined mass tolerance.
Maximum of Fixed Baseline Correction Range The maximum value of the specified retention time range. The range is selected using
the following options:
1 st fixed range
2 nd fixed range
Minimum of Fixed Baseline Correction Range The minimum value of the specified retention time range. The range is selected usin g
the following options:
1 st fixed range
2 nd fixed range
Noise Reduction Mode The defined mode to reduce noise.
Number of Smoothing Points The defined number of input data points used to generate each output data point.

Peak Spectrum Bunch The number of single spectra to be bunched (averaged) to form the spectrum a t t h e
peak maximum.
Relative Noise Reduction Threshold The specified threshold value used to include only mass peaks with great er re l at ive
intensities in the spectrum.
Right Region Bunch The number of single spectra which are bunched (averaged) after the end of a peak.

Smoothing Type The selected smoothing algorithm type applied to the data to reduce signal noise.

7.25 System Suitability Test Case Details

Variable Sub Function Description

Channel N/A Allows the selection of the channels on which the tests will b e
performed
Evaluation Formula N/A Returns the evaluation formula used for the system suitabilit y
test case.
Fail Actions N/A List of actions taken in if system suitability test fails.
Incomputable Interpretation N/A Displays the result of the system suitability test when the t e st
condition cannot be evaluated.
Injection Condition N/A Displays condition used to select the injections for the syste m
suitability test.
MaximumNumberOfInjections N/A Maximum number of injections for which a statistical
calculation is performed.
MinimumNumberOfInjections N/A Minimum number of injections for which a statistical
calculation is performed.
Name N/A Name of the system suitability test case.
Number N/A Number of the system suitability test case.

Number of Decimal Places N/A Specified decimal places to which the evaluation re su lt a n d
reference value are rounded.
Number of Fail Actions N/A Number of fail actions for the test case.

Number of Pass Actions N/A Number of pass actions for the test case.
Operator N/A Comparison operator used to compare the values of the
evaluation formula with the specified reference value.
Pass Actions N/A Overview of actions that are executed.
Peak Specification N/A Condition used to select the peak for the system suitability test
case.

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Variable Sub Function Description

Reference Value Formula Return formula of Formula that is used to compare the ‘first’ or ‘second’
reference values to the evaluation formula.
Statistics N/A Result of the used statistics function.

7.26 Spectral Library Screening Parameters

Variable Description
Hit Threshold Hit threshold specified in the processing method.
Is Spectral Library Filter Active Returns if the spectral library filter is currently active.

Is Spectral Library Used Returns if a spectral library identified by number or name is used.
Library Spectral Filter Optionally selects that only spectra matching the defined conditions will be included in
the search
Match Criterion Match criterion specified for spectral library screening in the processing method (Least
Square, Weighted Least Square, or Correlation).
Number of Spectral Libraries Number of spectral libraries listed in the processing method.
Spectral Library Returns the name of a spectral library identified by name.

Spectrum Derivative Returns the spectrum derivative setting for spectral library screening def ined b y t he
processing method.
Wavelength Range Maximum Maximum of the wavelength range used for spectral library screening.

Wavelength Range Minimum Minimum of the wavelength range used for spectral library screening.

7.27 UV Spectra Settings

Variable Description
Baseline Correction Baseline correction mode for UV spectra specified in the processing method.

Left Region Bunch Left bunch width for peak-dependent baseline correction of UV spectra as specified in
the processing method.
Match Criterion Match criterion for UV spectra comparison specified in the processing method (L e ast
Square, Weighted Least Square, or Correlation).
Maximum of Fixed Baseline Correction Range Returns the end time of the (first or second) fixed baseline correctio n ra n ge f o r UV
spectra as defined in the processing method.
Minimum of Fixed Baseline Correction Range Returns the start time of the (first or second) fixed baseline correction ra nge f or UV
spectra as defined in the processing method.
Peak Purity Threshold Peak purity threshold value for UV spectra comparison def ine d i n t he p roce ssi n g
method.
Peak Spectrum Bunch Peak spectrum bunch width for UV spectra defined in the processing method.
Right Region Bunch Right bunch width for peak-dependent baseline correction of UV spectra as speci fie d
in the processing method.
Spectrum Derivative Spectrum derivative setting for UV spectra comparison def ine d i n t he p roce ssi n g
method (None, 1st Derivative, or 2nd Derivative).
Wavelength Range Maximum End wavelength of the wavelength range that was used for UV spectra comparison.

Wavelength Range Minimum Start wavelength of the wavelength range that was used for UV spectra comparison.

7.28 Detection Parameters

The variables that Chromeleon can show are the same as the values that are defined in the processing method (see 5.3.1
for more details).

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Chromeleon 7

7.29 Component
The variables that Chromeleon can show are almost the same as the values that are defined in the component table in the
processing method (see 5.3.1.2 for more details).
There is one additional variable w hich can’t be seen in the processing method editor.

Variable Description
XIC Detection Reference Rule A text label describing whether a detection reference rule is set f o r t h e c o mpo nen t
record or not.

7.30 Peak Group

The variables that Chromeleon can show are the same as the values that are defined in the peak group table in the
processing method (see 5.3.4 for more details).

7.31 Instrument Method

Variable Description
Comment Instrument method comment.
Creation Date & Time Format date/time as text The instrument method creation date and time can have the fol lowing
formats:
Default date/time format
ISO 8601 date/time
Localized long date
Localized short date
Time offset only
Time with seconds and time offset
Time with time offset

Time in universal coordinated The time in coordinated universal time standard format.
time
Time offset in hours The time offset from your local time based on the Windows settin gs o f
your local computer (including any daylight savings time a dju st me nts
that apply)
Time using local time zone The conversion of date and time to your local time zone with the
following formats:
• Format date/time as text

• Default date/time format

• ISO 8601 date/time
• Localized long date
• Localized short date
• Time offset only
• Time w ith seconds and time offset
• Time w ith time offset
• Time offset in hours

Creation Operator Full Name Full user name of the user who created the instrument method.
Job Title Job title of the user who created the instrument method.

User Name User id of the user who created the instrument method.

Data Vault The data vault where the instrument method is stored.
Directory Directory where the instrument method is stored.

Instrument Name of the instrument associated with the instrument method.

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Variable Description
Last Update Date & Time Format date/time as text The date and time of when the last update of an instrument method was
performed can have the following formats:
Default date/time format
ISO 8601 date/time
Localized long date
Localized short date
Time offset only
Time with seconds and time offset
Time with time offset
Time in universal coordinated The time in coordinated universal time standard format.
time
Time offset in hours The time offset from your local time based on the Windows settin gs o f
your local computer (including any daylight savings time a dju st me nts
that apply)
Time using local time zone The conversion of date and time to your local time zone with the
following formats:
Format date/time as text
Default date/time format
ISO 8601 date/time
Localized long date
Localized short date
Time offset only
Time with seconds and time offset
Time with time offset
Time offset in hours
Last Update Operator Full Name Full name of the user who last saved changes to the instrument
method.
Job Title Job title of the user who last saved changes to the instrument method.

User Name User id of the user who last saved changes to the instrument method.
Name Instrument method name.

Server Name of the PC that the instrument was connected to.

Version Comment Comment for this version.

Computer Name Name of the computer on which this version was created.

Data Vault Name of the data vault.

Date & Time Date and time when the version was created. The same sub funct ion s
as for other date & time variables are available
• Format date/time as text
• Time in universal coordinated time
• Time offset in hours
• Time using local time zone

• Format date/time as text

• Default date/time format
• ISO 8601 date/time
• Localized long date
• Localized short date

• Time offset only

• Time w ith seconds and time offset
• Time w ith time offset
• Time offset in hours

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Chromeleon 7

Variable Description
Number Version number.
Operator Information about the user who created the ve rsi on. Th e sa m e su b
functions as for other operator variables are available. These are
Full Name, Job Title and User Name.

7.32 Mass Spectrometry

Variable Description
Device Information All variables in section 7.33 become available.
Mass Spectrum All variables in section 7.17 become available.

Spectra Count Number of mass spectra scans comprising the selected chromatographic peak.

Status Log Individual instrument status values recorded during the data acquisition.
Tune Data Values of individual tune data parameters.

7.33 MS Device

Variable Description
Device Name Name of device.

Firmware Version Device firmware version.

Hardware Version Device hardware version.

Model Model of device.

Name Name of device.

7.34 MS Detection Parameters

When Cobra or Chromeleon 6 algorithm is active, the variables that Chromeleon can show are the same as the values that
are defined in the processing method (see 5.3.1 for more details).

Variable Description
Algorithm Name of the detection algorithm (Cobra, Chromeleon 6, Genesis o r I CI S ) u se d f o r
mass spectrometry.
Area Noise Factor (ICIS) Noise level multiplier used to determine the pea k e d ge a ft er t h e l ocat ion o f t h e
possible peak.
Area Scan Window (ICIS) Number of scans on each side of the peak apex.
Area Tail Extension (ICIS) Number of scans past the peak endpoint used in averaging the intensity.

Baseline Window (ICIS) Number of scans over which to look for a local minima.

Calculate Noise As (Genesis) Returns the specified parameter to calculate the signal-to-noise v a lue s a s RM S o r
Peak to Peak.
Constrain Peak Width (Genesis, ICIS) Constrained peak width of a component during peak integration of a chromatogram
Enable Valley Detection (Genesis) Enables / disables valley detection.

Expected Peak Width (Genesis) Expected peak width in seconds, provided that valley detection is enabled.

Minimum Peak Width Minimum number of scans in a peak.

Multiplet Resolution Minimum separation in scans between the apexes of two potential peaks.

Minimum Scans in Baseline (Genesis) Minimum number of scans specified to calculate a baseline.
Mulitplet Resolution (ICIS) Minimum separation in scans between the apexes of two potential peaks.

Noise Method (ICIS) Algorithm used for determining the noise level.

Peak Height (Genesis, ICIS) Percent of the total peak height (100%) that a signal is above t he b a se line b ef ore
integration is turned on or off.

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Variable Description
Peak Noise Factor (ICIS) Noise level multiplier used to determine the potential peak signal threshold.
Peak S/N Cutoff (Genesis) Returns the specified peak signal-to-noise cutoff value.

Rise Percentage (Genesis) The defined percentage of the valley bottom that the peak t ra ce ca n ri se a bo ve a
baseline (before or after the peak) before valley detection peak integration criteria a re
applied.
RMS (ICIS) The calculated noise as RMS.
S/N Threshold (Genesis) The current signal-to-noise threshold for peak integration.

Tailing Factor (Genesis, ICIS) Maximum ratio of the trailing edge to the leading side of a constrained peak.

Valley Depth (Genesis) Returns the signal-to-noise range used for valley detection.

7.35 Peptide
The Peptide category contains variables w hich w ere either imported from a peptide w orkbook import or computed during
NTMS processing.

Variable Description
Charge Charge state of the peptide.
Chemical Formula Chemical formula of the component entered in the component table.

Composite Score Result of the composite scoring test.

Isotope Isotope related report variables. See section 7.36.

Isotopic Dot Product Isotopic dot product value used to evaluate isotopic dot product scoring.

Mass Accuracy Mass accuracy value used to evaluate mass accuracy scoring for the nth mass trace in t h e
mass trace settings list.
Mass Accuracy Mass The actual mass that is derived from the data and used in the Mass Accu ra c y co mposi t e
scoring
Molecular Mass Molecular mass of the component entered in the component table.

Name Peptide name.

Number of Charge States (Peptide Variable) Number of charge states of the peptide.

Number of Isotopes in Observed Isotopic Number of isotopes in the observed isotopic distribution.
Distribution

Number of Isotopes in Theoretical I so t op ic Number of isotopes in the theoretical isotopic distribution.

Distribution
Observed Isotopic Distribution Observed isotopic distribution.

Peak Apex Alignment Standard deviation between confirming peak apexes.

Retention Time Nominal retention time defined in the component table.

Theoretical Isotopic Distribution Theoretical isotopic distribution.

Window/(Component) Identification Window settings defined in the component table.

7.36 Isotope
The Isotope category is accessed by using the Isotope(n) variable of the Peptide category w here n refers to the isotope
number.

Variable Description
Auto Filter Text definition of the scan filter that was used to select a m ass sp e c t ru m a t a sp e c ific
retention time.
Collision Energy Activation energy of the first precursor of the MS confirming peak, if a precursor i s d e f in ed
by the filter.
End Time Ending retention time of the MS extraction
Extraction Time MS extraction time value, i.e. the retention time at which the apex of the peak is expected.

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Chromeleon 7

Variable Description
Extraction Window Settings Period of time which is subtracted from and added after the apex time at which the p eak i s
expected to create the retention time range.
Ion Coelution Ion coelution value of the peak ratio.

Mass Ranges List of the mass ranges used for the extraction of ion chromatograms.
Number of Smoothing Points Data points used for the selected smoothing algorithm to reduce noise.

Precursor Mass Mass of the first precursor of the MS confirming peak, if a precursor is defined by the filter.
Ratio Window Specified window width value (%) of the peak ratio assigned to the component.

Ratio Window Type Selected window type of the peak ratio assigned to the component: Absolute or Relative.

Smoothing Algorithm Name of the smoothing algorithm used to reduce noise.

Start Time Start retention time of the MS extraction.

Target Ratio Value of the peak target ratio assigned to the component.

7.37 Non-Targeted MS Processing (SIEVE)

Non-Targeted MS Processing category variables may only be used in the Summary Table of the Report Designer category
or Interactive Results in the Data Processing category.

Variable Description
Algorithm Algorithm used for non-targeted MS processing

Alignment Bypass Whether the alignment step is bypassed or not

Alignment Min Intensity Minimum signal intensity for alignment algorithm to take into consideration

Correlation Bin Width Width, in Daltons, of MS segment to correlate reference TIC to unknown TIC data point
Description Text description of non-targeted MS processing experiment. Does not affect results

Frame Selects and creates the Frame category (see section 7.38) based on frame ID

m/z Max The start of the m/z range in which the algorithm is permitted to create a frame.
m/z Min The end of the m/z range in which the algorithm is permitted to create a frame

m/z Width The width (in ppm) of the frame created for signal detection

Max Threads Maximum number of logical CPU cores which the algorithm is allowed to run on
Maximum Frames Maximum number of frames that the algorithm is allowed to detect before stopping.
Name Name of the non-targeted MS processing experiment. Does not affect results
Peak Intensity Threshold Minimum signal intensity required to be observed for algorithm to define a frame as valid

Peak Threshold Pct The percent of the reference peak used for filtering frames

Peak Threshold Peak Type The source of the rreference peak used for filtering frames (TIC, BPC, or N/ A if n ot a ut o-
computed)
Peak Threshold Type How the threshold level is computed (fixed or auto-computed)

Reference Index Injection number of reference when reference mode is set to Relative
Reference Mode Mode in which reference injection is defined – ‘Relative’ if based on an in ject ion n u mbe r,
‘Fixed’ if based on explicit injection inside or outside of sequence
Reference URI Path to reference injection if reference mode is set to Fixed.

Result Status Result of non-targeted peak detection after

RT Alignment Limits Maximum allowed retention time transformation of unknown TIC datapoint when aligning t o
reference TIC
Scan Filters MS scan filters used for non-targeted MS processing
Tile Increment Number of scans by which the tile size is incremented

Tile Maximum Maximum tile size

Tile Size Initial size (in number of scans) of a tile that correlates base peak a l ign men t a cro ss t h e
reference and unknown injections

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Variable Description
Tile Threshold Correlation threshold at which the tile size is incremented to the next larger size.
Time Start Start time of the range in which the algorithm is permitted to create a frame

Time Stop End time of the range in which the algorithm is permitted to create a frame

Time Width The width (in min) of the frame created for signal detection
Type Type of differential analysis carried out. Chromeleon only executes AvsB type experiments.

Version Version of algorithm used for non-targeted MS processing

7.38 Non-Targeted MS Processing (BioPharma Finder)

Non-Targeted MS Processing category variables may only be used in the Summary Table of the Report Designer
category or Interactive Results in the Data Processing category.

Variable Sub-Variable Description

Component Average experimental (observed) mass of the nth result component from the
Mass Exp
Results target injection.
Charge State Charge state of the nth result component from the target injection.

Component Number Component number of the nth result component.

Control Avg Mass Exp Average experimental (observed) mass of the nth result component from the
control injection.
Control Charge State Charge state of the nth result component from the control injection.
Control M/Z Mass-to-charge ratio of the nth result component from the control injection.

Experimental (observed) monoisotopic mass of the nth result component from

Control Mono Mass Exp
the control injection.
Control MS Area MS area of the nth result component from the control injection.

Control RT (min) Retention time of the peak corresponding to the nth result component from the
control injection.

Retention time of the start of the peak corresponding to the nth result
Control RT Start (min)
component from the control injection.
Retention time of the end of the peak corresponding tonth result component
Control RT Stop (min)
from the control injection.
M/Z Mass-to-charge ratio of the nth result component from the target injection.

Max MS Area Maximum MS area of the nth result component from the target injection.

Experimental (observed) monoisotopic mass of the nth result component from

Mono Mass Exp
the target injection.
MS area of the nth result component from the target injection. It displays the
MS Area
area for the component, specific to each individual raw data file.

MS Area Ratio MS ratio of the target vs. control injection of the nth result component from the
target injection.

Retention time of the peak corresponding to the nth result component from the
RT (min) target injection. It displays the retention time for the component from the first
raw data file.

Retention time of the start of the peak corresponding to the nth result
RT Start (min) component from the target injection. It displays the retention time for the
component from the first raw data file.

Retention time of the end of the peak corresponding to the nth result
RT Stop (min)
component from the target injection.
Results Status N/A Reports the outcome of applying the filtering results criterion on the list of
Results Components.

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Chromeleon 7

7.39 Intact Protein Deconvolution

Intact Protein Deconvolution category variables may be used as standalone parameters or in the Summary Table of the
Report Designer category or Interactive Results in the Data Processing category.

Variable Sub-Variable Description

Chromatogram Chromatogram Type Type of plot displayed in the chromatogram pane.
Parameters
End Scan Number End scan number of the chromatographic data from which the source mass spectrum
will be extracted.
End Time Ending time of the chromatographic data from which the source mass spectru m wi ll
be extracted.
Is High Sensitivity Whether the chromatographic peak detector performs a seco n d p ass a t a h i g her
sensitivity.
Mass Range High Highest m/z value of the mass range used as input to the deconvolution.

Mass Range Low Lowest m/z value of the mass range used as input to the deconvolution.
Range Display Type Criterion used to determine the range of chromatographic data from which the source
mass spectrum will be extracted.
Relative Intensity Threshold Intensity threshold for peaks in the chromatogram.

Restricted Time Whether the entire chromatogram is displayed in the chromatogram pane.

Start Scan Number Beginning scan number of the chromatographic data from which t h e so u rc e ma ss
spectrum will be extracted.
Start Time Beginning time of the chromatographic data from which the source mass sp e ct ru m
will be extracted.

Multiconsensus Merge Tolerance Mass tolerance that components from individual files must satisfy to be merged into a
Merge Multiconsensus component.
Parameters
Merge Tolerance Type Unit of measure for the Merge Tolerance report variable.

Minimum Required Occurrences Minimum number of single raw data files that must be included in a Multic on se nsu s
component for it to be considered valid.
RT Tolerance Maximum separation in retention time that components from individu al re su lt f ile s
must satisfy to be merged into a Multiconsensus component.
ReSpect Adduct Mass Custom adduct mass of a component.
Parameters
Charge Center Number of adduct ions used during electrospray (ESI) processing.
Charge High Maximum charge state to be deconvolved.

Charge Low Minimum charge state to be deconvolved.

Choice of Peak Model Index Appropriate peak model for the data.

Do Use Isotopic Profiles Whether isotopic profiles are used to identify components.

High Number Adjacent Charges Maximum number of charge state peaks that must appear in a row for components of
the minimum output mass and maximum output mass.
Intensity Threshold Scale Intensity threshold scale required to display peaks in a chromatogram.
Is Calculate XIC Whether an extracted ion chromatogram (XIC) is calculated for each detected
component from a range of deconvoluted spectra.
Is PPM Tolerance Unit of measure for the mass difference of the same ion in different scans.

Low Number Adjacent Charges Minimum number of charge state peaks that must appear in a row for components of
the minimum and maximum output masses.
Mass Tolerance Global allowable error for the m/z values of peaks in a charge state se rie s a s t h e y
appear in the input spectrum.
Min Peak Significance Numerical value (in standard deviations) that determines whether a peak is
considered legitimate and retained.
Negative Charge Whether the data was acquired in negative charge mode durin g t h e e lect rosp ra y
(ESI) process

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Variable Sub-Variable Description

Noise Compensation Whether the ReSpect algorithm improves signal detection wh ere t he n oise l evel
varies across the data.
Noise Rejection Degree of confidence that a peak is plausible.

Number of Peak Models Number of peak models generated to determine the width that a peak must h a ve t o
be associated with a compound.
Output Mass High Maximum value of the required mass range.
Output Mass Limit High Ending value of the output mass range.

Output Mass Limit Low Starting value of the output mass range.

Output Mass Low Minimum value of the required mass range.

Peak Model Width Scale Number of regions used to determine the peak wi d t h re qu ired f or a p e ak t o b e
associated with a compound
Quality Score Threshold Minimum protein quality score required for a component to be considered valid.

Relative Abundance Threshold Height of the smaller overlapping isotopic cluster used to resolve overlapping isotopic
clusters.
Resolution at 400 m/z Resolution of the source spectrum at an m/z value of 400.

Target Peak Mass Expected target mass to use when calculating the peak model.
Target Peak Shape Left Numerical value for the left side of the peak (determines the peak sharpness required
for a peak to be associated with a compound).
Target Peak Shape Right Numerical value for the right side of the peak (determines the peak sharpness
required for a peak to be associated with a compound).

Result Apex RT CV (coefficient of variation) percentage of the apex retention time of a component.
Component
Apex RT %CV Apex retention time of a component.
Charge State Count Number of charge states of a component.

Component ID Numerical position of a component in the component list.

Condition Condition of a component.

Delta Mass Delta mass of a component.

Detected Interval Count Number of detected intervals of a component in the injection results.
Drug Load Drug load of a component.

End Retention Time End retention time of the range of the chromatogram that you want to view.
Fractional Abundance Fractional abundance of a component.
High Charge State Range Maximum charge state to be deconvolved.

High Retention Time Maximum retention time of the range of the chromatogram that you want to view.

High Scan Range End scan of the range of the chromatogram that you want to view.
Intensity Sum of the intensities of the peaks for a charge state.

Intensity Percent CV CV (coefficient of variation) percentage of the intensity of a component.

Low Charge State Range Minimum charge state to be deconvolved.

Low Retention Time Minimum retention time of the range of the chromatogram that you want to view.

Low Scan Range Beginning scan of the range of the chromatogram that you want to view.
Mass Mass of an identified component.

Mass Percent CV CV (coefficient of variation) percentage of the mass of a component.

Mass Std. Dev. Standard deviation of delta masses for all the charge states of an identified
component, in Daltons.

Results obtained when matching the measured masses of components detect ed by

Matched Charges Chromeleon to the masses of target sequences specified by the use r. (O p ens t h e
Matched Charges report category.)
Matched Mass Error Error associated with the best target sequence that matches this component.

Modification of the target sequence that best matches a specific component with in a
Modification
given tolerance.

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Chromeleon 7

Variable Sub-Variable Description

Number of Files Observed Number of raw data files in which the component was detected.

Standard deviation of delta masses for all the charge states of an identified
PPM Std. Dev.
component, in parts per million.
Protein Name Name of the target sequence that matches this component within a given tolerance.

Ratio of the abundance of a specific peak to the abundance o f t h e p ea k wi t h t h e

Relative Abundance
highest abundance.
Score Quality score of a deconvolved component.

Score Percent CV CV (coefficient of variation) percentage of the score of a component.

Start Retention Time Starting retention time of the range of the chromatogram that you want to view.
Theoretical Mass Theoretical mass of a component.

Result The number of components in the deconvolution results.

Component
Count
Sliding Window Average Width RT Retention time (width) of a sliding window.
Parameters

Biggest Gap RT Maximum allowed separation in retention time between two successi ve i nd ividua l
members of a merged component.

Merge Tolerance Numerical value indicating how close in mass two components in successive sli din g
windows must be to qualify as a single component.
Merge Tolerance Type Unit of measure for the Merge Tolerance report variable.

Minimum number of sliding window intervals that a component must appear in t o b e

Min Cycles
considered valid.
Offset Percent Offset between successive sliding windows as a percentage value.
Offset Scans Offset between successive sliding windows as a number of scans.

Offset Type Mode used to specify the offset between successive sliding windows.
Start Time Beginning of the retention time range that a single deconvolution applies to.

Stop Time End of the retention time range that a single deconvolution applies to.

Xtract Adduct Mass Custom adduct mass of a component.

Parameters

Charge Carrier Type Type of adduct ion used during electrospray (ESI) processing.

Charge Range High Maximum charge state to be deconvolved.

Charge Range Low Minimum charge state to be deconvolved.

Tolerance toward errors when the spectrum intensity is much higher than e xp ec t ed
Consider Overlaps
for the theoretical isotopic cluster.
Custom Distribution Table Type of isotope table used.

Allowable margin of error when calculating the ratio of the most abundant isoto pe t o
Expected Intensity Error
the next isotope higher in mass in the isotope series.

Quality of a match between a measured isotope pattern and an averaging distribution

Fit Factor
of the same mass.
Whether an extracted ion chromatogram (XIC) is calculated for each detected
Is Calculate XIC
component from a range of deconvoluted spectra.

Is Negative Ion Whether data was acquired in negative charge mode during the electrosp ra y (E S I)
process.
Min Intensity Minimum intensity threshold used to filter out possible background noise.
Minimum Charge States Minimum number of charge states required to produce a component.

Output Mass Limit High Ending value of the output mass range.

Output Mass Limit Low Starting value of the output mass range.

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7.40 Frame
The Frame category is accessed by using the Frame(n) variable of the Non-Targeted MS category w here n refers to the
Frame ID or from the Report Formula Editor of the Frame Table.

Variable Description
Avg_intensity The average intensity of the peaks in the selected frame of the sample injection

Base Component Component ID of the pattern recognition cluster root element. If the PR Element variable i s
less or greater than 0, the base component will return 0
Charge The expected charge state based on rudimentary observed isotopic mass distribution. This
does not take into account isotopic ratios.
Component ID Unique ID number of a component cluster after pattern recognition clustering

Component Score Returns the component score.

Frame ID Unique ID of the frame independent of any pattern recognition clustering

Mass Observed m/z for frame

Molecular Weight Molecular weight of frame adjusted for m/z ratio, charge state, and adduct
PR Element ID of a frame within a component cluster

PR Root Frame ID of root element within a component cluster

PR Size Number of elements within a component cluster

Ratio Unknown to reference ratio of AUC of signal – not to be confused with AUC of a peak

Reference_avg_intensity The average intensity of the peaks in the selected frame of the reference injection

Retention Time Retention time of the frame

Weighted Mass Weighted mass of the specified frame

7.41 Report Template

Variable Description
Creation Date & Time Format date/time as text The report template creation date and time ca n h a ve t he f ollo wing
formats:
Default date/time format
ISO 8601 date/time
Localized long date
Localized short date
Time offset only
Time with seconds and time offset
Time with time offset

Time in universal coordinated The time in coordinated universal time standard format.
time
Time offset in hours The time offset from your local time based on the Windows settin gs o f
your local computer (including any daylight savings time a dju st me nts
that apply)

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Chromeleon 7

Variable Description
Time using local time zone The conversion of date and time to your local time zone with the
following formats:
• Format date/time as text

• Default date/time format

• ISO 8601 date/time
• Localized long date
• Localized short date
• Time offset only

• Time w ith seconds and time offset

• Time w ith time offset
• Time offset in hours

Creation Operator Full Name Full user name of the user who created the report template.
Job Title Job title of the user who created the report template.

User Name User id of the user who created the report template.

Current Sheet Name The current sheet name

Current Sheet Number The current sheet number

Data Vault Name of data vault where the report template is stored.
Directory Directory where the report template is stored.

Last Update Date & Time Format date/time as text The date and time of when the last update of a re port t e mpla te wa s
performed can have the following formats:
Default date/time format
ISO 8601 date/time
Localized long date
Localized short date
Time offset only
Time with seconds and time offset
Time with time offset

Time in universal coordinated The time in coordinated universal time standard format.
time
Time offset in hours The time offset from your local time based on the Windows settin gs o f
your local computer (including any daylight savings time a dju st me nts
that apply)
Time using local time zone The conversion of date and time to your local time zone with the
following formats:
• Format date/time as text
• Default date/time format

• ISO 8601 date/time

• Localized long date
• Localized short date
• Time offset only
• Time w ith seconds and time offset

• Time w ith time offset

• Time offset in hours

Last Update Operator Full Name Full name of the user who last saved changes to the report template.
Job Title Job title of the user who last saved changes to the report template.

User Name User id of the user who last saved changes to the report template.
Name Name of the report template.

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Variable Description
Number of Sheets Number of sheets of the report template.
Version Comment Comment for this version.

Computer Name Name of the computer on which this version was created.

Data Vault Name of the data vault.

Date & Time Date and time when the version was created. The same sub funct ion s
as for other date & time variables are available
Format date/time as text
Time in universal coordinated time
Time offset in hours
Time using local time zone
Format date/time as text
Default date/time format
ISO 8601 date/time
Localized long date
Localized short date
Time offset only
Time with seconds and time offset
Time with time offset
Time offset in hours
Number Version number.
Operator Information about the user who created the ve rsi on. Th e sa m e su b
functions as for other operator variables are available. These are
Full Name, Job Title and User Name.

7.42 eWorkflow
These variables are only available to the eWorkflow editor.

Variable Description
Description Description of the eWorkflow.

Instrument Used Name of the instrument used by the eWorkflow.

Name Name of the eWorkflow.

State eWorkflow state.

Type eWorkflow Type.

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Chromeleon 7

8 Electronic Signatures
Chromeleon supports the use of electronic signatures. The follow ing signature levels are available:
• Submit
• Review

• Approve
Electronic signatures can be enabled and disabled for each sequence separately (see section 4.3.2.4). Electronic signatures
are automatically enabled for new sequences created w ith the Sequence Wizard. If new sequences are created w ith the
eWorkflow Wizard, the eWorkflow defines whether electronic signatures are enabled or not (see section 3.4.1.2).
On applying a signature, the follow ing details are automatically recorded:

• User Name
• Full Name
• User Job Title
• Date and Time Signature w as executed
• Signature Comment

The Electronic Signature process includes the creation of an electronic report (see section 5.9). The procedures for applying
electronic signatures are as follow s:

8.1 Submit Signature

In the Console:
Select sequence to be signed in Data category.
Click the Submit button on the Sequence Control Bar.
–OR–
If the sequence is new or incomplete, click the dow n arrow next to the Submit button on the Sequence Control Bar and clic k
Submit.
If the electronic report does not yet exist, the Chromatography Studio w indow opens. Create the electronic report, and then
submit the sequence and report in the Studio.
In the Chromatography Studio:
In the Electronic Report category, on the Home ribbon, in the Signature group, click Submit button.
Signature dialog:
When the Submit Signature dialog box opens, enter your User Name and Signature Passw ord.
(Optional) In the Comment box, add any comments that might be helpful. These comments w ill be displayed in the Console
on the Signature tab page in the sequence Properties dialog box and on the Signature State page in the Studio.
Click OK.
The electronic report changes to an electronic signature. After a sequence has been electronically signed, the sequence
cannot be modified unless the signatures are first removed. This protects sequence reports that have been accepted as
correct by "freezing" the current state of the results. In addition, the icon for the next signature step (if defined) is enabled.
When the sequence is signed a unique checksum is created and saved inside the sequence. Changes cannot be made to
the sequence w ithout undoing the signature.

8.2 Review Signature

In the Console:
Select sequence to be signed in Data category.
Click the dow n arrow next to the Review button on the Sequence Control Bar and click Review .
In the Chromatography Studio:

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In the Electronic Report category, on the Home ribbon, in the Signature group, click Review button.
Signature dialog:
When the Submit Signature dialog box opens, enter your User Name and Signature Passw ord.
(Optional) In the Comment box, add any comments that might be helpful. These comments w ill be displayed in the Console
on the Signature tab page in the sequence Properties dialog box and on the Signature State page in the Studio.
Click OK.

8.3 Approve Signature

In the Console:
Select sequence to be signed in Data category.
Click the dow n arrow next to the Approve button on the Sequence Control Bar and click Approve.
In the Chromatography Studio:
In the Electronic Report category, on the Home ribbon, in the Signature group, click Approve button.
Signature dialog:
When the Submit Signature dialog box opens, enter your User Name and Signature Passw ord.
(Optional) In the Comment box, add any comments that might be helpful. These comments w ill be displayed in the Console
on the Signature tab page in the sequence Properties dialog box and on the Signature State page in the Studio.
Click OK.

8.4 Remove Signature

In the Console:
Select sequence in Data category.
Click the dow n arrow next to the Signed button on the Sequence Control Bar and click Remove Submit.
In the Chromatography Studio:
In the Electronic Report category, on the Home ribbon, in the Signature group, click Remove button.
Signature dialog:
When the Submit Signature dialog box opens, enter your User Name and Signature Passw ord.
Optional) In the Comment box, add any comments that might be helpful. These comments w ill be displayed in the Console
on the Signature tab page in the sequence Properties dialog box and on the Signature State page in the Studio.
Click OK.

8.5 Verify Report

After a report has been signed, it can be checked at any time later to verify that the data is still free of unauthorized
manipulations.
In the Chromatography Studio, click the Electronic Report category bar and open an electronic report.
On the Home ribbon, in the Signature group, click Verify. You can monitor the report data being verified in the progress
w indow. When the progress bar has reached 100%, the verification process is completed.

8.6 Report Signed results

In the Chromatography Studio, click the Electronic Report category bar and open an electronic report.
On the Home ribbon, in the Print & Export group, you can either print or export to pdf the signed electronic report.

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9 Chromeleon Services Manager

The Chromeleon Services Manager (Figure 63) provides details on the status of the Chromeleon services. It also provides
access to the Instrument Controller Service and the Chromeleon Instrument Configuration Manager.

Figure 63: Chromeleon Services Manager

9.1 Instrument Controller Service

The follow ing options are available for the instrument controller service:

Function Description
Start Starts the Chromeleon instrument controller.
Stop Stops the Chromeleon instrument controller.

Start service on system start Starts the Chromeleon instrument controller automatically at computer startup.

Configure instruments Launches the Instrument Configuration Manager (see section 10).
Manage Services Expands the dialog to show controls for starting a nd st o p ping Ch rome leo n
series.

9.1.1 Instrument Controller Service – Manage Services

When the Manage Services button is clicked, the dialog expands to show a list of the Chromeleon services (See Figure 64) ,
along w ith their current state (started/stopped). Services may be stopped, started or restarted by selecting the services of
interest and using the buttons provided.
Note that Local Admin privileges are required to change the state of te services.

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Figure 64: Chromeleon Services Manager - Expnded

9.2 Other Chromeleon services

The icon and text indicate the status of the other Chromeleon services. If any of the local or remote services become
unavailable, ‘Show Details’ becomes active. In order to manage other Chromeleon services or perform administrative tasks
open the Administration Console (section 11).

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10 Instrument Configuration Manager

The instrument configuration manager is the Chromeleon program that is used to connect instruments to the instrument
server.
New instruments are created here, and individual instrument modules are assigned. For a list of supported instruments
please refer to the “List of Supported Instruments” document. Figure 65 show s a typical instrument configuration.

Figure 65: Instrument Configuration Manager

10.1 Properties
The follow ing instrument controller properties can be set:

10.1.1Access Control
Function Description
Add User or Group Allows specific users or groups to be allowed access to a Data Vault.

Roles Allows specific roles to be assigned to users or groups when working with ob ject s
within the Data Vault. These roles may differ from the login role of the user.

10.1.2Queue Settings
Function Description
Automatically upload finished remote sequences Allows automatic upload of sequences to remote location when finished.

Enforce Save Electronic Report Enforces that, for all Sequences created on this instrument, the Save E lect ronic
Report (after acquiring) option is selected and cannot be changed by a user
Enforce Print report Enforces that, for all Sequences created on this instrument, the Print report (a f te r
acquiring) option is selected and cannot be changed by a user
Enforce Export report Enforces that, for all Sequences created on this instrument, the Export report (after
acquiring) option is selected and cannot be changed by a user
Enforce Print/Export report Enforces when, for all Sequences created on this instrument, an y re p ort wi ll b e
generated. Options are:
After whole sequence (default)
After each injection

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Note: Instead of using access control on the Chromeleon instrument controller, it is possible to define access control for
each instrument on the instrument controller.

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11 Administration Console
The Chromeleon Administration Console (Figure 66) is a central access point for administrative tasks. In the Chromeleon
Administration Console, you can:
• manage users in the User Manager
• manage licenses in the License Manager

• plan and organize tasks w ith the Scheduler

• define global policies
• configure the discovery service and monitor other Chromeleon services
• manage data vaults
• manage Organizational Units

Figure 66: Administration Console

11.1 License Manager

This program provides licenses for all PCs running Chromeleon. There are 2 main license types – Instrument Controller and
Client. The License Manager can be used to manage the licenses. In the Chromeleon License Manager, you can
• assign client licenses to users, client stations, or instrument controllers
• assign instrument licenses to instrument controllers
• update your license

• check how many licenses are currently in use and how many are available

11.1.1Client Licenses
The follow ing license options can be granted to Clients:

License Option Description

Data Client License for data reprocessing on a network PC without instrument control. Th e
license supports multitasking and reports from the followin g p art ia l me th ods:
single- and multiple-point calibration with various fit models, integration, ratio test,
user programs, etc.

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License Option Description

Instrument Operation Enables accessing a local or remote Instrument Contro ller f o r o pe rat ing t h e
Instruments connected to the Controller.
Compliance Tools This license supports additional compliance features:
• Data Audit Trails and Versioning
• User management
Electronic Signatures
Report Designer Pro This license extends the report and calculation features. In addition, it su p p ort s
calculations using formulas and the functions listed in sections 5.8.26 and chart s
(section 5.8.7).
Virtual Column Basic This license enables virtual column for isocratic analysis.

Virtual Column Complete This license enables virtual column including gradients.
Standard Instrument Integration Dedicated license for Standard instrument integration (SII).

SDK Developer Enables execution of un certified in-process SDK applications

SDK Runtime Enables execution of certified signed in-process SDK applications

Non-targeted MS Data Processing This license enables access to the Non-targeted MS Data Processing ca te go ry
of the Studio
Intact Protein Deconvolution This license enables access to the Intact Protein Deconvolution category o f t h e
Studio

11.1.2Instrument Controller Licenses

The follow ing license options can be granted to Instrument Controllers:

License Option Description

Instrument Controller The Instrument Controller license (without additional features) allows control and
signal acquisition without spectra from 6 Class 1instruments, of which 4 ca n b e
fully controlled Dionex instruments. The number of Channels is not limited.
Instrument Class 1 The number of Class 1 instruments (= uncontrolled or Thermo Scientific
instruments) that can be connected to the Instrument Controller (up to a
maximum of 6). All instrument controllers are provided with this license.
Instrument Class 2 The number of Class 2 instruments (= third-party GCs) that can be connected t o
the Instrument Controller (up to a maximum of 6).
Instrument Class 3 The number of Class 3 instruments (=third-party LCs) that can be connect ed t o
the Instrument Controller (up to a maximum of 2).
3D Data Acquisition Additional license to acquire digital 3D data from 3D-capable detectors.

SQ / QqQ GC-MS Data Acquisition Enables recording of GC, single quadrupole and triple quadrupole MS data
LC-MS Data Acquisition Enables recording of LC-MS data for currently supported instruments.

IC Control SE A special low-cost control license for operating a single low-cost ion
chromatograph.
Fraction Collection Enables the fraction collection support.

The “Installation Mode” can be enabled or disabled. If enabled, administrators do not need to configure fixed license
features for the available instrument controllers. The instrument controller license request w ill be automatically assigned
w ithout user interaction.

11.1.3License Overview
The License Overview provides details of how many Client and Instrument Controller licenses are currently in use and how
many are available for the entire Chromeleon Domain.

11.1.3.1 Per-Organizational Unit License Overview

Below the License Overview item, license allocations for each Organizational Unit can be view ed.

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Chromeleon 7

Figure 67: Per-Organizational Unit License Overview

The <Global> option details the licenses assigned to the <Global> Organizational Unit. These licenses can be used by any
user, instrument or client in the entire Chromeleon Domain.
The <Org Unit Name> option(s) detail the licenses assigned to each Organizational Unit. These licenses are only available
for use by users, instrument, or clients w hich are members of this Organizational Unit.

11.1.4Manage Licences
The Manage Licenses option opens the Manage Licenses dialog box w here you can View , Add, Activate and Remove
license codes.

Figure 68: Manage Licenses dialog

The follow ing options are available:

Function Sub function Description

Add N/A Opens the License Initialization Codes dialog (see 11.1.4.1.

Remove YES / NO Removes the selected license code from the system.
Activate N/A Opens the License Activation dialog (see 11.1.4.2)

Deactivate N/A Opens the License Deactivation dialog (see 11.1.4.3)

Details N/A Opens the Details dialog (see 11.1.4.4)

Assign Org Unit N/A Opens the Assign Organizational Unit dialog (see 11.1.4.5)

Close N/A Closes the Manage Licenses dialog

11.1.4.1 License Initialization Codes dialog

Figure 69: License Initialization Codes dialog box

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This dialog allow s a new License Initialization Code (LIC) to be added. Codes are checked for validity w hen the Add button
is pressed.

11.1.4.2 License Activation Dialog

Figure 70: License Activation dialog

The follow ing options are available

Function Sub function Description

Web Activation N/A Contacts the Chromeleon activation website and automatically activates
the license (if it is valid and is not already activated for another system)
Manual Activation <URL> Follow the URL to open the Chromeleon activation website for m an ua l
activation of a license
<QR Code> Use the QR code on a suitable device to open the activation website for
manual activation of a license
LIC N/A Read-only display of the currently selected LIC(s)
LRC N/A Read-only display of the License Request Code (LRC) for t he cu rren t
LIC(s)
LAC N/A Text field for typing or pasting a License Activation Code (LAC) from the
Chromeleon activation website

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Chromeleon 7

11.1.4.3 License Deactivation dialog

Figure 71: License Deactivation dialog

The follow ing options are available

Function Sub function Description

Web Deactivation N/A Contacts the Chromeleon activation website and automatically
deactivates the license (if it is valid and is n o t a lre ady a c t iva te d f o r
another system)
Manual Deactivation YES / NO Instantly removes LIC from Chromeleon and creates a License
Deactivation Code which must be manually entered in the Chrome leo n
activation website if this LIC is going to be used again o n t h is o r a n y
other Chromeleon system.

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11.1.4.4 Details dialog

Figure 72: License Code Details dialog

Displays the follow ing read-only details of the currently selected License Initialization Code (LIC):

Function Description
Code License Initialization Code (LIC
Serial Number Serial number of the LIC

Status Status of the LIC (Activated, Pending, Expired)

Version Version of Chromeleon to which this LIC is applicable

Date added Date the LIC was added to Chromeleon

Date activated Date the LIC was activated

Date expires Date the LIC will expire (only applies to time-based evaluation licenses)
License details List of features and number of entitlements granted by this LIC

11.1.4.5 Assign Organizational Unit dialog

Figure 73: Assign Organizational Unit dialog

Enables license code (LIC) to be assigned to an Organizational Unit. The license entitlements provided by the code may
only be used by the assigned Organizational Unit.
The follow ing options are available:

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Chromeleon 7

Function Sub function Description

Organisation Unit N/A Dropdown list of all available Organizational Units to which the lice nse
can be assigned.
Save N/A Saves changes and closes the dialog

Cancel N/A Closes the dialog without saving changes

11.2 Scheduler
The Chromeleon 7 Scheduler is a service that handles all remote data processing requests in Chromeleon.

11.2.1Scheduler (Chromeleon Domain)

11.2.1.1 Task List

Function Description
Enabled The user can disable or enable tasks. Tasks are only carried out if enabled.
New tasks can be created by clicking ‘Create new task’ button. Listed tasks can be edited by double click.

11.2.1.2 Audit Trail

Function Description
Show audit trail records from … to … The audit trail lists scheduler events from the defined time period.

11.2.1.3 Service Account

Function Sub function Description

Local System N/A The Local System account is a predefined local accoun t o f
the operating system.
User Account Domain Domain of user account to be used by scheduler service.
User User name to be used by scheduler service.

Password This is used to set the logon password for defined user.
Retype Password Confirmation of logon password for user.
The service account settings can only be changed after stopping the scheduler service.

11.2.1.4 Service Log

Function Description
Show audit trail records from … to … The service log lists scheduler service events from the defined time period.

11.2.1.5 About

Function Description
Delete entries older than … month(s) Change retention period setting of Scheduler Audit Trail

11.2.1.6 Scheduler Task

General

Function Sub function Description

Name N/A Name of the task.

Owner N/A Displays the name of the owner of the task.

Description N/A (Optional) Free text entry to provide a more detailed

description of the tasks.
Enabled N/A Activates the task.

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Function Sub function Description

Specify additional settings that affe ct If the task fails, restart every: Specifies the time interval at which the Scheduler ret rie s t o
the behavior of the task start a task.
Attempt restart up to ... Specifies the number of attempts allowed to start a task. T o
allow an unlimited (infinite) number of attempts to st a rt t h e
task, select or type –1 in the times box.

Schedule
This page configures how often a task is scheduled.

Function Sub function Description

Created N/A Date and time task were created.
Perform this task N/A Options to execute task; Manually, Hourly, Daily, Weekly, o r
Monthly.
Time Settings None Specify whether the task is started immediately or at a
specified time.
Every X hour(s) Specify whether the task is executed every h our o r e ve ry
number of hours.
At a specified time every day. At … Specify time of day that task will be executed once a day.

At a specified day of the we ek. … Specify when the task is executed once a week at a
at …. specified day and time.
At a specified day of the month. On Specify when the task is executed once a month at a
… at …. specified day and time.
Expire N/A Specify a date after which the task will end.

Items
This page determines a predefined query that generates a result list of the source sequences to be copied or moved.

Function Description
None Option if you do not want to transfer a sequence

Chromeleon 7 Defines the location of an existing injection query. Path of the predefined in ject ion
query can be typed into the All sequences returned by query b ox o r [ . .. ] c an b e
clicked to navigate to the required query.
Chromeleon 6 Copies existing sequences from a Chromeleon 6 data source. Chromeleon 6 Use r
ID and Password if required are entered into the given input b oxes. T e st b ut t on
checks whether login succeeded.
Path of the Chromeleon 6 query file can be typed into the All sequences re t u rne d
by query box or [...] can be clicked to navigate to the required query.

Action
This page view s and manages the actions performed w ith the current task.

Function Description
New Creates a new action item. The following actions can be created: copying a
sequence, moving a sequence and running an external program.
Remove Removes a selected action item from the list.

Destination Defines settings for the destination folder (Copy and Move tasks only):

Data vault: Select the destination data vault.

Folder formula: Type a name or formula in the box to determine t h e n ame o f t h e

destination folder or alternatively click {...} to browse. Free text can also be typed t o
determine a folder name.

If sequence in the destination folder already exists: Specifies the b eh avior o f t h e

scheduler if a sequence with the same name already exists in the destination folder.
Options; Do not copy and Overwrite.

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Function Description
Select external program to be executed Defines settings for external programs: Program/script, Add arguments (opt ion al),
Wait until external program terminates, Wait up to ... seconds and Do not wa it f o r
external program to terminate.

11.3 User Database

The user database manages all Chromeleon user security functions such as user id and passw ords, privilege and access
levels and electronic signature settings.

11.3.1Toolbar
The tool bar has four buttons; The save policies button is enabled, if the policies have changed. The report button creates a
printable HTML file for the currently selected OrgUnit. The Audit Trail show s the User Management Audit Trail. The help
button show s the online help for the currently selected policy.

11.3.2User Database Policies

All global security policies are defined in this part of the user database (for example minimum passw ord length).

11.3.2.1 Client Inactivity

Function Description
Lock any client station that waits for Select this option to automatically lock the Chromeleon client if there has b e e n n o
user input (for example, the mouse is not used, and no keys are pressed)
Minutes without receiving user input Set a specified time of inactivity before client automatically locks.

Close the Chromeleon Console and S t ud io o n a ny Select this option to automatically close the Chromeleon client if there has been n o
client that waits for user input (for example, the mouse is not used, and no keys are pressed)
Note that if there are unsaved changes then the client will not be closed.
Minutes without receiving user input Set a specified time of inactivity before client automatically locks.

11.3.2.2 Logon User Name

Function Sub function Description

Logon User Name Blank Ensures that the user name field o f t he l og on win dow i s
always blank.
Most Recent User Inserts the user name of the most recent user in the use r i d
field of the logon window.
Windows User Name Inserts the Windows user id into the user name field o f t h e
logon window.
Force Windows User Name Inserts the Windows user id into the user name field o f t h e
logon window. This user id cannot be changed.

11.3.2.3 LDAP Logon

Function Description

Delegate password verification to the operating When activated the Chromeleon logon password verifications are delegated to t h e
system operating system. In the Domain/Domain controller enter the domain (s) t o wh ich
these settings shall apply.
Domain Controller Specify the domain or domain controller.

Allow silent logon with current windo ws u se r n a me When activated the Chromeleon logon is performed automatically with the Windows
and password credentials.
Exclude users from LDAP authentication Users excluded from LDAP authentication. Excluded users wi l l u se a se p a rat e
Chromeleon logon and signature password.

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11.3.2.4 Concurrent Logon

Function Description
Allow multiple Chromeleon Conso le lo gon s o f t h e If this function is deactivated users can logon only to a single Chromeleon Conso le
same user in different Windows session. session at every computer or windows session connected to the same Chromeleon
domain.

11.3.2.5 Password Character Sets

Function Sub function Description

Password Character Sets Enforce at least … of the followin g Set requirement for passwords to contain a defined numb er
character sets for new passwords of characters (ranging from 0 to 4) from categories;
Lower case letters (a…z)
Upper case letters (A…Z)
Number (0…9)
Other characters

11.3.2.6 M inimal Password Length

Function Description
Minimum password length Defines the minimum number of characters a user may u se f o r t he ir lo gin a nd
signature passwords.

11.3.2.7 Password Attempts

Function Sub function Description

Locking Account/Signature Lock user’s account or signature Allows locking the user’s account after t h e se t n u mbe r o f
permission, if corresponding trials entering the wrong password.
password is not entered correctly

Send email notification when a u se r Enable Checking this box will generate an email notification if a user
account is locked account is locked.
Mail recipient(s) Defines the email addresses (or Chromeleon usernames) t o
whom the notification should be sent
Send email notification when a u se r Enable Checking this box will generate an email notifi ca tio n i f t h e
signature password is locked signature password of a user account is locked.
Mail recipient(s) Defines the email addresses (or Chromeleon usernames) t o
whom the notification should be sent

11.3.2.8 Password History

Function Description

Number of recent passwords, that cannot be used Determines the number of unique recent passwords a user must use before an o ld
again password can be reused. It can be set between 0 and 20; if set to 0, then e nf orce
password history is disabled.

11.3.2.9 Electronic Signature

Function Description
Submitter and Reviewer must be different When activated the user who submits the signed sequence must be different f ro m
the user who reviews it.
Submitter and Approver must be different When activated the user who submits the signed sequence must be different f ro m
the user who approves it.
Reviewer and Approver must be different When activated the user who reviews the signed sequence must be differen t f ro m
the user who approves it.

Removing a signature requires the signature When enabled undoing a signature requires the user to enter a password.
password

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Function Description
A sequence will be ready for LIMS transfer When a sequence transitions Electronic Signature state, Chromeleon will inform an
external application (e.g. Thermo Scien tif ic S amp leMa nag er L I MS) t h a t t h e
sequence’s results are ready for transfer. Options are:
Never
When an electronic report is saved
When the sequence is submitted
When the sequence is reviewed
When the sequence is approved
* Requires appropriate external application add-in to be available t o Ch ro meleo n
client. In the case of SampleManager, this requires 12.1 SP1 or later.

11.3.2.10 Signature Programs

Function Sub function Description

Run external application on signature N/A An external application can be run for each signature acti on
event in Chromeleon (Submit, Review, Approve, Remove
Signature).
Program file A program file can be associated that will be executed by the
console, after all other actions of a signat ure a ct ion h ave
been successfully finished.
Parameter Parameters can also be defined that will be evaluated in t h e
context of the sequence. The parameters may contain report
variables associated with Sequence, Gene ral a nd G lob al
Functions categories. Section 7.X

11.3.2.11 Administrator Password Recovery

If a user w ith administrator privileges cannot logon to the Chromeleon AdminConsole any more (e.g. forgotten passw ord,
account is locked) there is a procedure so that users w ith Window s administrator credentials can still logon to the
AdminConsole. To get this done you have to be a user w ith Window s administrator privileges on the computer w here the
Chromeleon User Management Service is installed and running. The AdminConsole needs to be started w ith Window s
administrator credentials on this computer. After entering the w rong passw ord for the user account w hich couldn’t logon
anymore a <Passw ord Recovery> button appears on the Logon Dialog. Pressing this button, you have to enter the
passw ord for the Window s administrator user account once again and after that you are logged on to the AdminConsole
successfully. The Administrator Passw ord Recovery policy controls w hether this procedure is possible or not.
If Organizational Units are enabled (see 11.4.2 for details) this user database policy is only available for the so-called
<Global> OrgUnit.

Option Description
Enable Allows to apply the password recovery procedure.

Disable Prevent the usage of the password recovery procedure.

Disable permanently Prevents the usage of the password recovery procedure permanently . O nc e t h is
option is saved there is no way to enable it again.

11.3.2.12 User Account Restrictions

If Organizational Units (OrgUnits) are enabled (see 11.4.2 for details) then these user database policies are only available
for the <Global> OrgUnit. All other OrgUnits must follow these policies.

Function Description
Allow delete user accounts Controls whether user accounts can be deleted at all.

Allow rename user accounts Controls whether user names can be changed. Changing the casing of user names
is always allowed.
Allow reuse user names Controls whether user names which are deleted or renamed can be reused again.

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11.3.3Chromeleon Users
An unlimited number of users each having an enforced unique ID can be created. How ever, there is a limitation relating to
the maximum netw ork message size (WCF quota). The limit depends on the length of user names, job titles, passw ord
history, etc. but approximately equates to 100000 users.

11.3.3.1 Toolbar
The tool bar has six buttons; The Create New User button opens a w izard that guides you through defining user properties
(section 11.3.4) of the new user account. The Delete User(s) button w ill remove one or more users that are selected in the
user list. The Retire User(s) button deactivates one or more selected users in the list and invalidates the passw ords (except
for users w ith LDAP authentication). The Reactivate User(s) button reverts one or more selected users in the list from the
retire state. The report button creates a printable HTML file of the list of users, including all user settings and memberships.
The help button show s the online help for the relevant section relating to managing users.

11.3.3.2 User List

The user list is a grid control that supports grouping and filtering. This grid control is read-only.
The follow ing features are supported:
• Copy of row s to the clipboard (as simple text).
• Double-click on a row opens the according object for editing. The selection in the tree jumps to the object, the editor
control opens at the right side.
• Data can be sorted by one or multiple columns.
• Data can be grouped by one or multiple columns.
• Data can be filtered by one or multiple columns.
• The columns can be dragged to new positions.
• The column layout is preserved (saved in the user profile).

11.3.4User Properties
All security settings specific to a user id are set in this area of the database e.g. login and signature passw ords , pas sw or d
expiry settings, etc. When creating a new user, an existing user’s properties as detailed in this section can be cloned w ith
the exception of their passw ords.

11.3.4.1 Toolbar
The toolbar has three buttons. The Save User button saves any change of the user properties. The Report button creates a
printable HTML file of the complete user database and the currently selected OrgUnit. The Reset Passw ord button opens a
dialog to reset the passw ord of the currently selected user.

11.3.4.2 General

Function Description
User Name User name for logon and signature purposes. Once assigned this cannot be
modified. It is not possible to create duplicate user ID’s.
Full Name Full printed user name is entered here

Job Title An optional user job title can be entered here

Organizational Unit Associate organizational unit that user belongs to

Email Address Defines an email address that can be used for notifications

11.3.4.3 Password

Function Description
Set the logon password This is used to set the logon password for a new user and is also used to re se t a
user’s password. Passwords can be automatically generated.
The password cannot be changed by the user Prevents the user from changing their current password.
The user must change logon password on next logon. Forces the user to change their logon password when the next logon to
Chromeleon.
The password must be periodically changed Forces the user to change their logon password x
Day(s)/Week(s)/Month(s)/Year(s) after they last changed their password.

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Function Description
Account Locked Locks the account.

11.3.4.4 Signature Password

Function Description
Set the signature password This is used to set the signature password for a new user and is also used to reset
a user’s signature password. Passwords can be automatically generated.
The password cannot be changed by the user Prevents the user from changing their current password.

The user must change the password on next Forces the user to change their signature password when performing t he ir n ext
signature. signature action.
The password must be periodically changed Forces the user to change their signature password x
Day(s)/Week(s)/Month(s)/Year(s) after they last changed their password.
Signature Locked Locks the signature and prevents it being used.

11.3.4.5 Access Groups

Show s the access groups that a user is assigned to. It is possible to assign/un-assign access groups to a user here.

11.3.4.6 Roles

Function Description
Default logon role Allows a default role to be preselected for every logon of a user, e ven if t he la st
logon was with a different role.
Select the Roles where the user will be a member Shows the roles that a user is assigned to. It is possible to assign/un-assign ro le s
to a user here.

11.3.4.7 M anage Users

Allow s to enable or disable detailed user administration rights. This page is only available for users w ith full administrator
rights in the user database.

Function Description
Allow all user management operations Allows to this user all user database administration rights.

Manage user database policies Controls whether this administrator user can change anything in the user database
policies
Manage access groups Controls whether this administrator user can create, delete or modify access
groups in the user database.
Manage roles Controls whether this administrator user can create, delete or modify ro le s i n t h e
user database, e.g. to enable a certain privilege in a role.
Create users Controls whether this administrator user can create users using the ‘Cre a te Ne w
User’ wizard.
Create users via clone Controls whether this administrator user can create users via cloning a n a lrea dy
existing one even though the ‘Create users’ option is disabled.
Cloneable Users … Defines the users this administrator user can select when creating a new use r vi a
the clone mode.
Modify users Controls whether this administrator user can change any property (e.g . Fu ll u se r
name, Title, etc…) of any user record in the user database. Assigning new acce ss
groups or roles is controlled via a further option.
Reset password of users Allows this administrator user to reset the password of any user in the user
database even though the ‘Modify users’ option is disabled.
Delete users Controls whether this administrator user can delete users. The Delete Users option
is only available if the corresponding user database policy option (Use r A cco u nt
Restrictions -> Allow delete user accounts) is enabled.
Assign access groups Controls whether this administrator user can assign access g ro u p s t o a ny u se r
record.
Assignable access groups … Defines those access groups which can be used by this administrator u se r wh en
he wants to assign access groups to any user record.

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Function Description
Assign roles Controls whether this administrator user can assign roles to any user record.
Assignable roles … Defines those roles which can be used by this administrator user when he wants to
assign roles to any user record.
Copy settings from … Copies settings of the Manage User page from another user record.

11.3.4.8 Profiles

Function Description
Name Functional area of Chromeleon (read-only) that has b e en st o red t o t h e u se r’s
profile.
Value Details of the change (read-only) that was made and stored to the user’s profile.

11.3.5Access Groups
An unlimited number of access groups can be created, and an unlimited number of users can be placed in each access
group. These groups can be assigned to Chromeleon Data Vaults (4.1) and folders (4.2), and also the Chromeleon
Instrument Controller and Instruments (9). Once assigned, only members of the groups w ill be able to access the objects.
Access groups are given a unique name and can also be given a description. One access group can be assigned to one
organizational unit, but must be uniquely identified across all organizational units that exist in the Chromeleon Domain.

11.3.5.1 Toolbar
The tool bar has four buttons; The Create New Access Group button opens a dialog to define Access Group name and
description. The Delete Access Group(s) button w ill remove one or more access groups that are selected in the access
group list. The report button creates a printable HTML file of the list of access groups, including all access group settings
and members. The help button show s the online help for the relevant section relating to managing users.

11.3.5.2 Access Group List

The access group list is a grid control that supports grouping and filtering. This grid control is read-only.
The follow ing features are supported:
• Copy of row s to the clipboard (as simple text).
• Double-click on a row , opens the according object for editing. The selection in the tree jumps to the object, the
editor control opens at the right side.
• Data can be sorted by one or multiple columns.

• Data can be grouped by one or multiple columns.

• Data can be filtered by one or multiple columns.
• The columns can be dragged to new positions.
• The column layout is preserved (saved in the user profile

11.3.6Roles
An unlimited number of roles can be created in Chromeleon and an unlimited number of users can be assigned to each role.
A user may be assigned to more than 1 role and each role can have different privilege settings (section 11.3.6.3).
One role can be assigned to one organizational unit, but must be uniquely identified across all organizational units that exist
in the Chromeleon Domain.

11.3.6.1 Toolbar
The tool bar has four buttons; The Create New Role button opens a dialog to define Role name, description and privileges.
The Delete Role(s) button w ill remove one or more roles that are selected in the roles list. The report button creates a
printable HTML file of the list of roles, including all role settings, privileges and members. The help button show s the online
help for the relevant section relating to managing users.

11.3.6.2 Roles List

The access group list is a grid control that supports grouping and filtering. This grid control is read-only.

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The follow ing features are supported:

• Copy of row s to the clipboard (as simple text).
• Double-click on a row , opens the according object for editing. The selection in the tree jumps to the object, the editor
control opens at the right side.
• Data can be sorted by one or multiple columns.
• Data can be grouped by one or multiple columns.
• Data can be filtered by one or multiple columns.
• The columns can be dragged to new positions.
• The column layout is preserved (saved in the user profile

11.3.6.3 General
The privileges that can be assigned to each role are as follow s:

Instrument Configuration

• Modify Instrument Controller Security Settings • Modify Instrument Configuration

• Modify Instrument Security Settings

ePanel
• Create ePanel • Add ePanel
• Delete ePanel • Export ePanel
• Design ePanel • Import ePanel

Instrument Method

• Create Instrument Method • Copy Instrument Method

• Delete Instrument Method • Move Instrument Method
• Modify Instrument Method • Rename Instrument Method
• Modify Instrument Method Script

Daily Instrument Audit Trails

• Copy Instrument Audit Trail • Delete Instrument Audit Trail

• Move Instrument Audit Trail • Rename Instrument Audit Trail

Instrument Control
• Control Instrument • Change Qualification Interval
• Take Over Instrument Control • Override Qualification
• Control Queue • Approve Qualification
• Control Instrument w hile Queue Is Running • Manual Injection
• Change Performance Limit • Execute On-demand MS Auto tune /Calibration

• Execute On-demand MS Manual Tune /Calibration • Execute On-demand MS Auto Tune /Calibration in a
Sequence
• Show Instruments Overview for Local Instruments
• Unrestricted Instruments in Instruments Overview
• Show Instruments Overview for All Instruments
• Show Instruments Overview for Favorite Instruments

Data Vault Basics

• Create Data Vault • Modify Security Settings

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• Mount/Dismount Data Vault • Modify List of Custom Variables

• Rename Data Vault • Restore Versions
• Modify Versioning Mode • Modify List of Custom Formulas

Folders

• Create Folder • Move Folder

• Delete Folder • Make Folder Read-Only
• Rename Folder • Remove Folder Read-Only
• Copy Folder • Modify Folder Security Settings

Injection Queries

• Create Injection Query • Move Injection Query

• Delete Injection Query • Execute Injection Query
• Modify Injection Query • Rename Injection Query
• Copy Injection Query

Audit Trail Queries

• Create Instrument / Data Audit Trail Query • Move Instrument / Data Audit Trail Query
• Delete Instrument / Data Audit Trail Query • Rename Instrument / Data Audit Trail Query
• Modify Instrument / Data Audit Trail Query • Execute Instrument / Data Audit Trail Query
• Copy Instrument / Data Audit Trail Query • Create Instrument / Data Audit Trail Query Report

Sequences
• Create Sequence • Rename Sequence w ith Raw Data
• Create Sequence via Wizard • Copy Sequence
• Create Sequence via eWorkflow • Move Sequence
• Create Sequence via Save As • Delete Sequence
• Create Sequence via Save As w ith Raw Data • Delete Read-Only Sequence
• Create Sequence from Injection Query Results • Make Sequence Read-Only
• Create Sequence from Worklist • Remove Sequence Read-Only
• Modify Sequence • Modify Running Sequence
• Rename Sequence • Rename Sequence
• Modify When Visible View s are Updated

Injections
• Copy Injection • Manually Create or Delete Channels
• Add New Injection • Delete Finished or Interrupted Injection
• Insert New Injection Betw een Finished or Interrupted • Delete Individual Channel/Audit Trail
Injections

• Modify Finished or Interrupted Injection • Lock Injections

• Change Status of Injections With Raw Data Back To • Unlock Injections
Idle

eWorkflow

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• Create eWorkflow • Run eWorkflow ‘Ready’

• Modify eWorkflow • Run eWorkflow ‘Retired’
• Rename eWorkflow • Send eWorkflow to File
• Delete eWorkflow • Import eWorkflow from File
• Run eWorkflow ‘Approved’ • Override Access Control

• Run eWorkflow ‘In Development’ • Modify w hen Visible View s for Sequence are Updated
• Modify eWorkflow Auto Reporting Settings • Modify Sequence Preview

Manual Data Processing

• Manipulate Peaks • Delete Peak Manipulations
• Edit Injection Specific XIC Detection Settings

Processing Methods
• Create Processing Method • Move Processing Method
• Delete Processing Method • Rename Processing Method

• Modify Processing Method • Manage Component Variables

• Modify Processing Method - Restricted • Update Detection Algorithm Version
• Copy Processing Method

Spectral Libraries
• Create Spectral Library • Move Spectral Library
• Delete Spectral Library • Rename Spectral Library
• Modify Spectral Library • Add Spectrum
• Copy Spectral Library • Delete Spectrum

Report Templates
• Create Report Template • Copy Report Template
• Delete Report Template • Move Report Template
• Modify Report Template • Protect Report Template
• Rename Report Template • Unprotect Report Template

Electronic Report
• Create Electronic Report • Move Electronic Report
• Delete Electronic Report • Print Electronic Report
• Copy Electronic Report • Export Electronic Report

Reporting
• Print Results • Export ADF
• Export PDF • Print or Export Unsaved Data
• Export XLS • Call External Program

• Export Text • Modify Default Print Settings

• Export AnDI • Modify Default Export Settings
• Export GAML • Allow Formula Customization
• Export Raw File • Modify Custom Formulas

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View Settings
• Create View Settings • Rename View Settings
• Delete View Settings • Copy View Setting
• Modify View Settings • Move View Settings

Electronic Signatures
• Sign as Submitter • Remove Signature w hen Review ed
• Sign as Review er • Remove Signature w hen Approved
• Sign as Approver • Modify Signature Requirements

• Remove Signature w hen Submitted

Archive
• Import Chromeleon Data • Send to File
• Import Non-Chromeleon Data

Administration
• Manage User Database • Overw rite Default Comment
• Manage Licenses • Modify Global Security Settings

• Manage Global Policies • Close Locked Clients

• Manage Scheduler • Revoke Data Transaction Lock
• Manage eWorkflow Tags • Manage Maintenance Window
• Manage Privileged Actions • Manage Updater Service and Repository

Administration Audit Trail

• View Administration Audit Trail • Copy Administration Audit Trail Query

• Show Logon Events of All Users • Move Administration Audit Trail Query
• Create Administration Audit Trail Query • Delete Administration Audit Trail Query
• Modify Administration Audit Trail Query • Execute Administration Audit Trail Query

• Rename Administration Audit Trail Query • Create Administration Audit Trail Report

Chromeleon XPS
• Manage User Interface • Use Client User Interfac

Process Analyser
• Configure Analyzers • Start Analyzers
• Stop Analysers • Start OPC Server
• Stop OPC Server

11.3.6.4 Logon

Function Description
Logon Role Defines whether or not role members can select the role when logging on.

Use special set of access groups Enables a set of access groups to be defined for the role which replace the access
groups of the user at logon.

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11.3.6.5 M embers

Function Description
Role Members Defines the users that are members of the role.

11.3.6.6 Licenses

Function Description

Select the licenses requested from license service, i f Licenses that will be requested from the Chrome leo n clie nt wh en t h e ro l e i s
this role has been selected as logon role selected at logon.

11.3.7Audit Trail
Chromeleon logs information about all events related to the user database in User Database Audit Trails in a dedicated
audit trail table.

Function Description
Reload Reloads the audit trail table.

Report Creates a HTML report containing the current records of the User Database A ud it
Trail.
Show Changes Opens a new window showing the changes of the administration object in re sp ect
of the selected administration audit trail record.
Filtering Provides a filtering option for each of the columns in the audit trail.

Grouping Allows the audit trail to be grouped by any of the columns available.
Show logon events Filters whether the audit trail table should contain all successful a nd f aile d l ogo n
operations or not.
More Extends the current date/time for the audit trail to an earlier start time. The end time
for the date/time range is always the current day / time.
Query Opens a new Administration Audit Trail Query window. See section 4.7 for details.

11.4 Global Policies

Global policy settings that apply for all netw orked computers running Chromeleon connected to the same Chromeleon
domain.

11.4.1Toolbar
The tool bar has four buttons; The Save Policies button is enabled, if the policies have changed. The Report button creates
a printable HTML file for the currently selected OrgUnit. The Audit Trail button creates a printable HTML file of the list of
roles, including all role settings, privileges and members. The help button show s the online help for the currently selected
policy.

11.4.2User Mode
Function Description
Enable User Mode Enables or disables user mode. With disabled user mode, th e u se r d a t aba se
cannot be modified.
Enable Organizational Units Enables or disables Organizational Units. In the navigation tree the User
Database node is replaced by an Organizational Units node.

11.4.3Host Name Resolution

Function Sub function Description
Host Name Resolution Use names provided by Chromeleon uses the network address provided by the
workstations (default) workstation

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Function Sub function Description

Always use NetBIOS names. If the check box is selected, then the client will conve rt a n y
Check this if your network does not fully qualified domain names (FQDNs) in resource addresses
fully support DNS. to simple NetBios names before attempting communica tio n
with the resource. This solves a problem for users where the
network uses WINS resolution only (i.e. no DNS) for the
intranet and where TCP/IP settings for some wo rkst a t ion s
within that intranet causes them to publish FQDNs to
discovery. Users whose Chromeleon domain spans multiple
Windows domains should not use this option.
Always use Fully Qualified Domain If the check box is selected, then Chromeleon wi ll con vert
names. Check this if your net work any NetBIOS names in resource addresses to fully qualifie d
only resolves FQDNs. domain names before attempting communicatio n wi th t he
resource. This solves communication problems ca u se d b y
networks that resolve only fully qualified domain names, n o t
short domain names.

11.4.4Multi-User Logon
Function Description

Allow multiple users to logon within the same win dows If enabled, concurrent access to Chromeleon by multiple users on the same P C
session concurrently is allowed.
When a user logs on, lock all other client sessions If enabled, client sessions of all other users on the same PC are locked as so o n
as another user logs on.

11.4.5Injection Locking
Function Description
Enable locking of single injections If enabled, locking and/or unlocking of injections in the Console or
Chromatography Studio is allowed.

11.4.6Remote Data Vaults

Function Description
Show local Data Vaults of remote systems You can either show all data vaults when the function is enabled or hide remo te
local data vaults from the data tree to show only data vaults that are local on your
computer, network data vaults, and data vaults marked favorite.

11.4.7Instrument Audit Trails

Function Description
Automatically archive instrument audit trails If enabled, the scheduler will copy daily instrument audit tra ils t o t h e lo ca tio n
configured in ‘to’ field.
Automatically delete instrument audit trails If enabled, the scheduler will delete daily instrument audit trails o l de r t ha n t h e
configured time range.

11.4.8Detection Algorithm Version

Function Description
Offer option for existing processing methods to update to Select the check box if it is desirable to allow users an upgrade option for existing
the latest detection algorithm version processing methods during use.
Detection Algorithm Version Select how to handle stored detection algorithm version with opt ion s t o e it her
keep currently used or update to latest, in a processing method for each o f t h e
specific creation actions:
Create sequence from worklist
Create sequence via “Save As…”
Create sequence via eWorkflow
Create sequence via wizard

11.4.9User Templates Location

Function Description

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Function Description
User Templates Locations User specified locations that can store user created reporting object t e mpla te s
which can then be listed as categories. Locations can be specified for;
Report Templates
Report Tables
Plots
Result Charts

11.4.10 Watermark
Function Description
Print with watermark If enabled, reports printed by Chromeleon will have a watermark.

11.4.11 UI Customizations
Function Description

Display “QC Sample” for injections of type “Check If enabled, all visual references to “Check Standards” in the Console, Studio and
Standard” Reports will be replaced with “QC Sample”. When a sequence is cre a t ed , t h is
setting is saved with the sequence. Thereafter, when the sequence is viewed, if
the stored setting does not match the current system setting, a message is
displayed.
Show injection Target mass detection columns If enabled, the following columns will be available for display i n t h e se q u en ce
table:
Target Formula or Mass
Target Negative Adducts
Target Positive Adducts
Show Non-Targeted MS Processing category If enabled, Non-Targeted MS Processing category is available to be accessed in
the studio
Show Intact Protein Deconvolution category If enabled, Intact Protein Deconvolution category is available to be accesse d i n
the studio
Maximum Instruments in Overview Limits the number of instruments which can be disp laye d i n t he I nst ru me nt
Overview in the Chromeleon Console.

11.4.12 Privileged Actions

Function Sub function Description
Settings Requires Authorization Select authorization and/or comment requirements for users when t h ey
perform a specific operation. Privileged actions apply to all Data V a ult s
that have the Versioning and Privileged Actions enabled (se e se ct io n
Requires Comment 4.1.2). Privileged actions authorization and/or comments settings can be
enabled or disabled using the Select All or None buttons o r u si n g t h e
grouping or individual check boxes.
Default Comment The Default Comment can be any free text or can be one entry selected
from the Standard Comments tab.
Standard Comments N/A To help users save time and to keep wording consistent in audit t ra ils,
you can create a list of standard comments. All users se l e c t f ro m t h e
same list.

11.4.13 Email Configuration

Test Configuration button tests the configured email notification settings and sends an email to the recipient(s) if successful.

Function Description
Sender Enter the email address of the sender.

Mail Server Address Enter the mail server address.

Enable TLS/SSL connection Click this check box to use TSL/SSL when connecting to the mail server.
Port Number Enter the Port Number of the mail server you want to connect to.

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Function Description

Authenticate on SMTP Server usi ng lo gg ed o n Use r Select which credentials to use for sender authentication on the mail se rve r. I f
Credentials the check box is checked the credentials of the currently logged on user wi ll b e
used otherwise enter the email address and password o f t h e A ut hen ticat ion
User.

11.4.14 Station Audit

Function Description
Enable Station Audit Trail logging If enabled, Station Audit Trail logging will be active.

11.4.15 License
Function Sub function Description

Enable notifications Checkbox Enables the notifications

when license is about
to expire or when Mail recipient(s) Defines one or more email addresses (or Chromeleon
license is in grace usernames) to whom the notifications will be sent
period
Notifications sent when the ti me t o Defines (in days) the time before expiration that the
license expiration is less than notifications will begin to be sent.
Resend email notifications every Defines (in hours) how often the notifications will be sent.

11.4.16 Raw Data

Function Description
Enable raw data verification If enabled, Chromeleon will validate raw files to verify data integrity.

11.4.17 Updater
Function Sub function Description
Distributed caching Checkbox Enables distributed caching to reduce overa ll d ownlo ad
time.
Transfer Rate Defines the transfer rate for sending data from each
Updater Server.
Overall transfer rate Defines the overall transfer rate for sending data f rom a ll
Updater Servers.
Map drive letter Defines the drive letter which the Updater service will u se
to mount the installation kit.
Central updater host name Used to define the name of a computer that will h o st t he
Central Updater Service and repository. If left b lan k, t h e
default central updater host is the Ch ro mele on Do main
Controller.

11.4.18 Audit Trail Events

The properties of all enabled audit trail events are copied into new ly created sequences if the datavault properties “Enable
versioning and data audit trails” and “Enable audit trail events” (see section 4.1.1) are enabled as w ell. There is only a single
property for every audit trail event w hich signals w hether the audit trail event is enabled or not. Audit trail events are only
recorded for sequences.

Audit Trail Ev ent Type Description

Ext. Report Template Changed This audit trail event is recorded in the sequence data audit trail if t h e e xt ern al
report template of the sequence is used to create and report
(print/export/electronic report) and the external report template has been
modified since the creation of the sequence or since its last use to create reports
(print/export/electronic report).

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Audit Trail Ev ent Type Description

Ext. Spectral Library Changed This audit trail event is recorded in the sequence data a ud it t ra il i f t h ere a re
external spectra library references in the processing method of the sequence, the
processing method is modified and/or a report (print/export/electronic re p ort ) is
created for an injection associated with such a processi n g m et hod a nd a n y
spectra library reference has been modified since the most recent report
(print/export/electronic report) or the most recent modification of the proce ssi n g
method.
Manual Command Interference This audit trail event is recorded in the sequence data audit trail if there has been
a manual command execution during an injection run.
Instrument Error Occurred This audit trail event is recorded in the sequence data audit trail if an instru men t
error occurred during an injection run.
Processing Method Changed This audit trail event is recorded in the sequence data audit trail if any processing
method in the sequence is changed.
Injection Changed This audit trail event is recorded in the sequence data audit t ra il i f a u se r h a s
changed any property of any injection in the sequence.
Injection List Changed This audit trail event is recorded in the sequence dat a a ud it t ra il i f i nje ctio n
records are added or removed from the sequence.
Instrument Method Changed This audit trail event is recorded in the sequence data audit trail if any instrument
method in the sequence is changed.
Report Template Changed This audit trail event is recorded in the sequence data audit t ra il i f a n y re port
template which is located in the sequence is changed.
Chromatogram Changed This audit trail event is recorded in the sequence data audit trail if any
chromatogram modification is committed. The m od ifica tio ns co ve r m anu al
integrations, manual peak assignments and injection sp e cific X I C d et ect ion
settings (see 5.4.3.3 for more details).
Sequence Properties Changed This audit trail event is recorded in the sequence data audit trail if any sequen ce
property (e.g. comment, instrument, default report template, etc…) is changed by
a user.
Additional Sequence Start This audit trail event is recorded in the sequence data audit trail if a sequence is
started for any additional run.

11.4.19 Auto Reporting Settings

Function Description
Maximum number of active jobs Defines the number of active auto reporting jobs which will run concurren tly o n
each Auto Reporting Server. Once this number of active jobs is re a ch ed, a ny
additional job requests are queued.

11.5 Define Policies in Organizational Units

If Organizational Units are enabled, each organizational unit contains modules for User Database Policies and Global
Policies w hich can have inherited or independent policy settings.

11.5.1Separate Policy Settings for Organizational Units

If Organizational Units are enabled the follow ing option is available in the Global Policies and User Database Policies
modules of the <Global> Organizational Unit:

Function Description
Allow separate policy settings for Organizational Units This policy is locked by the <Global> organizational unit. All ch an ge s
apply to all organizational units. Click the ch e ck b o x t o u nlo ck t h e
policy so it can be changed for other organizational units.

This policy can be changed for other organizational units. Changes t o

the policy affect the <Global> organizational unit and all organizational
units which use the global settings for this policy. Deselect t he ch eck
box to lock the policy so it can only be changed in the <Global>
organizational unit.

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11.5.2Use <Global> Settings

This option is available in the Global Policies and User Database Policies modules of all other organizational units, but only
available if the ‘Allow separate policy settings for Organizational Units’ check box in the <Global> organizational unit is
enabled:

Function Description
Use <Global> Settings The check box is checked by default. The policy uses the se t t in gs o f
the <Global> organizational unit. Clear the check box to enable
different settings for the organizational unit.

The check box is cleared. Independent policy setting s a re e na bled .

Select the check box to use the global settings.

11.6 eWorkflow Tags

Tags for eWorkflow s can be defined w hich can then be used to organize and group eWorkflow s to reduce a large list of
eWorkflow s to those eWorkflow s which are relevant for the respective user.

11.6.1Toolbar
The tool bar has three buttons; The Create New Tag button used to generate predefined eWorkflow tags. The Delete Tag
button removes the selected eWorkflow tag from the predefined list in the Administration Console. The help button show s
the online help for eWorkflow tags in Administration Console.

11.6.2Create New Tag

Function Description
Tag Name User defined name for Tag.
Comment Optional comment providing description of tag.

11.7 Domain Resources

The Domain Resources displays summary information from the Discovery service of all Chromeleon Consoles, computers,
Instruments, Instrument Controllers, Data Vault Services, and Data Vaults currently registered w ith the Chromeleon Domain
Controller. There are separate tree nodes for each supported service type (All Resources, Computers, Data Vaults,
Instruments, Chromeleon Consoles and System Printers) w hich w hen selected display a tab page w ith aggregated data
items. The grid control on each tab page supports grouping and filtering and is read-only. Information in these tables can
help you manage the domain and troubleshoot problems.

11.7.1All Resources

11.7.1.1 Toolbar
The tool bar has nine buttons; The Save button saves changes after removing an item from the table. The report button
creates a printable HTML file of the list of resources. The Audit Trail button displays the Data Audit Trail w indow for domain
resources. The Manage Data Vaults displays the Data Vault Manager if the selected item is a local data vault service. The
Show Vault Properties displays the Data Vault Properties for a selected data vault. The Configure Instrument button opens
the Instrument Configuration Manager connected to instrument controller of the selected instrument w ith that instrument
expanded in the tree. The Configure Instrument Controller button opens the Instrument Configuration Manager connected to
the selected instrument controller. The Add System Printer opens the Add System Printer w indow if the selected item is a
Print Service (see 11.7.1.4). The Installation and Maintenance button opens the Installation and Maintenance sub menu
(see 11.7.1.3). The Remove button removes the selected item(s) from the table view only.

11.7.1.2 All Resources Context M enu

The follow ing context menu operations are also available:

Function Description
Manage Data Vaults... Displays the Data Vault Manager if the selected item is a local data vault service. If the data va ult
service is remote, an error message is displayed. If more than one data vault service is selected i n
the grid control the option is greyed out.

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Chromeleon 7

Show Data Vault Properties... Displays the Data Vault Properties for the selected data vault. I f m ore t h an o n e d at a va ult i s
selected in the grid control the option is greyed out.

Show Data Vault Manager Audit Displays the Data Audit Trail window for the selected Data Vault Manager.
Trail...
Configure Instrument... Displays the Instrument Configuration Manager connected to the selected instrument. If
configuration of the instrument PC is already active or not possible, an error message is displayed.
If more than one instrument is selected in the grid control the option is greyed out.
Configure Instrument Controller... Displays the Instrument Configuration Manager connected to the selected instrument controller. I f
the Instrument Configuration Manager is already active or establishing a connection is not possible,
an error message is displayed. If more than one instrument controller is selected in the grid control
the option is greyed out.

Show Instrument Configuration Aud it Displays the Data Audit Trail window for the selected instrument controller.
Trail...
Updater Repository Displays the contents of the Updater Repository on the selected computer if it is an Updater Server
(see 11.7.1.4)
Show Station Audit Trail... Displays the Data Audit Trail window for the host computer of the selected item.

Add System Printer... Displays the Add System Printer window if the selected item is a Print Service (see 11.7.1.5)

Edit System Printer... Displays the Edit System Printer window if the selected item is a Printer (see 11.7.1.6)
Run IQ Triggers Chromeleon IQ on the selected computer to run.

View IQ Report Opens and displays the most recent IQ Report from the select ed comp ut er o n t he comp ut er
running the Chromeleon Administration Console.
Remove Removes the selected item(s) from the table view only.

11.7.1.3 Installation and Maintenance sub menu

Category Function Description

Updater Updater Repository Displays the contents of the Updater Repository on t h e
selected computer if it is an Updater Server (see
11.7.1.4)

Installation Run IQ Triggers Chromeleon IQ on the selected co mput er t o

Qualification run
View IQ Report Opens and displays the most recent IQ Report from th e
selected computer on the computer running the
Chromeleon Administration Console.

11.7.1.4 Updater Repository window

Displays the contents of the Updater Repository on the target computer.

Toolbar
The toolbar has three buttons; The Empty button empties the Updater Repository on the target computer. The Delete
button deletes the selected package from the Updater Repository on the target computer. The Refresh button refreshes the
view .

11.7.1.5 Add System Printer window

Function Description

Available Printers on <target Print Allows a printer configured on the target Print Service computer to be selected for use as a System
Service computer> Printer
Alias Enter a name by which the System Printer will be known throughout Chromeleon

Org. Unit Displays the Organizational Unit to which the selected Print Service computer belongs

11.7.1.6 Edit System Printer window

Function Description

Available Printers on <target Print Allows a printer configured on the target Print Service computer to be selected for use as a System
Service computer> Printer

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Alias Displays the name by which the System Printer is known throughout Chromeleon

Org. Unit Displays the Organizational Unit to which the selected Printer’s Print Service computer belongs

11.7.2Computers

11.7.2.1 Toolbar
The tool bar has seven buttons; The Save button saves changes after removing an item from the table. The Report button
creates a printable HTML file of the list of resources. The Audit Trail button displays the Data Audit Trail w indow for domain
resources. The Manage Data Vaults displays the Data Vault Manager connected to the data vault service of the selected
computer. The Configure Instrument Controller button opens the Instrument Configuration Manager connected to the
selected instrument controller. The Installation and Maintenance button opens the Installation and Maintenance sub menu
(see 11.7.2.3). The Show “Push Notification” subscriber list opens the Push Notification subscriber list dialog.

11.7.2.2 Computers Context M enu

The follow ing context menu operations are also available:

Function Description
Manage Data Vaults... Displays the Data Vault Manager if the selected item is a local data vault service. If the data v a ult
service is remote, an error message is displayed. If more than one data vault service is selected i n
the grid control the option is greyed out.

Show Data Vault Manager Audit Displays the Data Audit Trail window for the selected Data Vault Manager.
Trail...
Configure Instrument Controller... Displays the Instrument Configuration Manager connected to the selected instrument controller. I f
the Instrument Configuration Manager is already active or establishing a connection is not possible,
an error message is displayed. If more than one instrument controller is selected in the grid control
the option is greyed out.

Show Instrument Configuration Aud it Displays the Data Audit Trail window for the selected instrument controller.
Trail...
Set Maintenance Window... Displays the Maintenance Windows Settings for the selected workstations (see section 11.7.2.3).

Updater Repository Displays the Updater Repository window for the selected computer (see section 11.7.1.3)
Show Station Audit Trail... Displays the Data Audit Trail window for the host computer of the selected item.

Run IQ Triggers Chromeleon IQ on the selected computer to run

View IQ Report Opens and displays the most recent IQ Report from the select ed comp ut er o n t he comp ut er
running the Chromeleon Administration Console.
Remove Removes the selected item(s) from the table view only.

11.7.2.3 Installation and Maintenance sub menu

Category Function Description

Set Maintenance N/A Opens the Maintenance Windows Settings for the
Window selected computer(s) (see section 11.7.2.4)
Updater Create Updater Package Opens the Create Updater Package dialog (see
11.7.2.5)
Updater Repository Displays the contents of the Updater Repository on t h e
selected computer if it is an Updater Server (see
11.7.1.4)

Installation Run IQ Triggers Chromeleon IQ on the selected co mput er t o

Qualification run
View IQ Report Opens and displays the most recent IQ Report from th e
selected computer on the computer running the
Chromeleon Administration Console.

11.7.2.4 M aintenance Window Settings

The Maintenance Window Settings prevent the selected w orkstation(s) displayed in the Computers Summary from using
instruments configured in Chromeleon for a set time.

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Chromeleon 7

Function Sub function Description

Define Maintenance Window N/A Select to enable all other options. If the workstation is curre nt ly u nd er
maintenance, clearing the check box cancels the maintenance window.

Start of maintenance Enter the start dates and times of the maintenance window.
period

End of maintenance Enter the end dates and times of the maintenance window.
period
Open Ended Select this check box to remove the End of maintenance period se t t ing
and keep the maintenance window open-ended.
In time zone Select the time zone of the selected workstation. If the workstation's time
zone is different from your local time zone, your corresponding local start
and end times are displayed below the Start of maintenance period and
End of maintenance period.
Notification period Select how far in advance users are notified of the maintenance window.
Select from the predefined settings or by manually entering the days and
hours.

Enforce maintenance Allows the user to select when to start enforcement:

window
• Don’t enforce stop
• Stop after completed sequence
• Stop after completed injection

Download software Allows the selection of a Chromeleon Updater Package for inst alla tio n
update during the Maintenance Window

11.7.2.5 Create Updater Package wizard

The Create Updater Package w izard guides the user through the process of creating an Updater Package for installation
during a Maintenance Window . The follow ing parameters are defined by the Wizard:

Parameter Description
Package Source Defines the folder containing an installation package.

Package Name Defines the name by which the package will be known throughout Chromeleon..

11.7.3Data Vaults

11.7.3.1 Toolbar
The tool bar has six buttons; The Save button saves changes after removing an item from the table. The report button
creates a printable HTML file of the list of resources. The Audit Trail button displays the Data Audit Trail w indow for domain
resources. The Manage Data Vaults displays the Data Vault Manager connected to the data vault service of the selected
computer. The Show Vault Properties displays the Data Vault Properties for a selected data vault. The Remove button
removes the selected item(s) from the table view only.

11.7.3.2 Data Vaults Context M enu

The follow ing context menu operations are also available:

Function Description
Manage Data Vaults... Displays the Data Vault Manager and connects to the data vault service of the selected computer.
If the data vault service is remote, an error message is displayed. If more than one d a ta vau lt i s
selected in the grid control the option is greyed out.
Show Data Vault Properties... Displays the Data Vault Properties for the selected data vault. I f m ore t h an o n e d at a va ult i s
selected in the grid control the option is greyed out.
Show Data Vault Manager Audit Displays the Data Audit Trail window for the Data Vault Service of the selected Data Vault.
Trail...
Show Station Audit Trail... Displays the Data Audit Trail window for the host computer of the selected item.
Remove Removes the selected item from the table view only.

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11.7.4Instruments

11.7.4.1 Toolbar
The tool bar has five buttons; The Save button saves changes after removing an item from the table. The report button
creates a printable HTML file of the list of resources. The Audit Trail button displays the Data Audit Trail w indow for domain
resources. The Configure Instrument button opens the Instrument Configuration Manager connected to instrument controller
of the selected instrument w ith that instrument expanded in the tree. The Remove button removes the selected item(s) from
the table view only.

11.7.4.2 Instruments Context M enu

The follow ing context menu operations are also available:

Function Description
Configure Instrument... Displays the Instrument Configuration Manager connected to the selected instrument. If
configuration of the instrument PC is already active or not possible, an error message is displayed.
If more than one instrument is selected in the grid control the option is greyed out.
Show Instrument Configuration Aud it Displays the Data Audit Trail window for the selected instrument controller.
Trail...
Show Station Audit Trail... Displays the Data Audit Trail window for the host computer of the selected item.

Remove Removes the selected item(s) from the table view only.

11.7.5Chromeleon Consoles

11.7.5.1 Toolbar
The tool bar has four buttons; The Save button saves changes after removing an item from the table. The report button
creates a printable HTML file of the list of resources. The Audit Trail button displays the Data Audit Trail w indow for domain
resources. The Remove button removes the selected item(s) from the table view only.

11.7.5.2 Chromeleon Consoles Context M enu

The follow ing context menu operations are also available:

Function Description
Show Station Audit Trail... Displays the Data Audit Trail window for the host computer of the selected item.

Remove Removes the selected item(s) from the table view only.

11.7.6System Printers

11.7.6.1 Toolbar
The tool bar has four buttons; The Save button saves changes after removing an item from the table. The report button
creates a printable HTML file of the list of resources. The Audit Trail button displays the Data Audit Trail w indow for domain
resources. The Remove button removes the selected item(s) from the table view only.

11.7.6.2 System Printers Context M enu

The follow ing context menu operations are also available:

Function Description
Show Station Audit Trail... Displays the Data Audit Trail window for the host computer of the selected item.

Edit System Printer... Displays the Edit System Printer window for the selected item (see 11.7.1.5)
Remove Removes the selected item(s) from the table view only.

11.8 Local Machine

This page provides tools to manage resources on the local machine, i.e. the computer the administration console is running
on.

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Chromeleon 7

11.8.1Manage Data Vaults

11.8.1.1 Data Vault Manager

The Data Vault Manager (Figure 74) enables a user to create, upgrade, mount, or dismount and configure Chromeleon Data
Vaults.

Figure 74: Data Vault Manager

The follow ing options are available:

Function Sub function Description

Local Data Vaults Lists all Chromeleon 6 and 7 data vaults that are st o re d o n t h e l ocal
system.
Name Name of the Data Vault.

Database Schema Database schema.

Create… N/A Creates a new local or network Data Vault.

Mount… N/A Mount a dismounted Chromeleon 7 Data Vault.

Chromeleon 6… N/A Mounts a Chromeleon 6 Datasource.

Dismount N/A Removes a Chromeleon 6 or 7 Data Vault.

Upgrade Schema N/A Performs a manual Data Vault schema upgrade.

Configure N/A Configure Multi-User Data Vault (see section 11.8.1.2).

Audit trail... N/A Opens Data Vault Management Audit Trail dialog (see section 12)

Refresh N/A Refreshes display of Data Vaults.

Service Settings... N/A Configure Data Vault service settings (see section 11.8.1.3).

11.8.1.2 Configure M ulti-User Data Vault

Multi-user data vault(s) can be configured on the system w here the data vault is hosted.

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Figure 75: Data Vault Manager

The follow ing options are available:

Function Sub function Description

Load balancing server(s) Lists all load balancing servers. Master system is displayed in t he f i rst
line of the list. Additional load balancing servers can be added or
removed. The master cannot be removed.
Server Load balancer name.

Type Load balancer type.

Status Load balancer status.

Organizational unit N/A Associate organizational unit that Multi-User Data Vault belongs to.

11.8.1.3 Data Vault Service Settings

Figure 76: Data Vault Manager

The follow ing options are available:

Function Sub function Description

Local System N/A The Local System account is a predefined local accoun t o f
the operating system.
User Account Domain Domain of user account to be used by data vault service.
User User name to be used by data vault service.

Password This is used to set the logon password for defined user.

Retype Password Confirmation of logon password for user.

This service can be used for load N/A Enables Data Vault service to be used as a load balancer.
balancing

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Chromeleon 7

11.9 Configure Discovery

The Discovery Service maintains a central index of various Chromeleon resources (instrument controllers, data vaults, and
clients) that these resources use to maintain aw areness of each other and establish communications.

11.9.1Discovery Configuration

Figure 77: Discovery Service Configuration

The follow ing options are available:

Function Sub function Description

Chromeleon Domain Controller N/A The locator control displays the current location and contains a drop text
box and a button to browse for other locations.
Organizational Unit N/A Associate organizational unit that discovery service belongs to.

Notifications (choose at least one) Receive push Clients subscribe to receive notifications about updates to Discovery (on
notifications by default).

Poll for updates e v e ry Client machines simply poll the domain controller discovery service f or
... sec resource information on a regular interval of x seconds.
Connection Security Require enhanced New certificates for the communication between different Ch rome leo n
connection security Services and Chromeleon client applications have been int rod uced in
(Chromeleon 7.2 S R5 order to enhance transport security.
and above) If checked the Chromeleon services will communicate via new Windows
Communication Foundation (WCF) hosts based on a n ew ce rt ificat e
created using SHA-256 hash algorithm.
If unchecked the old legacy hosts will be started additionally and enable
clients with Chromeleon versions <7.2 SR5 to connect.

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12 Administrative Audit Trails

A common audit trail view er control/window is used for all of the follow ing audit trail view s:
• Organizational Unit
• Global Policies

• User Management
• eWorkflow Tags
• Discovery
• Instrument Configuration
• Data Vault Management

• Station
• License Management
Figure 78 show s the such an audit trail view er control/window .

Figure 78: Administrative Audit Trail

The data audit trail offers the follow ing toolbar controls:

Function Description
Reload Reloads the data audit trail from the Data Vault.
Report Creates a report of the data audit trail.

Show Changes Opens the details window, if details are available for the selected audit trail record.

Show Logon Events Filters whether the audit trail table should contain all successful a nd f aile d l ogo n
operations or not. This option is only available for audit trails where user
management records are considered (Organizational Unit, User Management)
Filtering Provides a filtering option for each of the columns in the audit trail.

Grouping Allows the audit trail to be grouped by any of the columns available.
More Extends the current date/time for the audit trail to an earlier start time. The end time
for the date/time range is always the current day / time.
Query Opens a new Administration Audit Trail Query window. See section 4.7 for details.

The audit trail displays the follow ing default columns, but the actual list depends on the context of the audit trail:

Function Description
Date/Time The date and time of the audit trail record.

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Chromeleon 7

Function Description
Operator The user who made the modifications or triggered the event.
Operation The type of modification or event.

Computer Name The name of the computer from where the modification was m a de o r t he e v ent
was triggered.
Application The name of the application that made the modification or triggered the event.

Application Version The version of the application that made the modification or triggered the event.
Comment Comment entered by the user or the application about the modification.

Additional Information Additional information where available.

Object The modified object.

Org. Unit The organizational unit of the object.

Category The category (Global Policies, User Management, etc…) of the audit trail re co rd.
This column only appears if multiple categories are considered.
Old Value The value prior to any modification.

New Value The resulting value after any modification.

Object Type The type of object that has been modified.

Host Name Indicates the host name of the computer where a particular resource was running.

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13 Time Zone Information

A tooltip provides additional information about time zone offset and how it translates to local machine date time. The tooltip
appears under the mouse pointer w hen it is hovering over a Date and Time w ith offset field. The tooltip is available in
ePanels Audit Trail control, Console folder details, Sequence Inject Time and Associated items, Data Vault, Folder and
Injection Properties, and all audit trails.
Figure 79 show s the time zone tooltip.

Figure 79: Time Zone Tooltip

When the mouse pointer is rested over a date and time the follow ing information is displayed:
• The time offset from Coordinated Universal Time (UTC)
• The time offset from your local computer (including any daylight savings time adjustments that apply)
• The conversion of this date and time to your local time zone

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Chromeleon 7

14 Changes Introduced in Version

14.1 7.2
3D View 123
Absolute Value 317
Add 6
Adds table 13
Agilent ICF configuration 14
AnDI/NetCDF file for mat 301
Apply scaling to all plots passim
Arithmetic Combination 107
Available algorithm version 346, 347
Blank Run injection Record 346
CAS 73, 114
Check for Errors 307
Chem. For mula 73, 74, 114
Compar ison passim
Consolidated Table 144, 260
Convert 22, 56
CORREL 299
Data Audit Trail 145, 326
Database Statistics 35, 39
Date Modified 12
Deleted Items 22, 34, 51
Der ivatives 109
Detection Algorithm 327
Displaying Imported Results 319
Export GAML 388
Export AnDI 388
Extracted Ion Chromatograms 71, 114
Filter Peaks 256
For mat 38
GA ML file format 301
Grouping 303, 304, 305, 306
Grouping Options 257, 264
Groups 13
GUID 37, 323
Header Row s passim
Hit Mass Spectrum 341
Hit Spectrum 344
Import Non- Chromeleon Data 389
Import Type 327
Imported Data 319
Injection Overlay 214
Injection Rac k View 40, 95, 145, 245
Interactive Settings passim
INTERCEPT 299
Label 125, 155
Legend 101, 200, 210, 238
Library Spectral Filter 76, 353
Mass Spectra 95
mass spectral plot 13, 223
Mass Spectrometry 356
Mass Spectrum 328, 342
Metadata 328
Mol. Mass 73, 114
Monitor Baseline 10
MS 105
MS & Results 57
MS Components 95, 229
MS Detection 84
MS Detection Settings 145
MS Dev ice 356
MS Dev ice Information 145, 280
MS Instrument Method (XRAW) 145, 275
MS Library Screening 87, 351

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MS Quantitative 94
MS Raw Spectra 144, 264
MS Settings 86, 351
MS Signal Extraction Parameter 329
MS Spectral Library 21, 34, 311
MS Status Log 145, 280
MS Tune Report 145, 275
Netw ork 390
Non- Chromeleon data 4, 8
Options 134, 144
Overlay order 103
Override Access Control 388
Peak Purity and Identification 339, 346
Pow er Law 109
Pr oportional 215
Queue Settings 30
Re- injections 37, 324
Report Column passim
Report Mode 317
Result For mula Statistics 37, 38
Round Value 317
Signal Axis 198, 209, 237
Signature Programs 382
SLOPE 299
SmartLink passim
Smooth Channel 110
SQ / QqQ GC- MS Data Acquisition 373
SST/IRC 77
System Suitability IRC 145
Table Channels 256
Test Case Overall Result 324
Test Case Spec ific Result 324
Tic k mar k intervals 198, 209, 236
Time mark intervals passim
Trace 1300 command 14
Triggers 104, 213
TriPlus RSH command 14
TriPlus RSH Status 14
Update Detection Algorithm Version 388

14.2 7.2 SR1

Acquisition List 89
Autodilution 77, 80, 81
ChemStation Data Import 9
Composite Scor ing 83, 339, 340, 347, 350
Configure Multi- User Data Vault 400
Custom For mulas 307
Custom For mulas Editor 6
Customizable Titles 112, 124, 129, 136, 141
Data Vault Service Settings 401
Discovery Configuration 402
Exponential Function 317
Export MS raw File – new privilege 388
Export MS raw file format 301
Fraction Collection – new license 373
Fraction Tray Pane 146
Fraction Tray Plot 245
Fraction Tubes 104, 213
Fractionation - Fraction Table 280
Fractionation - Tube Table 281
Host Name Resolution 390
Inhibit Integration for TIC 87, 352
LC- MS Data Acquisition – new license 373
Load balancing 401
Logarithm 317

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Chromeleon 7

Logarithmic scale for calibration 111

Log-log linear transformation 111
Logon Roles 389
Mass Precision 86
Mass Spectrometer Instrument Methods 53
Modify Custom For mulas – new privilege 388
Modify List of Custom For mulas – new privilege 387
MS Component Table Export 89
Natural Logar ithm 317
Number of recent passw ords, that cannot be used again 381
Open MS raw file w ith registered application 24
Organizational Units 383, 385, 390
Passw ord change restriction 383, 384
Passw ord complexity 381
Peak to Valley Ratio 333
Standard Instrument Integration – new license 373
User Report Templates Locations 392

14.3 7.2 SR2

AutoDilution 77
Autoscale in fixed time range 100, 199, 210,
237
Autoscale in time range or peak 100, 199, 209,
237
Autoscale in v isible time range 100, 199, 210,
237
Autoscale on peak 100, 199, 210,
237
Calculated Mass 322
CE Area 331
Detection parameter label 105, 172
Errors passim
Exclude users 380
Frame 363
Frame Table 144, 265
Launch 13
Manual commands 104, 213
Manual Commands 105, 200, 215, 238
Manual Injection 386
Method of noise calculation 335
Non-Targeted MS Processing 55
NTMS Chromatogram Plot Pane 178
NTMS Frame Plot Pane 176
NTMS Frame Report Pane 178
NTMS Mass Spectra Pane 178
NTMS Pr ocessing Pane 175
NTMS Ribbon Bar 174
Pr ovides embedded PDF 13
QD Calibration 88
QD Quantitative 94
Remove All Manual Assignments 98
Remove Manual/Automatic Assignment 98
Requires Reference Peak 114
Selected peak 105
Selected peak label 105, 172
Signal parameters 104, 213
Time interval for noise calculation 335, 336
TriPlus 100 LS command 14
TriPlus 100 LS status panel 14

14.4 7.2 SR3

AutoFilter Filtering 172
Baseline Corrected 344
Baseline Correction 344
Calibration Levels 68
Chromeleon data file format 301
Chromeleon data files 4

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Chromeleon PQ 5
Comment 30, 395
Concentration Level Tolerances 74
Confirming Peak Ion Ratios 72
Copy 169
Create MS Channel 169
Data Range for Extracted Ion Chromatograms 71
Data Range for MS Components 84
Define Polic ies in Organizational Units 394
Display “ QC Sample” for injections of type “ Chec k Standard” 392
eWor kflow Tags 27, 395
Export Chromatogram 169
Extract MS Channel(s) 80, 82
From <date> to <date> 312
Full Scan Mode 91
Instrument Selection 32
ISQ 90
Level 19, 49, 314
Level Check 323, 332
Level Tolerance High A mount 332
Level Tolerance High Response 332
Level Tolerance Low Amount 332
Level Tolerance Low Response 332
Line & Fill Styles 171
MS AutoFilters 168
Neutral Loss Scan Mode 92
Next Day 19
Next Injection 314
Nor malize signal 103, 165, 212, 213
Nor malize time 103, 213
Open Chromeleon Studio 33
Peak Character ization 171
Peak Label 171
Plot Details 170
Pr ecursor Ion Scan Mode 91
Pr evious Day 19
Pr evious Injection 314
Pr oduct Ion Scan Mode 91
Pr operties 170
QED Scan Mode 91
Relative CE Area 333
Remote Data Vaults 391
Retention Time Standard Peak Area Ratio 64
Run eWorkflow ‘Approved’ 388
Run eWorkflow ‘In Development’ 388
Run eWorkflow ‘Ready’ 388
Run eWorkflow ‘Retired’ 388
sampler positions w hen the eWorkflow is launched 32
Sampler start position 32
Scale 170
Separate Policy Settings for Organizational Units 394
Show Description at Launch 27
Show local Data Vaults of remote systems 391
SIM Scan Mode 91
SRM Scan Mode 90
Tag Name 395
The list of eWorkflow s in the navigation area can be grouped and filtered 26
Tolerance [%] 68
Toolbar 380, 390, 395
Troubleshooting 11
Try Launch 32
TSQ Quantiva and TSQ Endura 90
UI Customizations 392
Use <Global> Settings 395
User Mode 395
XICs 72
Zooming and Navigating in the MS AutoFilters pane 168

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Chromeleon 7

14.5 7.2 SR5

Access Group List 385
Administrative Audit Trails 403
All Resources 395
All Resources Context Menu 395
Audit trail 400
Audit Trail 380
Bulk Import 9
Chromeleon 6 data files (*.c mb) 8
Chromeleon Consoles 399
Chromeleon Consoles Context Menu 399
cmb 9
Computers 397
Computers Context Menu 397
Connection Security 402
Create Sequence from Injection Query Results 387
Create Sequence via Save As 387
Create Sequence via Save As w ith Raw Data 387
Data Vault Management Audit Trail 400
Data Vaults 398
Data Vaults Context Menu 398
Default logon role 384
Domain Resources 395
Email Configuration 392
Enable pr ivileged actions 34
For mat date/time as text passim
Imports multiples of Chromeleon data files 9
Instruments 399
Instruments Context Menu 399
Last Fixed Calibration Update Date and Time 348
Last Fixed Calibration Update Operator 348
Maintenance Window Settings 397
Manage Maintenance Window 389
Manage Pr ivileged Actions 389
Overwrite Default Comment 389
Pr ivileged Actions 392
Raw Data 393
Reactivate User(s) 383
Retire User(s) 383
Roles List 385
Send email notification w hen a user account is loc ked 381
Send email notification w hen a user signature passw ord is locked 381
Station Audit 393
Time in universal coordinated time passim
Time offset in hours passim
Time us ing local time zone passim
Time Zone Infor mation 405
Toolbar passim
User List 383

14.6 7.2.6
Amount Ratio for Variable Internal Standard 75
Chromatogram Report Variables 328
Chromeleon XPS Per missions 389
Component Match by Mass Spectrum 65
Detection Settings - Reference Mass Spectrum 70
Electronic Signatures 389
eWor kflow Notification Settings 30
General User Pr operties 383
Injection Report Variables 322
License Notifications 393
MS Component Table Import 88
MS Components Plot Signal Axis 163
MS Plot - Show Detected Mass Info 155, 226

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Passw ord Attempts 381

Sequence Notifications 39
Sequence Table Target Mass Support 37
UI Customizations 392

14.7 7.2.7
Ad Hoc Libraries Search Window – Multiple Library Search Function 133
Autorepeat Areas - Tw o Repeat Levels 303, 304
Chromatogram Plot Property - MS Quantitation Channel 104, 214
Import - Empow er Data 9
MS Component Plot Properties - Reference Injection 163, 165, 229, 232

14.8 7.2.8
Admin Console - Ready for LIMS transfer 382
Cobra Integration - Fixed Baseline 59
Component Table - Context Menu 63
eWor kflow - Auto-reporting Settings 30, 31
Instrument ePanel - Fluidic Configuration 11
Instrument Controller Queue - Enforce Export 370
Instrument Controller Queue - Enforce Pr int 370
Sequence Properties - Autogenerate Report 39
Sequence Properties - Export 39
Sequence Properties - Pr int 39
Tentatively Identified Peaks - CAS Number 168
Tentatively Identified Peaks - Add To Component Table 168
Tentatively Identified Peaks - Amount 346
Tentatively Identified Peaks - CAS Number 346
User Management - User Account Restrictions 382
XIC Extraction - Include in Calibration 73

14.9 7.2.9
BioPhar ma Finder Workbook Import 89
Data Processing - Linking Internal Standards 66
Data Processing – Multiple Variable Internal Standards 38, 66
ePanel Control - Instrument Data Brow ser 13
Execute On-demand Auto tune 386
Export Notification 301
Intact Protein Deconvolution 190
Intact Protein Deconvolution Report Variables 360
IPD Chromatogram Pane 196
IPD Chromatogram Report Object 234
IPD Component Results Pane 195
IPD Component Results Report Table 267
IPD Deconvoluted Spectrum 200
IPD License 373
IPD Mass Deconvoluted Spectra Report Object 238
IPD Mass Source Spectra Report Object 241
IPD Processing Method Pane 191
IPD Processing Parameters Pane 194
IPD Processing Parameters Report Table 269
IPD Ribbon Bar 190
IPD Source Spectrum Pane 204
LIMS transfer 382
Modify When Visible View s are Updated 387, 388
Notifications 301
On- Demand View Updating 174
Peak Grouping - General 68, 69, 332, 349
Peak Grouping - Report Category 350, 354
Peak Grouping - Report Table 144, 270
Peak Grouping - Results 271
Pr ocessing Method - Peak Group Table 75
Save Electronic Report 30, 31, 39, 370

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Chromeleon 7

System Printers 396, 399

UI Cusomitzations 392
Update Vis ible View s For MS Data 30, 38
Updater Package 398
Updater Repository 389

14.10 7.2.10
Allotrope Export 301, 388
Autoreporting Settings 39
Bulk Copy XIC Detection Settings 115
Close Client After Inactivity 380
Component Match - New Options 64
Configure Autoreporting 30, 31
Edit Peptide Name 64
Effective Smoothing Width ( Cobra) 327
Enforce Pr int/Ex port Report 370
Execute MS AutoTune in a Sequence Priv ilege 386
Execute MS Manual Tune Privilege 386
Injection Specific XIC Detection Settings 115, 327, 388
IPD Chromatogram 236
IPD Processing Parameters Report Table 283
IPD Results Table 196
IPD Source Spectrum 206, 242
Modify Running Sequence Pr ivilege 387
Multiple Component Assignments 98, 258
NTMS Frame Report Variables 363
NTMS Pr ocessing Parameters Pane 179
NTMS Pr ocessing Parameters Report Table 266
NTMS Pr ocessing Setup 175
Peak Highlight 101, 164, 211, 230
Pr ocessing Parameters Pane 283
QC Check Ter minology 392
SIEV E Processing Parameters Report Table 286
SmartLink By Injection 172, 174
SmartLink Pane By Injection 131, 138, 158, 167
SmartLink Report Object By Injection passim
Tentatively Identified Peaks 168
TraceFinder compound data store 89
Update XICs Window 72
Updater 393
Updater Repository 396
User Database - Manage Users 384
User Database - Reset Passw ord 383
Versioning - Read-only Studio Window 46, 47, 312, 313
View Settings 56

14.11 7.3
Additional Mass Spectrum Report Variables 342
Audit Trail Events – Configuration 393
Audit Trail Events – Configuration Report 278
Audit Trail Events – Data Audit Trail Window 313
Audit Trail Events – Report Table 277, 326
Data Audit Trail Report - Show Details 277, 326
Diagnostic Tests 11
eWor kflow – Default Assignments 28
eWor kflow – Link Instruments 28
eWor kflow - Notification Settings dialog 31
Extracted 3D Channel Units 81
Instrument Overview grid 20
Instrument Queue – Current and Pending view 17
Instrument Queue – Manual Upload of Sequences 18
Manage Licenses – License Activation 375
Manage Licenses – License Deactivation 376
Manage Licenses – License Details 377

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 Chromeleon 7

Manage Licenses – License Initialization Codes 374

Manage Licenses – Overview 374
Maximum Instruments in Overview 392
Peak Label for Undetected Components 102
Pr ocessing Parameters Pane 194
Show Instruments Overview for All Instruments 386
Show Instruments Overview for Favorite Instruments 386
Show Instruments Overview for Local Instruments 386
Unrestricted Instruments in Instruments Overview 386
User Database Policies - Concurrent Logon 381

14.12 7.3.1
Administration Audit Trail Query 4, 49, 390, 403
Atlas detection algorithm 61
Auto Reporting Settings 394
BioPhar ma Finder Component Results Report Table 290
BioPhar ma Finder Processing Parameters Report Table 287
Command line – Import CSV Wor klist 32
Composite Scor ing Parameters Report Table 282
CSV Sequence Import 4
Data Audit Trail Query 4, 44
Detection Reference XIC 116, 162, 327, 354
Domain Resources - Installation and Maintenance Menu 396
Elemental Compos ition (Ad Hoc Window ) 151
Elemental Compos ition ( Property tab) 155
eWor kflow – Autosampler Tray Sharing Options 29
eWor kflow - Copy Options 29
eWor kflow Wizard – Allow Sequence Edits 27
Filter Isotopes – Pr ocessing Method 83
Filter Isotopes – Report Variables 332, 351
Injection Query 4, 40
Instrument Audit Trail Query 4, 47
Instrument Overview - Stop and Start Queue 20
Instrument Queue - Postpone and Reactivate 18
Instrument Queue – Sequence Incomplete 17
Manage Licenses - Assign License to Organizational Unit 374, 377
Manage Services 368
Mass Accuracy Mass 357
Mass Tolerance per component 74, 86
MS Baseline 342
MS Noise 340, 343
MS Signal To Noise 343
Non-Targeted MS Processing ( BioPhar ma Finder) Report Variables 359
Non-Targeted MS Processing Category (BioPhar ma Finder) 180
NTMS Algorithm Selection 38
NTMS Autoprocessing 31, 39
Peak Threshold Pct – SIEV E Report Table 287
Peak Threshold Pct – SIEV E Report Variable 358
Peak Threshold Peak Type – SIEV E Report Table 287
Peak Threshold Peak Type – SIEV E Report Variable 358
Peak Threshold Type – SIEV E Report Table 287
Peak Threshold Type – SIEV E Report Variable 358
Peptide Group ( MS Component Table) 74
Peptide Group ( Peptide Table) 88
Per-Organizational Unit License Overview 373
Sequence Features tab 30
Sequence tabs – Associated Items 24
Sequence tabs - Custom For mulas 25
Sequence tabs – Custom Sequence Variables 25
Simulated Abundance 331
Simulated Mass 331
Summed Charge State Confir ming Peak Area 340
Summed Confir ming Peak Area 340
XIC Display Options 165

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Page 414 Functional Specifications, 7.3.1, Rev. 1.0