Analyst® 1.6.

2 Software

Getting Started Guide

RUO-IDV-05-0267-A
Release Date: April 2013
This document is provided to customers who have purchased AB SCIEX equipment to use in the
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Contents

Foreword. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
Technical Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
Chapter 1 Create Hardware Profiles and Projects . . . . . . . . . . . . . . . . . . . . . . . . 9
Hardware Profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
Create a Hardware Profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10
Add Devices to Hardware Profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13
Troubleshoot Hardware Profile Activation . . . . . . . . . . . . . . . . . . . . . . . . . . . .14
Projects and Subprojects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
Project Organization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
About Subprojects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .16
Create Projects and Subprojects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17
Create a Subproject . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .18
Copy a Subproject . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19
Installed Projects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .20
Back up the API Instrument Project . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .20
Chapter 2 Tune and Calibrate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
About Tuning and Calibrating . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21
Automatically Tune and Calibrate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21
Back up Instrument Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .22
Restore Instrument Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .22
Optimize the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23
Verify or Adjust Performance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23
Results Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23
Chapter 3 Create Basic Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
About LC Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .25
Create Mass Spectrometry Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .25
Create an Acquisition Method using a Q1 MS Scan Type . . . . . . . . . . . . . . .26
Create an Acquisition Method using a Q1 MI Scan Type . . . . . . . . . . . . . . . .29
Create an Acquisition Method using an MRM Scan Type . . . . . . . . . . . . . . . .30
Add or Remove Devices From Acquisition Methods . . . . . . . . . . . . . . . . . . . . . .32
Add or Remove an LC Device . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .32
Modify LC Pump Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33
Set Autosampler Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33
Set Integrated Syringe Pump Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . .34
Set Column Oven Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .35
Set Switching Valve Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .35
Set Diode Array Detector Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .36
Set Analog to Digital Converter Properties . . . . . . . . . . . . . . . . . . . . . . . . . . .37
Change Acquisition Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .38
Add an Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .38
Copy an Experiment into a Period . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .38
Copy an Experiment within a Period . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .38

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Add a Period . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .39

Chapter 4 Create and Submit Batches. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Queue Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .41
Set Queue Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .41
Create and Submit a Batch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .42
Add Sets and Samples to a Batch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .42
Acquire Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .44
Set Sample Locations in the Batch Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . .45
Select Vial Positions Graphically using the Locations tab (Optional) . . . . . . .46
Set Quantitation Details in the Batch Editor (Optional) . . . . . . . . . . . . . . . . . .47
Stop Sample Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .47
Import and Submit Batch Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .48
Build a Batch as a Text File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .48
Import a Batch as a Text File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .48
Batch and Acquisition Method Editor Tips . . . . . . . . . . . . . . . . . . . . . . . . . . . .49
Batch Editor Right-Click Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .50
Queue States and Device Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .50
Queue States . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .51
View Instrument and Device Status Icons . . . . . . . . . . . . . . . . . . . . . . . . . . . .52
Queue Right-Click Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .53
Chapter 5 Analyze and Process Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Overview of Spectral and Chromatographic Data . . . . . . . . . . . . . . . . . . . . . . . .57
Analyze Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .57
Open Data Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .58
Navigate Between Samples in a Data File . . . . . . . . . . . . . . . . . . . . . . . . . . .58
View Experimental Conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .59
View the Data in Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .60
View ADC Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .61
Obtain Basic Quantitative Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .61
Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .62
Chromatograms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .62
TICs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .62
Show TICs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .63
XICs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .63
BPCs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .66
Generate BPCs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .66
XWCs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .67
Generate XWCs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .67
DAD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .68
View DAD data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .68
TWCs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .68
Generate TWCs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .68
Adjust the Threshold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .69
Data Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .70
Work with Graphs in Panes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .70
Zoom in on a Graph . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .72
Label Graphs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .73
Overlay and Sum Spectra or Chromatograms . . . . . . . . . . . . . . . . . . . . . . . .73

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 Contents

Perform Background Subtractions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .75

Smoothing Algorithms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .78
Smooth Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .78
Centroid Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .80
Save and Open Processed Data Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .81
Contour Plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .82
Work with Contour Plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .82
Fragment Interpretation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .84
Work with the Fragment Interpretation Tool . . . . . . . . . . . . . . . . . . . . . . . . . .84
Show Formula Differences for Fragments . . . . . . . . . . . . . . . . . . . . . . . . . . . .85
Library Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .86
Connect to a Library Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .87
Work with Library Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .90
Search for a Similar Spectrum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .91
Chapter 6 Analyze and Process Quantitative Data . . . . . . . . . . . . . . . . . . . . . . . 97
Quantitative Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .97
About Quantitation Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .97
About Results Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .98
Create Quantitation Methods and Generate Results Tables . . . . . . . . . . . . . .98
Define the Layout of Results Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .102
Sort Data in Results Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .103
Results Table Right-Click Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .106
Peak Review and Manual Integration of Peaks . . . . . . . . . . . . . . . . . . . . . . . .107
Integrate Peaks Manually . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .107
Peak Review Right-Click Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .112
Calibration Curves . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .112
Work with Calibration Curves . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .113
Calibration Curve Right-Click Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .114
Sample Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .116
Review Sample Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .116
Metric Plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .117
Generate Metric Plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .117
Chapter 7 Reporter Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
Analyst Software Reporter Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .123
Reporter User Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .124
Generate Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .125
Appendix A Calibration Ions and Solutions . . . . . . . . . . . . . . . . . . . . . . . . . . . .127
Appendix B Parameters and Scan Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .129
About Instrument Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .129
Source-Dependent Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .129
Compound-Dependent Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .130
Quadrupole- and LIT-Mode Scan Parameters . . . . . . . . . . . . . . . . . . . . . . .130
LIT Mode Scan Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .131
Detector Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .132
Scan Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .132
Scan Techniques . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .132

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Quadrupole-Mode Scan Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .132

LIT (Linear Ion Trap)-Mode Scan Types . . . . . . . . . . . . . . . . . . . . . . . . . . . .133
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135

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Foreword

This guide is for operators who are new to the Analyst® software. You can use the procedures to
learn how to use the software and the mass spectrometer.

WARNING! Risk of personal injury or instrument damage. If you need to

move the system, contact a Field Service Employee (FSE) to assist you.

Related Documentation
The guides and tutorials for the mass spectrometer and the Analyst software are installed
automatically with the software and are available from the Start menu: All Programs > AB SCIEX
> Analyst. A complete list of the available documentation can be found in the Help. To view the
Analyst software Help, press F1.

Technical Support
AB SCIEX and its representatives maintain a staff of fully-trained service and technical
specialists located throughout the world. They can answer questions about the mass
spectrometer or any technical issues that might arise. For more information, visit the Web site at
www.absciex.com.

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Foreword

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Create Hardware Profiles and Projects
1
In this section, you will learn how to create a hardware profile. You can use this hardware profile
to create methods and batches in the following sections. You will also learn about the types of
files in the Analyst® software and how to create projects and subprojects.
Topics in this section:
• Hardware Profiles on page 9
• Projects and Subprojects on page 15

Hardware Profiles
You can set up multiple hardware profiles, but only one profile can be active at any time. A
hardware profile tells the Analyst software what mass spectrometer and devices you want to use,
and how the mass spectrometer and the devices are configured and connected to the computer.
Each hardware profile must include a mass spectrometer. Before creating an acquisition method,
make sure that all devices you want to use in the method are included in the hardware profile,
including a syringe pump, if your instrument comes with an integrated syringe pump. Only
peripheral devices included in the active hardware profile can be used when creating acquisition
methods.
When you create a hardware profile in the Hardware Configuration Editor, you must also
configure the peripheral devices that you add so that the software can communicate with them.
Configuring the peripheral devices requires two procedures: setting up the physical connections
and configuring the software to communicate with the peripheral devices. When the software is
installed, the driver required for each peripheral device is also installed. After the peripheral
devices are physically connected to the computer, you can set up the appropriate configuration
information.
For information about setting up the physical connections, refer to the Peripheral Devices Setup
Guide. For a list of the supported peripheral devices, refer to the Analyst software Installation
Guide.
Topics in this section:
• Create a Hardware Profile on page 10
• Add Devices to Hardware Profiles on page 13
• Troubleshoot Hardware Profile Activation on page 14

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Create Hardware Profiles and Projects

Create a Hardware Profile

You can add peripheral devices to this hardware profile.
1. On the Navigation bar, under Configure, double-click Hardware Configuration.
Figure 1-1 Hardware Configuration Editor Dialog

2. In the Hardware Configuration Editor dialog, click New Profile.

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Figure 1-2 Create New Hardware Profile

3. In the Profile Name field, type a name for the profile.

4. Click Add Device.
In the Available Devices dialog, in the Device Type field, Mass Spectrometer is the
default value (Figure 1-3).

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Figure 1-3 Available Devices Dialog

5. In the Devices list, select the mass spectrometer and then click OK.
6. In the Devices in current profile list, select the mass spectrometer and then click
Setup Device.
7. Select the features on the Configuration tab and Communication tab as required.
8. Click OK to return to the Create New Hardware Profile dialog.
9. Click Add Device and then add and configure each device that you are using with
the mass spectrometer. Refer to Add Devices to Hardware Profiles on page 13.
10. On the Create New Hardware Profile dialog, click OK.
11. To activate the hardware profile, on the Hardware Configuration Editor, click the
hardware profile and then click Activate Profile.
A green check mark is shown next to the profile.

Tip! You do not have to deactivate one hardware profile before activating
another. Just click the hardware profile that you want to activate and then
click Activate Profile; the other profile is deactivated automatically.

12. Click Close.

13. Next steps: You can either create projects and subprojects or you can optimize the
instrument. Refer to Create Projects and Subprojects on page 17 or Optimize the
Mass Spectrometer on page 23.

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Add Devices to Hardware Profiles

Only the devices configured in the active hardware profile and selected in the Add/Remove
Device Method dialog appear as icons in the Acquisition Method Browser pane.
1. Open the Hardware Configuration Editor.
2. In the Hardware Profiles list, make sure the hardware profile has been deactivated.
3. Click Edit Profile.
4. Click Add Device.
5. In the Available Devices dialog, in the Device Type list, select the device and then
click OK.
Figure 1-4 Available Devices Dialog

Note: Remember to add a mass spectrometer. Refer to Create a

Hardware Profile on page 10.

6. In the Devices in current profile list, select the device, and then click Setup
Device.
A dialog containing configuration values for the device opens.

Note: The Alias field may also be referred to as the Name box and may be
found on another tab, under Alias.

7. On the Communication tab, in the Alias field, type a name or other identifier for the
device.

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Note: For devices using serial communication, make sure that the serial
port selected matches the serial port to which the device is physically
connected. If you are using the serial expansion cable, the number
selected in the profile is the number on the cable plus two.

• If the device uses Serial Port as a communication interface, in the COM Port
Number list, select the COM port that the device is connected to.
• If the device uses Ethernet as a communication interface, type the IP address
assigned to the device by the administrator or use the corresponding host
name for the address.
• If the device uses a GPIB board as a communication interface, do not change
the settings for the GPIB board.
The rest of the preset values for the device are likely appropriate; do not change
them. For information about the Configuration and Communication tabs, refer to the
Help.
8. To restore the device preset values, on the Communication tab, click Set Defaults.
9. To save the configuration, click OK.
10. Repeat step 4 to step 9 for each device.
11. On the Create New Hardware Profile dialog, click OK.
12. To activate the hardware profile, on the Hardware Configuration Editor, click the
hardware profile and then click Activate Profile.
The check mark should turn green. If a red x is shown then there is a problem with
the hardware profile activation. Refer to Troubleshoot Hardware Profile Activation.

Tip! You do not have to deactivate one hardware profile before activating
another. Just click the hardware profile that you want to activate and then
click Activate Profile; the other profile is deactivated automatically.

13. Click Close.

Troubleshoot Hardware Profile Activation

1. Read the error message generated. Depending on the message, there may be an
issue with a device or how the communication is set up.
2. Verify that the peripheral device has power and is turned on.
3. Verify that the COM port assigned to the peripheral device is correct.

Tip! On computers with two built-in serial ports, the first port on the serial
port expansion card is usually COM3, even though the cable indicates P1.

4. Verify that the communication settings with the peripheral device (for example, dip
switch settings) are set correctly and match the settings in the Communication tab.
5. Turn off the power to the peripheral device, wait 10 seconds, and then turn it back
on.

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6. Wait until all peripheral device power-up activities are complete before trying to
activate the hardware profile again.
Some peripheral devices may require 30 seconds or more to complete their power-
up activities.
7. If the issue persists, delete the failing profile and then create a new one.
8. If you are still having issues, contact technical support.

Projects and Subprojects

Before you begin an experiment, decide where to store the files related to the experiment. Use
projects and subprojects for each experiment to manage your data better and compare your
results. For example, you can use subprojects to store the results for specific dates.
Topics in this section:
• Project Organization on page 15
• About Subprojects on page 16
• Create Projects and Subprojects on page 17
• Create a Subproject on page 18
• Copy a Subproject on page 19
• Installed Projects on page 20
• Back up the API Instrument Project on page 20

Project Organization
A project is a folder structure for organizing and storing sample information, data, quantitation
information and so forth. Within each project there are folders that can contain different types of
files; for example, the Data folder contains acquisition data files. Table 1-1 on page 15 describes
the contents of the different folders.
The software can access a project only if it is stored in a root folder. You cannot create projects in
a folder that has not been defined as a root folder.
The preset root folder is Analyst Data on the drive where the Analyst® software is installed. If you
want to store projects in other locations, you must create new root folders. Refer to the Help
system.
Table 1-1 Project Folders
Folder Contents
\Acquisition Methods Contains all acquisition methods used. Acquisition methods have the
.dam extension.
\Acquisition Scripts Contains all the acquisition batch scripts available.
\Batch Contains all the acquisition batch files used. Acquisition batches have
the .dab extension. It also contains a subfolder, Templates, that contains
acquisition batch templates. Batch templates have the .dat extension.
\Data Contains the acquisition data files (.wiff extension).

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Table 1-1 Project Folders (Continued)

Folder Contents
\Log Contains results of quantitation and compound optimization.
\Processing Methods Contains all qualitative data processing methods used.
\Processing Scripts Contains all data processing scripts available. Processing scripts stored
in the API Instrument project appear in the Scripts menu.
\Project Information Contains all project information and settings for the project. This folder
cannot be stored in a subproject.
\Quantitation Methods Contains all quantitation methods used. Quantitation methods have a
.qmf extension.
\Results Contains all quantitation results table files (.rdb extension).
\Templates Contains report templates (.rpt extension).

About Subprojects
A subproject contains a subset of the folders in the project. All subprojects must contain the same
folders. Subprojects can be very useful for organizing your data. For example, if you are running
samples of various compounds from different laboratories using the same acquisition method,
you could create subprojects to store the results for each laboratory, but leave the acquisition
method folder in the project. The acquisition method would then be available for use with
subproject or laboratory. Alternatively, if you were running samples over a period of several
weeks, you could store the results from each day in a separate subproject.

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Figure 1-5 Example of a Project and Subproject Folder Structure

Create Projects and Subprojects

If you want to use a subproject structure within a project, you must create a subproject when you
first create the project. You cannot create a subproject in an existing project that does not already
have a subproject structure.
1. Click Tools > Project > Create Project.
2. In the Project name field, type a project name.
3. If you want to use subprojects in this project, select the folders that you want to store
in the subprojects and then use the arrow buttons to move them to the Subproject
folders list.

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Figure 1-6 Create New Project/Subproject Dialog

Note: You cannot create a new subproject for a project that was not
originally created with a subproject.

4. If you are using subprojects, in the Subproject name field, type a name for the first
subproject or use the existing date.
5. If you want to use this project and subproject folder organization for all new projects,
select the Set configuration as default for new projects check box.
All new projects will be created with this folder configuration.
6. Click OK.

Create a Subproject
1. On the Project toolbar, in the Project list, select the project in which you want to
create a subproject.
2. Click Tools > Project > Create Subproject.
3. In the Subproject name box, type a name for the subproject or use the existing
date.

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4. Click OK.

Copy a Subproject
Note: You can copy a subproject from another project that has existing subprojects;
however, the copied subprojects may contain folders that also exist in the project folder.
When the same folders exist at both the project and subproject levels, the software uses
the project level folders.

1. Click Tools > Project > Copy Subproject.

The Copy Subproject dialog opens.
2. Click Browse to navigate to the subproject source and then click OK.
3. In the Source Subproject list, select the subproject to be copied.
4. Click Browse to navigate to the subproject destination.
5. In the Target Subproject field, type the name for the copied subproject and then
click OK.
6. Do one of the following:
• To copy all folders and files from the Subproject Source into the Subproject
Destination, select the Copy Contents check box.
• To copy only the folders in the same structure into the Subproject
Destination, make sure that the Copy Contents check box is cleared.
7. Click Copy.

Switch Between Projects and Subprojects

• On the Analyst software toolbar, from the project selection list, select the project or
subproject.
Figure 1-7 Analyst Toolbar

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Installed Projects
Three projects are installed with the software: API Instrument, Default, and Example.

API Instrument Project

The API Instrument project is unique and very important to the proper functioning of the
instrument. The API Instrument project contains the information required for tuning and
calibrating your instrument. This information includes parameter settings files, reference files,
instrument data files that contain calibration and resolution information, and the acquisition
methods used during automatic tuning. The API Instrument project also contains data files for
manual tuning runs that were performed using the Start button rather than the Acquire button.
These data files are saved automatically in the API Instrument project in the Tuning Cache folder
and named with the date and time they were created. The Tuning Cache needs to be emptied on
a regular basis.

Default Project
The Default project contains folders that are present in new projects and serves as a template for
new projects.

Example Project
The Example project contains sample methods and data files. You can practice working with the
Explore or Quantitate modes using the example data files. The example files are sorted into
subfolders by instrument type and application area.

Back up the API Instrument Project

You should routinely back up this project. You should also back up this project after routine
maintenance has been done.
1. To create the backup, copy the API Instrument project, paste it to a different location,
preferably to another computer, and then rename the folder. You should use the
date, and an instrument reference if you have more than one instrument, when you
rename the folder; for example, API Instrument__4000QTRAP3_010107
2. To recover the project, rename the current API Instrument folder, and then copy the
backup into the Projects folder and then change its name back to API Instrument.
Table 1-2 Icons on the Analyst Software Toolbar
Icon Name Function
New Subproject Click to create a subproject.You can create subprojects later in the
process only if the project was originally created with subprojects.
Copy Subproject Click to copy a Subproject folder.
You can copy a subproject from another project that has existing
subprojects; however, the copied subprojects may contain folders
that also exist in the project folder. When the same folders exist at
both the project and subproject levels, the software uses the
project level folders.

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2
In this section, you will learn how to use the Instrument Optimization software to tune, calibrate,
and optimize the mass spectrometer to get the best performance.
You should run the Verify instrument performance option weekly or after you clean the mass
spectrometer to confirm that the system is working properly. In general, the calibration and
resolution for quadrupole are fine for 3 to 6 months unless the system loses vacuum. For LIT
(linear ion trap) systems, the resolution should also be good for 3 to 6 months but the calibration
should be done approximately monthly. If the system loses vacuum then you should check the
calibration and resolution before using the system.

Tip! Perform maintenance tasks regularly to make sure that the mass spectrometer is
performing optimally. Refer to the Qualified Maintenance Person Guide.

About Tuning and Calibrating

Tuning the instrument is the process of optimizing the resolution and instrument parameters to
attain the best sensitivity and performance of the mass spectrometer. Optimizing the resolution
means adjusting the peak width and peak shape. You can tune and calibrate the instrument
either automatically or manually.

Caution: Potential Calibration Error. If the temperature changes by more than 2°C, then
the resolution and mass calibration might be affected.

Tip! Clean the Q0 region regularly to minimize the impact of charging (a significant
loss of sensitivity of the ions of interest over a short period of time) on the quadrupoles.
Refer to the Qualified Maintenance Person Guide.

Automatic tuning: The software performs resolution optimization and mass calibration, using
the Instrument Optimization wizard. For LIT instruments, MS3 optimizations are also performed.
Manual tuning: You can perform many of the instrument resolution optimizations and
calibrations manually.

Automatically Tune and Calibrate

Instrument Optimization is automatic instrument tuning software that tunes both quadrupole and
LIT modes and performs mass calibration. For quadrupole mode, it adjusts the resolution offsets.
For LIT mode, it optimizes AF3 and EXB. For MS3, it adjusts the Excitation and Isolation
coefficients. You can select one of the instrument performance options:
• Verify instrument performance: Tests the instrument performance but leaves the
instrument settings unchanged. A report is generated at the end of the test. You can
use this option weekly to check how well the instrument is performing.
• Adjust mass calibration only: Automatically checks and adjusts the mass
calibration. If the mass calibration has changed, then the software corrects it. You
can use this option weekly for LIT instruments, or monthly to check and adjust the
mass calibration if required.

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• Adjust instrument settings: Checks and adjusts the instrument settings and mass
calibration. The instrument settings are updated from the current settings to optimal
settings. You can use this option if instrument performance is poor or if the peak
shape is bad. Only experienced users should adjust the instrument settings.

Note: Old LIT methods must be updated with the new settings. This can
be done two ways. The first way is by toggling the LIT speed in the
advanced MS tab and then saving the method. The second way is by using
the Change All Methods script that is available from AB SCIEX technical
support.

• Reset selected scan modes to default values and adjust instrument settings:
Resets the instrument values to the factory preset values. Select this option if a
major component of the instrument is replaced or after the first installation. Only
FSEs should use this feature.
You can back up your current instrument parameters in case you want to restore them later. The
preset location for the instrument parameters is C:\Analyst Data\Projects\API
Instrument\Instrument Optimization\Instrument Settings Backups\User Created Backups.

Back up Instrument Parameters

1. On the Navigation bar, double-click Instrument Optimization.
2. Click File > Backup Instrument Settings Files in the Instrument Optimization
dialog.
3. Type a file name and then click Save.

Restore Instrument Parameters

1. On the Navigation bar, double-click Instrument Optimization.
2. Click File > Restore Instrument Settings Files in the Instrument Optimization
dialog.
3. Navigate to the instrument settings that you want to restore and then click Open.

Required material
• Tuning solutions that are supplied in the Standards Chemical Kit shipped with the
system. If needed, a new Kit can be ordered from AB SCIEX. For information about
the appropriate solutions that should be used in a system, refer to Calibration Ions
and Solutions on page 127.
• 5 ml, 1 ml, and 250 µl serial gas-tight syringes (1.0 ml will be used as reference).
• PEEK (red) sample tubing.
• Syringe pump, if using an instrument without an integrated syringe pump.

Prerequisites
• Make that you have a printer configured.
• Make sure that the spray is stable and that the proper tuning solution is being used.

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Optimize the Mass Spectrometer

The following procedure describes how to verify the performance of the instrument. For more
information on using the other instrument performance options, refer to the Help.
1. On the Navigation bar, under Tune and Calibrate, double-click Manual Tuning.
2. Run a calibration method and then confirm that there is a stable TIC.
3. Confirm that the peaks of interest are present in the spectrum.
4. On the Navigation bar, under Tune and Calibrate, double-click Instrument
Optimization.
5. Click Verify instrument performance and then click Next.
6. Click Approved Tuning and then click Next.
7. Select a Tuning Solution from the list.
Depending on the solution you choose, different modes are available.
• Click a polarity.
• If available, click Q1 and Q3 in the Quad section. If available, click the
required scan speeds.
• If available, click the scan speeds in the LIT section.
• If available, click Excitation in the MS/MS/MS section.
8. Click Next.
9. If the Select a mode page opens, select Automatic.
10. Click Next.
11. Click GO. In this example, the preset values are suitable.
The Verifying or Adjusting Performance screen opens. After the process has
completed, the Results Summary opens. Refer to the Help system.
12. Depending on what you had selected, you will be prompted to change solutions for
the various scan types and polarities.

Verify or Adjust Performance

The top left corner displays the part of the instrument that is being tuned.
Current Spectrum: This graph displays the spectrum of the current scan, the optimal scan
selected by the software, or the scan at the current parameter value when you are reviewing the
software results in interactive mode.
The Instrument Optimization Decision Plots, in the top right graph, dynamically display the
intensity versus voltage curves of the parameters that are currently being optimized.

Results Summary
The Results Summary is a record of any instrument settings changes that were made by the
Instrument Optimization software. This includes the location of data files and instrument settings
backups, as well as step-by-step changes and results during optimization. In addition, the
Results Summary displays a verification report. This report contains a snapshot of the mass

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spectrum for each relevant mass for the scan modes being verified. The spectrum is labelled with
the target mass, where the mass was found, mass shift, peak width, and peak intensity. The
spectrum can be used as a visual record of peak shape or scan mode performance. A summary
table of results follows the spectra. Refer to Figure 2-1 on page 24.
The Results Summary is saved as a document in the folder indicated at the top of the report. You
can print the Results Summary or you can open a previously saved Results Summary.
Figure 2-1 Results Summary

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3
In this section, you will learn how to create methods that you can use for data acquisition.
Topics in this section:
• About LC Methods on page 25
• Create Mass Spectrometry Methods on page 25
• Add or Remove Devices From Acquisition Methods on page 32
• Change Acquisition Methods on page 38

About LC Methods
Creating an acquisition method using a peripheral device, such as an HPLC, includes providing
the operating parameters for that device. If you are creating a new acquisition method file from
an existing file, you may decide to use some or all of the peripheral device methods in the
acquisition method.

Create Mass Spectrometry Methods

You create the mass spectrometer acquisition method using the Acquisition Method Editor.
Depending on the type of mass spectrometer configured and the scan type selected, different
fields and options are available. As you type the mass spectrometer parameters, the Acquisition
Method Editor validates the settings.
Topics in this section:
• Create an Acquisition Method using a Q1 MS Scan Type on page 26
• Create an Acquisition Method using a Q1 MI Scan Type on page 29
• Create an Acquisition Method using an MRM Scan Type on page 30
Spectral data can be acquired in one of three modes, as shown in Table 3-1 on page 25:
Table 3-1 Spectral Data Acquisition
Mode Description
Profile Profile data is the data generated by the instrument and corresponds
to the intensity recorded at a series of evenly spaced discrete mass
values. For example, for a mass range 100 Da to 200 Da and step
size 0.1, the instrument scans 99.95 to 100.05 (records as value 100),
100.05 to 101.15 (records as value 101)…199.95 to 200.05 (records
as value 200). The preset value is 0.1 Da.
Peak Hopping Peak Hopping is a mode of operating a mass spectrometer in which
large steps (approximately 1 Da) are made. It has the advantage of
speed (less data steps are made) but with the loss of peak shape
information. The preset value is 1.0 Da.

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Table 3-1 Spectral Data Acquisition (Continued)

Mode Description
Centroid The instrument scans as in Profile mode, but centroids the data,
replacing found peaks with the intensity-weighted center of gravity for
each peak. Centroiding has the advantage of significantly reducing file
size with a loss of peak shape information. The disadvantage is that if
data has been collected as a centroid it cannot be altered. It is
recommended to use Profile mode and centroid the data post-
acquisition.

You can create one of the following methods and use it in Create and Submit Batches on
page 41 to acquire data:
• Create an Acquisition Method using a Q1 MS Scan Type on page 26
• Create an Acquisition Method using a Q1 MI Scan Type on page 29
• Create an Acquisition Method using an MRM Scan Type on page 30

Required equipment
• Reserpine solution (refer to Table 3-2.) that is supplied in the Standards Chemical Kit
shipped with the system. If needed, a new Kit can be ordered from the manufacturer.
• 5 mL, 1 mL, and 250 µL serial gas-tight syringes.
• PEEK (red) tubing transfer line.
• Syringe pump.
Table 3-2 Reserpine Concentrations
System Reserpine Concentration
API 2000™ System and QTRAP® System 1 pmol/µl (1 µM)
API 3000™ System 0.167 pmol/µl (0.167 µM or 6:1)
API 4000™ System and 4000 QTRAP 0.167 pmol/µl (0.167 µM or 6:1)
System

API 5000™ System 0.0167 pmol/µl (0.0167 µM or 60:1)

Create an Acquisition Method using a Q1 MS Scan Type

Use the following procedure to create a method using the Q1 MS scan. The ion intensity is
returned for every requested mass in the scan range. You can save the acquisition method in the
Tutorial project that you created in Create Projects and Subprojects on page 17.
1. Make sure that a hardware profile containing the mass spectrometer and syringe is
active.
2. On the software toolbar, make sure that the appropriate project is selected.
3. On the Navigation bar, in Acquire mode, double-click Build Acquisition Method.
The Method Editor is shown with a method template based on the active hardware
profile.
4. In the Acquisition method pane, click Acquisition Method.

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5. On the Acquisition Method Properties tab, in the Synchronization Mode list,

make sure that No Sync is selected. For more information about synchronization
modes, refer to the Help.
6. In the Acquisition method pane, click the Mass Spec icon.
7. On the MS tab, in the Scan type list, select Q1 MS (Q1).
8. In the Polarity group, click Positive.
9. Clear Center/Width and Parameter Range check boxes if selected.
10. Type the following values:
Table 3-3 MS Tab Parameter Values
Field Value
Start (Da) 200
Stop (Da) 700
*Time (sec) (if available) 2.5
*Scan rate (Da/s) (if available) 200
Duration (min) 3
* These fields are instrument dependent.

11. Click the Advanced MS tab. Note that the scan mode is set to Profile and the step
size is 0.1 in the Step size field.
In this example, the quadrupole (Q1) is scanning a 600 amu mass range taking 0.1
Da steps; therefore, there are 6000 steps across the mass range. If this takes 2.4
seconds to scan, the dwell time is 0.4 ms per step. This is typically the fastest that
you want to scan a Q1 or Q3 scan based on standard calibration procedure. Proper
consideration for mass calibration should be taken if Q1 or Q3 are to be scanned
faster.

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Note: The step size and the time of the scan control the dwell time per
step for the scan. The dwell time is the length of time spent acquiring signal
at each step in a scan.

12. On the MS tab, click Edit Parameters.

13. Click the Source/Gas tab in the Parameter table dialog.
14. Type the following values:
Table 3-4 Source/Gas Tab Parameters
Source/Gas parameters Typical value
Curtain Gas (CUR) 20
IonSpray Voltage (IS) 5000
Temperature (TEM) 0
Ion Source Gas 1 (GS1) 15
Ion Source Gas 2 (GS2) 0

15. Click the Compound tab and then set the Declustering Potential (DP) to 90 and
leave the Entrance Potential (EP) at 10.
A value of 90 might not be optimal for your mass spectrometer but it is a good DP to
start with.
16. Click OK.
17. In the Acquisition method pane, click the Harvard Syringe Pump icon.
18. On the Syringe Pump tab, edit the syringe pump method to include Syringe
Diameter, Flow Rate, and Unit.
Figure 3-1 Harvard Syringe Pump Method Properties Tab

19. Save the acquisition method.

20. Next steps: You have created an acquisition method that you can now use to acquire
data for preliminary analysis. To create and submit batches, refer to Create and
Submit a Batch on page 42.

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Create an Acquisition Method using a Q1 MI Scan Type

Use the following procedure to create a method using the Q1 MI scan. The ion intensity is
returned for only the specified masses. You can save the acquisition methods in the Tutorial
project that you created in Create Projects and Subprojects on page 17.
1. Make sure that a hardware profile containing the mass spectrometer and syringe is
active.
2. On the software toolbar, make sure that the Tutorial project is selected.
3. On the Navigation bar, in Acquire mode, double-click Build Acquisition Method.
The Method Editor is shown with a new method based on the active hardware
profile.
4. In the Acquisition method pane, click Acquisition Method.
5. On the Acquisition Method Properties tab, in the Synchronization Mode list,
make sure that No Sync is selected. For more information about synchronization
modes, refer to the Help.
6. In the Acquisition method pane, click the Mass Spec icon.
7. On the MS tab, in the Scan type list, select Q1 Multiple Ions (Q1 MI).
8. In the Polarity group, click Positive.
9. Type the following values in the mass ranges table:
Table 3-5 MS Tab Parameter Values
Field Value
Q1 Mass (Da) 609
Time (msec) 100

Figure 3-2 MS Tab

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10. Click Edit Parameters.

11. Click the Source/Gas tab in the Parameter Table dialog.
12. Type the following values:
Table 3-6 Source/Gas Tab Parameter Values
Source/Gas parameters Typical value
Curtain Gas (CUR) 20
IonSpray Voltage (IS) 5000
Temperature (TEM) 0
Ion Source Gas 1 (GS1) 15
Ion Source Gas 2 (GS2) 0

13. Click OK.

14. Click the Compound tab and then set the Declustering Potential (DP) to 90 and
leave the Entrance Potential (EP) at 10.
A value of 90 may not be optimal for your mass spectrometer but it is a good DP to
start with.
15. In the Acquisition method pane, click the Harvard Syringe Pump icon.
16. On the Syringe Pump tab, edit the syringe pump method to include Syringe
Diameter, Flow Rate, and Unit.
Figure 3-3 Harvard Syringe Pump Method Properties Tab

17. Save the acquisition method.

18. Next steps: You have created an acquisition method that you can now use to create
and submit a batch. To create and submit batches, refer to Create and Submit a
Batch on page 42.

Create an Acquisition Method using an MRM Scan Type

Use the following procedure to create a method using the MRM scan. This scan is used in
quantitative applications. An MRM scan can be used to determine how much of a compound is in
a sample; and it is now used in pharmacokinetic analysis and increasingly in applied markets and
screening applications. You can save the acquisition methods in the Tutorial project that you
created in Create Projects and Subprojects on page 17.
1. Make sure that a hardware profile containing the mass spectrometer and syringe is
active.

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2. On the software toolbar, make sure that the Tutorial project is selected.
3. On the Navigation bar, in Acquire mode, double-click Build Acquisition Method.
The Method Editor is shown with a new method based on the active hardware
profile.
4. In the Acquisition method pane, click Acquisition Method.
5. On the Acquisition Method Properties tab, in the Synchronization Mode list,
make sure that No Sync is selected. For more information about synchronization
modes, refer to the online Help.
6. In the Acquisition method pane, click the Mass Spec icon.
7. On the MS tab, in the Scan type list, select MRM (MRM).
8. In the Polarity group, click Positive.
9. Type the following values in the mass ranges table:
Table 3-7 Mass Range and Dwell Time
Q1 Mass (Da) Q3 Mass (Da) Time (msec)
609 397.2 100

10. Click Edit Parameters.

11. Click the Source/Gas tab in the Parameter Table dialog.
12. Type the following values:
Table 3-8 Source/Gas Tab Parameters
Source/Gas parameters Typical value
Curtain Gas (CUR) 20
Collision Gas (CAD) 0
IonSpray Voltage (IS) 5000
Temperature (TEM) 0
Ion Source Gas 1 (GS1) 15
Ion Source Gas 2 (GS2) 0

13. Click the Compound tab and then change the Declustering Potential (DP) to 90
and the Collision Energy (CE) to 45.
14. In the Acquisition method pane, click the Harvard Syringe Pump icon.
15. On the Syringe Pump tab, edit the syringe pump method to include Syringe
Diameter, Flow Rate, and Unit.

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Figure 3-4 Harvard Syringe Pump Method Properties Tab

16. Save the acquisition method.

17. Next steps: You have created an acquisition method that you can now use to create
and submit a batch. To create and submit batches, refer to Create and Submit a
Batch on page 42.

Add or Remove Devices From Acquisition

Methods
With the Acquisition Method Editor, you can customize the acquisition method by adding or
removing HPLC peripheral device methods. If the required device icon is not in the Acquisition
Method Browser pane, then you can add the peripheral device only if it is included in the active
hardware profile.
Topics in this section:
• Add or Remove an LC Device on page 32
• Modify LC Pump Properties on page 33
• Set Autosampler Properties on page 33
• Set Integrated Syringe Pump Properties on page 34
• Set Column Oven Properties on page 35
• Set Switching Valve Properties on page 35
• Set Diode Array Detector Properties on page 36
• Set Analog to Digital Converter Properties on page 37

Note: The available parameters for the LC devices vary depending on the
manufacturer.

Add or Remove an LC Device

1. With a method file open in the Acquisition Method Editor, in the Acquisition method
pane, right-click Acquisition Method and then click Add/Remove Device Method.

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Figure 3-5 Add/Remove Device Method Dialog

2. Select or clear the check boxes beside the device method to add or remove the
device method.
3. Click OK.

Modify LC Pump Properties

Modify each device in the method in order for it to function properly for your method.
1. With an acquisition method file open in the Acquisition Method Editor, in the
Acquisition method pane, click the Pump icon.
The Pump Properties tab opens in the Acquisition Method Editor pane. Figure 3-6 on
page 33 shows an Agilent LC binary pump.
Figure 3-6 LC Pump Gradient Tab

2. Edit the LC pump method to include the pump conditions, including the flow rate and
sample composition, that you will be using during sample acquisition.
3. If required, on the Limits (Advanced) tab, edit the advanced pump parameters.
4. Save the method.

Set Autosampler Properties

1. Make sure that on the Acquisition Properties tab, the Synchronization Mode field
is set to LC Sync. The LC and the mass spectrometer will start simultaneously.
2. With a method file open in the Acquisition Method Editor, in the Acquisition method
pane, click the Autosampler icon.
The Autosampler Properties tab opens in the Acquisition Method Editor pane.
Figure 3-7 on page 34 shows an Agilent autosampler.

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Figure 3-7 Autosampler Properties Tab

3. If required, edit the Inject Details and Wash Details.

4. If required, click the Advanced Properties tab, and then type the needle and
advanced injection information.
5. Save the method.

Set Integrated Syringe Pump Properties

This procedure is for systems with built-in syringe pumps. To use this function with an external
syringe pump you must have a syringe pump with a serial port and the serial cable.
1. In the Acquisition method pane, click the Syringe Pump icon.
The Syringe Pump Properties tab opens in the Acquisition Method Editor pane.
Figure 3-8 Syringe Pump Properties Tab

2. In the Syringe Diameter (mm) field, type the syringe diameter.

3. In the Flow Rate field, type the flow rate.
4. In the Unit list, select the units of flow.
5. Save the file.

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Set Column Oven Properties

1. With a method file open in the Acquisition Method Editor, in the Acquisition method
pane, click the Column Oven icon.
The Column Oven Properties tab opens in the Acquisition Method Editor pane.
Figure 3-9 Column Oven Tab

2. Type the temperature of the column oven or column oven compartments in degrees
Celsius.
3. In the Temperature Tolerance field, type the temperature tolerance in degrees
Celsius.
4. In the Start Acquisition Tolerance field, type the start acquisition tolerance in
degrees Celsius.
5. If you are using the Agilent column oven, in the Column Switching Valve section,
select Time Table Used check box to add and remove entries from the time table at
the bottom of the pane, or select an option from the Position for the first sample in
the batch list and then click one of the sample positions options.
6. Save the file.

Set Switching Valve Properties

The switching valve can be used as a diverter or injection valve. Select the Manual Sync with
Valve synchronization mode if you are using the valve as an injector; choose any other mode if
you are using the valve as a diverter.
1. With a method file open in the Acquisition Method Editor, in the Acquisition method
pane, click the Valve icon.
The Valve Properties tab opens in the Acquisition Method Editor pane.

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Figure 3-10 Valve Properties Tab

2. Change the position names from their preset names, if required. The switching valve
is sometimes used to switch the flow of solvent to waste, or to a different column.
The preset position names are A and B.
• In the Change Position Names list, select a position.
• In the Change Position Names list, rename the preset position names A and
B to Inject and Divert or to Column and Waste, depending on how the valve is
plumbed.
3. In the Total Time (min) column, click a cell and then type the total time the valve will
remain in this position.
4. In the Position column, click a cell and then, in the Position list, select the valve
position.
5. Repeat step 3 and step 4 for each switch of the valve required during acquisition.
6. Save the file.

Set Diode Array Detector Properties

1. With a method file open in the Acquisition Method Editor, in the Acquisition method
pane, click the Diode Array Detector (DAD) icon.
The DAD Method Editor tab opens in the Acquisition Method Editor pane.

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Figure 3-11 DAD Method Editor Tab

2. Do one of the following:

• To scan one to five individual wavelengths, in the Operating Mode section,
click Signal Data and then edit the data requirements.
• To scan over a wavelength range, in the Operating Mode section, click
Spectral Data and then edit the data requirements.
3. Save the file.

Set Analog to Digital Converter Properties

1. With a method file open in the Acquisition Method Editor, in the Acquisition method
pane, click the Analog to Digital Converter (ADC) icon.
The Analog/Digital Convertor Properties tab opens in the Acquisition Method Editor
pane.
Figure 3-12 Analog to Digital Converter Properties Tab

2. In the Sample section, in the Rate (pts/sec) field, type the rate.

Note: The interval and rate are proportional to each other. When you
change the rate, the software automatically calculates the interval.

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3. Do the following to set the channel details:

• In the Channels field, click the channel name, and then select the check box
beside the name to include it in the method.
• In the Interpreted Value @ Full Scale field, type the appropriate value.
• In the Interpreted Unit field, type the appropriate unit.
The number of available channels is specified when setting up the ADC in the
hardware profile.
4. Save the file.

Change Acquisition Methods

You can add or delete periods and experiments to existing acquisition methods. You must have a
method open in Acquire mode to get the view.
Topics in this section:
• Add an Experiment on page 38
• Copy an Experiment into a Period on page 38
• Copy an Experiment within a Period on page 38
• Add a Period on page 39

Add an Experiment
1. In the period where you want to add an experiment, right-click, and then click Add
experiment.
An experiment is added below the last experiment in the period.

Note: You cannot insert an experiment, IDA criteria, or period. You can
only add an experiment at the end of the period.

2. In the Acquisition Method Editor pane, select the appropriate device or instrument
parameters.

Copy an Experiment into a Period

• In the Acquisition method pane, press Ctrl and then drag the experiment to the
period.
The experiment is copied below the last experiment in the period.

Copy an Experiment within a Period

• Right-click the experiment and then click Copy this experiment.
This is useful when you are adding the same or similar experiments and most or all
the parameters are the same as in IDA.

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Add a Period
• In the Acquisition method pane, right-click the Mass Spec icon, and then click Add
period.
A period is added below the last period created.
Table 3-9 Icon Quick Reference: Method Editor
Icon Name Function
Mass Spec Click to show the MS tab in the Acquisition Method Editor.

Period Right-click to add an experiment, add an IDA Criteria Level, or

delete the period.
Autosampler Click to open the Autosampler Properties tab.

Syringe Pump Click to open the Syringe Pump Properties tab.

Column Oven Click to open the Column Oven Properties tab.

Valve Click to open the Valve Properties tab.

DAD Click to open the DAD Method Editor. For more information on
DAD, refer to View DAD data on page 68.
ADC Click to open the ADC Properties tab. For more information on
ADC, refer to View ADC Data on page 61.

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4
In this section, you will learn how to create and submit batches and also how to monitor the
sample queue.
A batch is a collection of information about the samples that you want to analyze. When you
create a batch, you are telling the software the order in which you want to analyze samples.

Queue Options
Before you submit the samples, you can review and edit the queue conditions, such as the
maximum number of acquired and waiting samples and the maximum idle time.
The queue goes one by one through the list, running each sample with the selected acquisition
method. After all the samples have been acquired, the queue stops and the instrument goes into
Standby mode. In Standby mode, the LC pumps are turned off and some instrument voltages are
turned off.
You can modify the length of time the queue runs after the last acquisition has finished, before it
puts the instrument into Standby mode. For more information about the other fields in the Queue
Options dialog, refer to the Help.

Set Queue Options

1. On the Navigation bar, click Configure.
2. Click Tools > Settings > Queue Options.
Figure 4-1 Queue Options Dialog

3. In the Max Idle Time field, type the length of time the queue will wait after acquisition
is completed before going into Standby mode. The preset value is 60 minutes.

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If you are using gas cylinders, you may want to adjust this time to make sure that you
do not deplete the gas in the cylinders.
4. If you are using an LC method, before the run is started, make sure that there is
enough solvent in the reservoirs for the primary flow rate for all of the sample runs
and the Max. Idle Time.

Create and Submit a Batch

Use this workflow to create a batch. In this example, we will use the MRM scan that you created
previously. You can also go through the workflow twice more for practice, once using the Q1MS
and the second time using Q1MI methods.

Add Sets and Samples to a Batch

1. On the Navigation bar, under Acquire, double-click Build Acquisition Batch.
Figure 4-2 Batch Editor

2. On the Sample tab, in the Set list, type Test Set.

3. Click Add Set.
4. Click Add Samples to add samples to the new set.

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Figure 4-3 Add Sample Dialog

5. In the Sample name section, in the Prefix field, type a name for the samples in this
set.
6. To include the sample number as part of the full sample name, select the Sample
number check box.
7. If you have selected the Sample number check box, in the Number of digits field,
type the number of digits to include in the sample name. For example, if you type 3,
the sample names would be samplename001, samplename002, samplename003.
8. In the Data file section, in the Prefix field, type a name for the data file that will store
the sample information.
9. If you want the set name to be part of the data file name, select the Set name check
box.
10. Select the Auto Increment check box to increment the data file names
automatically.

Note: The data for each sample can be stored in the same or separate
data file. The names of the data file will have numerical suffixes starting
from 1.

11. In the Sub Folder field, type Test Data.

The folder is stored in the Data folder for the current project. If you leave the Sub
folder field blank, the data file will be stored in the Data folder and a subfolder will not
be created.
12. In the New samples section, in the Number field, type the number of new samples
to add and then click OK. For this example, add three samples.
The sample table fills with the sample names and data file names.

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Tip! Fill Down and Auto Increment options are available in the right-click
menu after you select a single column heading or several rows in a column.

13. On the Sample tab, in the Acquisition section, select the MRM method from the list.
You can run the batch twice more using the Q1MS and the Q1MI methods.

Tip! If you want to use different methods for some of the samples in this
set, select the Use Multiple Methods check box. The Acquisition Method
column is shown in the Sample table. You can select the acquisition
method for each sample in this column.

Depending on how your system is set up, you will have to type the information
specific for your autosampler. Even if the injection volume is set in the method you
can change it for one or more samples by changing the value in Inj. Volume column.
14. If you want to change the injection volumes from the volumes listed in the method, in
the Inj. Volume (µL) column, type the injection volume for each sample.
15. To set sample locations, do one of the following:
• Set Sample Locations in the Batch Editor on page 45
• Select Vial Positions Graphically using the Locations tab (Optional) on
page 46
16. (Optional) If you want to define quantitation details prior to submitting the batch, then
refer to Set Quantitation Details in the Batch Editor (Optional) on page 47.
17. Click the Submit tab.
18. If the Submit Status section contains a message about the status of the batch, do
one of the following:
• If the message indicates that the batch is ready for submission, proceed to
step 19.
• If the message indicates that the batch is not ready for submission, make the
changes as indicated by the message.
19. Click Submit.
The Acquisition dialog opens.
20. Save the file.

Acquire Data
The system should not be in Tune mode when you start sample acquisition. Also, if the system
has been previously run that day and has not yet been set to Standby, sample acquisition will
start automatically.
1. In Acquire mode, click View > Sample Queue.
The Queue Manager opens with all submitted samples.

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Figure 4-4 Queue Manager

2 3

Item Description
1 The Tune icon should not be pressed in.
2 Queue status should be Stand By.
3 Queue Server should be in Normal mode. For more information,
refer to Queue States on page 51.

2. Click Acquire > Start Sample.

3. Next steps: You can now analyze the data that you have just acquired. For more
information, refer to Analyze and Process Data on page 57 or Analyze and Process
Quantitative Data on page 97.

Set Sample Locations in the Batch Editor

If an autosampler is being used in the acquisition method, then the vial positions of the samples
must be defined in the acquisition batch. You can define the location on the Sample tab or on the
Locations tab. For more information on creating batches, refer to Create and Submit Batches on
page 41.

Note: Depending on the autosampler you are using, it may not be necessary to
type details in additional columns.

1. On the Sample tab, in the Set list, select the set for which you want to select sample
locations.
2. For each sample in the set, do the following if applicable:
• In the Rack Code column, select the rack type for the autosampler.
• In the Rack Position column, select the position of the rack in the
autosampler.
• In the Plate Code column, select the plate type for the autosampler.
• In the Plate Position column, select the position of the plate on the rack.
• In the Vial Position column, type the position of the vial in the plate or tray.
3. Save the file.

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Select Vial Positions Graphically using the Locations tab

(Optional)
1. In the Batch Editor, click the Locations tab.

2. In the Set list, select the set for which you want to select sample locations.
3. In the Autosampler list, select the autosampler that you are using.
The appropriate number of rack spaces for the autosampler you chose is shown in
the graphic rack display.
4. In the space associated with the rack you are using, right-click and then select the
rack type you are using.
The plates or trays you selected are shown in the rack.
5. Double-click one of the rectangles.
The circles depicting the wells or vials for the plate or tray appear.
6. To select whether samples are marked by row or column, click Row/Column
Selection. If the button shows a red horizontal line, the Batch Editor marks the
samples by row. If the button shows a red vertical line, the Batch Editor marks the
samples by column.
7. Click the sample wells or vials in the order to be analyzed. Click a selected well or
vial again to clear it.
8. Save the file.

Tip! It is also possible to auto fill in the samples by clicking the first and
final vial within a set with the Shift key held down. Multiple injections from
the same vial can be done by holding down Ctrl while clicking the vial
location (red circle changes to a green).

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Set Quantitation Details in the Batch Editor (Optional)

If you are using a Quantitation method with a batch and if you do not want to select quantitation
details post-acquisition then define the quantitation details prior to submitting a batch.
The appropriate Internal Standard and Standard columns appear in the Quantitation tab
according to the quantitation method selected in the Sample tab.
1. With a batch file open in the Batch Editor window, click the Quantitation tab.
2. Select the set containing the samples that you want to modify.
3. From the list in the cell, select a Quant Type for all the samples.
4. If applicable, type the peak concentration in the Analyte column.
5. If applicable, type the Internal Standard.
6. Repeat the preceding steps for each set in the batch.
7. Save the file.

Tip! The order of samples can be edited before you submit them to the
Queue. To change the order of a sample, when in the Submit tab, double-
click any of the numbers on the far left of the table (you'll see a very faint
square box), and then drag them to the new location.

Stop Sample Acquisition

There are three ways to stop a sample after it is in the sample queue and the instrument is
running. The following procedures shows you one way to stop sample acquisition. For more
information on the other ways to stop sample acquisition, refer to Table 4-4 on page 54. When
you stop a sample acquisition, the current scan finishes before the acquisition is stopped.
1. In the Queue Manager, click the sample in the queue after the point where you want
to stop acquisition.
2. Click Acquire > Stop Sample.
The queue stops after the current scan in the sample you selected is complete. The
sample status on the Queue Manager (Local) window changes to Terminated, and
all others following in the queue are Waiting.
3. When you are ready to continue processing the batch, click Acquire > Start
Sample.

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Import and Submit Batch Files

You can import a text file containing batch information instead of creating a batch in the Batch
Editor. If you have all the details for the samples you want to process in a spreadsheet, it is faster
to rearrange and import the data in the spreadsheet than to manually type the data into the Batch
Editor.
Before you import batch information from a text file, make sure the data in the file is organized
and formatted correctly. In particular, the column headings in the spreadsheet must match the
Batch Editor column headings.

Build a Batch as a Text File

To make sure that your text file includes the proper headings, you must create a batch using the
Batch Editor, export it as a text file, type the appropriate values in a spreadsheet editor, and then
import the file back into the Batch Editor. You can export a batch only if it contains at least one set
with at least one sample. If you save the text file, you can use it again later as a template.
1. Make sure that the active hardware profile includes all the devices you will use to
acquire your samples.
2. In the Batch Editor, create a single-set, single-sample batch.
3. Click File > Export.
The Save As dialog opens.
4. In the File name field, type the name you want to use for the text file, and then click
Save.
5. Open the text file in a spreadsheet program such as Microsoft Excel.
6. Type, or copy and paste, the details for the samples: one sample per row, with the
details under the appropriate headings.

Note: Do not delete any of the columns. The columns in the spreadsheet
must match the columns in the Batch Editor.

7. Save the modified text file as a .txt or .csv file and then close the spreadsheet
program.
The text file is now ready to be imported into the Batch Editor.

Import a Batch as a Text File

1. In the Batch Editor, in the Sample tab, right-click, and then click Import From > File.
The Open dialog opens.
2. Click the text file in which you saved the batch details, and then click Open.
If you are using an autosampler, then the Select Autosampler dialog opens.

Note: If you do not see the text file you saved, in the Files of type list,
select Microsoft Text Driver (*.txt; *.csv). Files with the extension .txt are
shown in the field.

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3. In the autosampler list, select the autosampler you are using, and then click OK.
The sample table fills with the details from the text file. You are now ready to submit
the batch.

Batch and Acquisition Method Editor Tips

Table 4-1 Tips
To do this... ...do this
To change the values in the table (for example, to change a sample name) click in a cell and
then type the new value.
To change all the values in a column click a column heading and then right-click. From the
simultaneously menu that is shown, use the Auto Increment and Fill
Down commands to change the values in the column.
This also works for multiple cells in the same column.
To change an existing acquisition from the list, select the method and then click Method
method Editor. To create a new acquisition method, from the list,
select None and then click Method Editor. Only
experienced users should use this feature.
Do not use this feature when you are using the Use
Multiple Methods option.
To apply a previously created select the method from the Quantitation menu.
quantitation method
To select more than one well or vial press Shift and click the first and last well or vial of the
at a time range you want to select.

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Batch Editor Right-Click Menu

The following options are available if you right-click in the Batch Editor table.
Figure 4-5 Batch Right-Click Menu

Menu Function
Open Click to open a batch file.
Import From Click to import a file.
Save As Batch Click to save the batch.
Save As a Template Click to save the batch as a template. Used with the Express View
feature.
Hide/Show Column Click to hide or show a column.
Save Column Settings Click to save the batch column settings.
Add Custom Column Click to add a custom column.
Delete Custom Column Click to delete a custom column.
Fill Down Click to fill the same data into the selected cells.
Auto Increment Click to automatically increment data into the selected cells.
Delete Samples Click to delete the selected row.
Select Autosampler Click to select an autosampler.

Queue States and Device Status

The Queue Manager shows queue, batch, and sample status, so that you can manage samples
and batches in the queue. You can also access detailed information about a particular sample in
the queue.

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Queue States
The current state of the queue is indicated in the Queue Server.
Figure 4-6 Queue Server Indicator Showing Normal Mode

Figure 4-7 Queue Server Indicator Showing Tune Mode

The first icon in Figure 4-6 on page 51 shows the queue state. The second icon indicates
whether the queue is in Tune mode (for tuning) or Normal mode (for running samples). Table 4-2
on page 51 shows the various queue states.
Table 4-2 Queue States
Icons State Definition
Not Ready In the Not Ready state, the hardware profile is
deactivated and the queue is not accepting any
sample submissions.

Stand By In the Stand By state, the hardware profile has been

activated, but all devices are idle. Pumps are not
running and gases are turned off.

Warming Up In the Warming Up state, the instrument and

devices are equilibrating, columns are being
conditioned, the autosampler needle is being
washed, and column ovens are reaching
temperature. The period of equilibration is selected
by the operator. From this state, the system can go
to the Ready state.
Ready In the Ready state, the system is ready to start
running samples and the devices have been
equilibrated and are ready to run. In this state, the
queue can receive samples and will run after
samples are submitted.
Waiting In the Waiting state, the system will automatically
begin acquisition when the next sample is
submitted.

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Table 4-2 Queue States (Continued)

Icons State Definition
Prerun In the Prerun state, the method is being
downloaded to each device and device equilibration
is occurring. This state occurs before the acquisition
of each sample in a batch.
Acquiring In the Acquiring state, the method is run and data
acquisition occurs.

Paused In the Paused state, the instrument has been

paused during acquisition.

View Instrument and Device Status Icons

Icons representing the instrument and each device in the active hardware configuration appear
on the status bar in the bottom right corner of the window.
You might want to view the detailed status of an LC pump to check if the LC pump pressure is
appropriate, or view the detailed status of the instrument to check the temperature of the source.
• On the status bar, double-click the icon for the device or instrument.
The Instrument Status dialog opens.
Table 4-3 Instrument and Device Status (showing the instrument icon)
Status Icon Background Color Description
Idle Green or yellow The device is not running. If the background
color is yellow, the device should be equilibrated
before it is ready to run. If the background color
is green, the device is ready to run.

Equilibrating Green or yellow The device is equilibrating.

Waiting Green The device is waiting for a command from the

software, from another device, or for some
action by the operator.
Running Green The device is running.

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Table 4-3 Instrument and Device Status (showing the instrument icon) (Continued)
Status Icon Background Color Description
Aborting Green The device is aborting a run.

Downloading Green A method is being transferred to the device.

Ready Green The device is not running, but is ready to run.

Error Red The device has encountered an error that

should be investigated.

Note: For each status the background color can also be red. This situation means that
the device encountered an error while in that status and should be investigated.

Queue Right-Click Menu

The following options are available if you right-click in the Queue table.
Figure 4-8 Queue Manager Right-Click Menu

Menu Function
Sample Details Click to open the Sample Details dialog.
Reacquire Click to reacquire a sample.
Insert Pause Click to insert a pause, in seconds, between two samples.
Delete Click to delete either the batch or the selected samples.
Move Batch Click to move the batch within the queue.

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Menu Function
Sort Click to sort by the preselect column.
Column Settings Click to change the column settings.

Icon Quick Reference: Acquire Mode

Table 4-4 Icons in Acquire Mode
Icon Name Function
View Queue Click to view the sample queue.

Instrument Queue Click to view a remote instrument station.

Status for Remote Instrument Click to view the status of a remote instrument.

Start Sample Click to start the sample in the queue.

Stop Sample Click to stop the sample in the queue.

Abort Sample Click to abort a sample acquisition in the middle of

the processing of that sample.
Stop Queue Click to stop the queue before it has completed
processing all the samples.
Pause Sample Now Click to insert a pause in the queue.

Insert Pause before Selected Click to insert a pause before a specific sample.
Sample

Continue Sample Click to continue acquiring the sample.

Next Period Click to start a new period.

Extend Period Click to extend the current period.

Next Sample Click to stop acquiring the current sample and to

start acquiring the next sample.

Equilibrate Click to select a method to use to equilibrate the

devices. This method should be the same as the one
you are using with the first sample in the queue.

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Table 4-4 Icons in Acquire Mode (Continued)

Icon Name Function
Standby Click to put the instrument in Standby mode.

Ready Click to put the instrument in Ready mode.

Reserve Instrument for Click to reserve the instrument for tuning and
Tuning calibrating.

IDA Method Wizard Click to start the IDA Method Wizard.

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5
In this section, you will use the sample files installed in the Example folder to learn how to view
and analyze data using the most common analysis and processing tools.

Overview of Spectral and Chromatographic Data

When you view data as a spectrum, you obtain mass-specific information about a compound. A
chromatogram gives you a general view of the data, usually time dependent when using an LC
column, but it does not tell you anything about the components of a peak. A spectrum, however,
looks at a particular peak and gives you the molecular weight of the corresponding compound,
which you can use to find more specific information. For example, while a chromatogram may
show only one peak, that peak can represent more than one compound; that is, different masses.
A spectrum shows all of the masses that make up a peak, including the intensity of each mass.
Chromatographic data can change in both time and intensity if there is a change in the
chromatographic conditions in a given sample. Spectral intensities may change, but the masses
are fixed because the mass of a compound does not change.
There are two ways to generate spectral data:
• If only one scan is acquired, by default the data is shown as a spectrum.
• From a chromatogram.
A typical spectrum is shown with the molecular weight, labeled with the m/z (mass/charge ratio),
on the x-axis. The intensity is shown on the y-axis.

Analyze Data
When you open a data file, different panes appear in windows, depending on the type of
experiment you performed. The software stores data in files with a .wiff extension. Wiff files can
contain data for more than one sample. In addition to .wiff files, the software can open .txt files;
however, .txt files contain data for only one sample.
You can view the information contained in a data file in table or graph form. Graphical data is
presented either as a chromatogram or as a spectrum. Data from either of these can appear as a
table of data points, and you can perform various sorting operations on the data.
You can open files containing existing data or data that is currently being acquired. You can also
view all experiment-related data in tabular form. The table pane consists of two tabs, the Data
List tab and the Peak List tab.The Data List tab contains experiment-related information, such as
acquisition time and scan intensity. The Peak List tab displays peak-related information such as
peak height, peak area, and baseline type.
If the data contains results from multiple experiments, you can create individual TICs (Total Ion
Chromatograms) for each experiment, and another TIC that represents the sum of all
experiments.
The preset TIC that represents the sum of all of the experiments is shown with a splitter tool
below the center of the x-axis.

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Open Data Files

1. Make sure that you are in the Example project.
2. On the Navigation bar, under Explore, double-click Open Data File.
The Select Sample dialog opens.
3. In the Data Files field, double-click Triple Quad and then click QuanData.wiff.
4. In the Samples list, select sample AP13-020, and then click OK.
The data acquired from your sample is shown. If you were still acquiring data, the
mass spectrum, DAD/UV trace, and TIC would continue to update automatically.

Tip! To turn off the automatic update on the mass spectrum, right-click
the mass spectrum and then click Show Last Scan. If there is a check
mark beside Show Last Scan, then the spectrum will update in real time.

Navigate Between Samples in a Data File

Table 5-1 on page 58 contains the navigation icons used in this procedure.

Note: If samples were saved in separate data files, then you will need to open each file
individually.

1. Open a data file that contains multiple samples. For this example, you can use
QuanData.wiff.
2. To skip to the next sample in the data file, click the icon with the arrow pointing to the
right. (Refer to Table 5-1 on page 58.)
3. To skip to a non-sequential sample, click the icon with the arrow curving to the right.
4. In the Select Sample dialog that opens, in the Sample list, select the sample you
want to view.
5. To go to the previous sample in the data file, click the icon with the arrow pointing to
the left.
Table 5-1 Navigation Icons on the Explore Toolbar
Icon Name Function
Open File Click to open files.

Show Next Sample Click to navigate to the next sample.

Show Previous Sample Click to navigate to the previous sample.

GoTo Sample Click to open the Select Sample dialog.

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View Experimental Conditions

The experimental conditions used to collect the data are stored in the data file along with the
results. The information contains the details of the acquisition method used: the MS acquisition
method (that is, the number of periods, experiments and cycles) including instrument
parameters, and peripheral HPLC device method (LC pump flow rate). It also contains the MS
resolution and mass calibration tables used for the sample acquisition. Table 5-2 on page 59
shows the software functionality available when you view the file information.

Note: If you have acquired data from more than one sample into the same .wiff file, the
file information pane will not refresh automatically as you scroll through the samples.
You will need to close the file information pane and then reopen it to view the details for
the next sample in the .wiff file.

• Click Explore > Show > Show File Information.

The File Information pane is shown below the graph.
Table 5-2 Right-Click Menu for Show File Information Pane
Menu Function
Copy Click to copy the selected data.
Paste Click to paste data.
Select All Click to select all the data in the pane.
Save To File Click to save data in an .rtf file.
Font Click to change the font.
Save Acquisition Method Click to save the acquisition method as .dam file.
Save Acquisition Method to Click to open the Specify Compound Information dialog.
CompoundDB Select the IDs and molecular weights to be saved in the
compound database.
Delete Pane Click to delete the pane.

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View the Data in Tables

• With a data file open, click Explore > Show > Show List Data.
The data is shown in a pane below the graph.

Table 5-3 RIght-Click Menu for the Spectral Peak List Tab
Menu Function
Column Options Click to open the Select Columns for Peak List dialog.
Save As Text Click to save the data as text file.
Delete Pane Click to delete the pane.

Table 5-4 Right-Click Menu for the Chromatographic Peak List Tab
Menu Function
Analyst Classic Click to open the Analyst Classic dialog.
Parameters
IntelliQuan Parameters Click to open the Intelliquan dialog.

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Table 5-4 Right-Click Menu for the Chromatographic Peak List Tab
Menu Function
Centroid Parameters Click to open the Centroid Parameters dialog.
Save As Text Click to save the data as text file.
Delete Pane Click to delete the pane.

View ADC Data

ADC (analog-to-digital converter) data is acquired from a secondary detector (for example from a
UV detector through an ADC card), and is useful for comparison with mass spectrometer data. If
you want to have ADC data available, you must acquire the data and the mass spectrometer data
simultaneously and save it in the same file.
1. Make sure that you are in the Example project.
2. On the Navigation bar, under Explore, double-click Open Data File.
The Select Sample dialog opens.
3. In the Data Files field, double-click Devices and then click Adc16chan.wiff.
4. In the Samples list, select a sample, and then click OK.
5. Click Explore > Show > Show ADC Data.
The Select ADC Channel dialog opens.

6. In the Channel list, select a channel, and then click OK.

The ADC data is shown in a new pane beneath the active pane.

Obtain Basic Quantitative Data

1. In the Peak List tab, right-click and select Show Peaks in Graph.
Peaks appear in two colors.
2. To change the peak finding algorithm settings right-click and then select either
Analyst Classic Parameters or Intelliquan Parameters, which ever is active.
3. To remove the colored peaks, right-click on the Peak List tab and clear Show Peaks
in Graph.

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Spectra
A spectrum is the data that is obtained directly from the mass spectrometer and normally
represents the number of ions detected with particular mass-to-charge (m/z) values. It is shown
as a graph with the m/z values on the x-axis and intensity (cps) represented on the y-axis. For a
more information about software functionality available when you are working with spectrums,
refer to Table 5-8 on page 70.
In the case of MS/MS data, the intensity is associated with two masses, the precursor ion mass
(Q1) and the product ion mass or masses (Q3).

Chromatograms
A chromatogram is a graphical display of the data obtained from the analysis of a sample. It plots
the signal intensity along an axis that shows either time or scan number. For more information
about software functionality available when you are working with chromatograms, refer to
Table 5-7 on page 69.
The software plots intensity, in counts per second (cps), on the y-axis against time on the x-axis.
Peaks above a set threshold are labeled automatically. In the case of LC/MS, the chromatogram
is often shown as a function of time. Table 5-5 on page 62 contains the description of the types of
chromatograms.
Table 5-5 Chromatograms
Types of chromatograms Purpose
TIC (Total Ion Chromatogram) A chromatographic display generated by plotting the intensity
of all ions in a scan against time or scan number.
XIC (Extracted Ion An ion chromatogram created by taking intensity values at a
Chromatogram) single, discrete mass value, or a mass range, from a series of
mass spectral scans. It indicates the behavior of a given mass,
or mass range, as a function of time.
BPC (Base Peak Chromatographic plot that displays the intensity of the most
Chromatogram) intense ion within a scan versus time or scan number.
TWC (Total Wavelength A chromatographic display created by summing all of the
Chromatogram) absorbance values in the acquired wavelength range and then
plotting the values against time. It consists of the summed
absorbances of all ions in a scan plotted against time in a
chromatographic pane.
XWC (Extracted Wavelength A subset of TWC. An XWC displays the absorbance for a
Chromatogram) single wavelength or the sum of the absorbance for a range of
wavelengths.
DAD (Diode Array Detector) A UV detector that monitors the absorption spectrum of eluting
compounds at one or more wavelengths.

TICs
A TIC is created by summing the intensity contributions of all ions from a series of mass scans.
You can use the TIC to view an entire data set in a single pane. It consists of the summed
intensities of all ions in a scan plotted against time in a chromatographic pane.

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If the data contains results from multiple experiments, you can create individual TICs for each
experiment and another TIC that represents the sum of all experiments.

Show TICs
When you open a data file, it is preset to appear as a TIC. However, if the experiment contains
only one scan, it is shown as a spectrum. For more information about using the available icons,
refer to Table 5-9 on page 71.
If the MCA check box is selected during acquisition of the data file, then the data file opens to the
mass spectrum. If the MCA check box is not selected, then the data file opens with the TIC.

View a TIC from a Spectrum

1. Make sure that you are in the Example project.
2. On the Navigation bar, under Explore, double-click Open Data File.
The Select Sample dialog opens.
3. In the Data Files field, double-click LIT and then click Reserpine.wiff.
4. In the Samples list, select a sample, and then click OK.
5. Click Explore > Show > Show TIC.
The TIC opens in a new pane.

Tip! You can also right-click inside a pane containing a spectrum and
then click Show TIC.

View a Spectrum from a TIC

1. Select a range in the spectrum.
2. Click Explore > Show > Show Spectrum.
The spectrum opens in a new pane.

Tip! You can also double-click in the TIC pane at a particular time to show
the spectrum.

XICs
An XIC is an extracted ion chromatogram created by taking intensity values at a single, discrete
mass value, or a mass range from a series of mass spectral scans. It shows the behavior of a
given mass, or mass range, as a function of time. The intensity of the ion, or the summed
intensities of all ions in a given range, is plotted in a chromatographic pane.

Generate XICs
You can generate XICs only from single period, single experiment chromatograms or spectra. To
obtain an XIC from multi-period or multi-experiment data you must first split the data into
separate panes by clicking the triangle that appear under the x-axis. For more information about
using the available icons, refer to Table 5-9 on page 71.

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There are several methods for extracting ions to generate an XIC, depending on whether you are
working with chromatographic or spectral data. Table 5-6 on page 64 contains a summary of
methods that can be used with chromatograms and spectra.
Table 5-6 Summary of XIC Generation Methods
Method Use with Use with Extraction
chromatogram spectrum
Selected range No Yes The selected range method extracts
ions from a selected area in a
spectrum.
Maximum No Yes The maximum method extracts ions
from a selected area in a spectrum
using the most intense peak in the
selected area. This creates an XIC
using the maximum mass from the
selected spectral range.
Base peak Yes No The base peak masses method can
masses be used only with BPCs (Base Peak
Chromatograms.) Using the Use
Base Peak Masses command to
extract ions results in an XIC with a
different colored trace for each mass.
If your selection includes multiple
peaks, the resulting XIC will have an
equal number of colored traces
representing each mass.
Specified masses Yes Yes The specified masses method
extracts ions from any type of
spectrum or chromatogram. You can
select up to 10 start and stop masses
for which to generate XICs.

Generate an XIC using a Selected Range

1. To select a range inside the pane, click and hold the left mouse button where you
want to start the range and then drag the cursor to the stop point and release.
The selection is highlighted in blue.
2. Click Explore > Extract Ions > Use Range.
An XIC of the specified selection is shown in a pane below the spectrum pane. The
experiment information at the top of the pane contains the mass range and the
maximum intensity in counts per second.

Generate an XIC using the Maximum Peak

1. Select a range in a spectrum.
The selection is highlighted in blue.
2. Click Explore > Extract Ions > Use Maximum.

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An XIC of the maximum peak specified selection is shown below the spectrum pane.
The experiment information at the top of the pane contains the mass range and the
maximum intensity in counts per second.

Generate an XIC using Base Peak Masses

1. In a BPC, select the peak from which you want to extract ions.
The selection is highlighted in blue.
2. Click Explore > Extract Ions > Use Base Peak Masses.
An XIC of the specified selection is shown below the spectrum pane. The experiment
information at the top of the pane displays the mass range and the maximum
intensity in counts per second.

Extract Ions by Selecting Masses

1. Select a spectrum or chromatogram.
2. Click Explore > Extract Ions > Use Dialog.
Figure 5-1 Extract Ions Dialog

3. Type the values for each XIC that you want to create. If you do not define a stop
value, the range will be defined by the start value that you entered.
• In the Start box, type the start value (lower value) for the mass range you want
to extract.
• In the Stop box, type the stop value (higher value) for the mass range you
want to extract.
4. Click OK.

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An XIC of the selection is shown below the chromatogram pane. The experiment
information at the top of the pane includes the mass/masses and the maximum
intensity in counts per second.

BPCs
A BPC displays the intensity of the most intense ion in every scan as a function of scan number
or retention time. It is useful in instances where the TIC is so dominated by noise that there is a
large offset and chromatographic peaks are hard to distinguish. It is also helps to distinguish
between co-eluting components. You can generate BPCs only from single period, single
experiment data.
The graph uses two colors, alternating each time the mass of the base peak changes. The color
changes are maintained when you manipulate the data by scrolling or zooming. For information
about selecting the colors used in the graph, refer to the Help.

Generate BPCs
BPCs can be generated only from single period, single experiment data. For more information
about using the available icons, refer to Table 5-9 on page 71.
1. Select an area within a TIC.
The selection is highlighted in blue.
2. Click Explore > Show > Show Base Peak Chromatogram.
The selections that you specified are shown in the Start Time and End Time fields.
Figure 5-2 Base Peak Chromatogram Options Dialog

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3. In the Mass Tolerance field, type the value to dictate the mass range used to find a
peak. The software finds the peak using a value twice the entered range (± the mass
value).
4. In the Minimum Intensity field, type the intensity below which peaks are ignored by
the algorithm.
5. In the Minimum Mass field, type the mass that determines the beginning of the scan
range.
6. In the Maximum Mass field, type the mass that determines the end of the scan
range.
7. To set the start and end times, select the Use Limited Range check box and do the
following:
• In the Start Time field, type the time that determines the start of the
experiment.
• In the End Time field, type the time that determines the end of the experiment.
8. Click OK.
The BPC is generated in a new pane.

XWCs
An XWC is a wavelength chromatogram created by taking intensity values at a single
wavelength, or by the sum of the absorbance for a range of several wavelengths

Generate XWCs
You can extract up to three ranges from a DAD spectrum to generate the XWC. For more
information about using the available icons, refer to Table 5-9 on page 71.
1. Open a data file that contains a DAD spectrum.
2. Anywhere in the pane, right-click and then click Extract Wavelengths.
Figure 5-3 Extract Wavelengths Dialog

3. Type start and stop values and then click OK.

The XWC opens in a pane below the DAD spectrum.

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DAD
You can view the DAD spectrum for a single point in time, or for a range of time as a Total
Wavelength Chromatogram. For more information about using the available icons, refer to
Table 5-9 on page 71.

View DAD data

You can view DAD data in chromatogram or spectrum form, the same as mass spectrometer
data.
1. Open a data file containing data acquired with a DAD.
2. The TWC, which is analogous to a TIC, is shown in a pane underneath the TIC.
3. In the TWC pane, click a point to select a single point in time, or highlight an area of
the spectrum to select a range of time.
4. Click Explore > Show > Show DAD Spectrum.
The DAD spectrum is shown in a pane below the TWC. The y-axis shows
absorbance and the x-axis shows wavelength.

Tip! If you close the pane with the TWC, you can open it again by clicking
a point anywhere in the TWC and then clicking Explore > Show > Show
DAD TWC.

TWCs
A TWC is a less commonly used chromatogram. It displays the total absorbance (mAU) as a
function of time. The TWC provides a way of viewing an entire data set in a single pane. It
consists of the summed absorbances of all ions in a scan plotted against time in a
chromatographic pane.
If the data contains results from multiple experiments, you can create individual TWCs for each
experiment, and another TWC that represents the sum of all experiments.

Generate TWCs
A TWC shows total absorbance (mAU) on the y-axis plotted against time on the x-axis. For more
information about using the available icons, refer to Table 5-9 on page 71.
1. Open a data file that contains a DAD spectrum.
2. Click Explore > Show > Show DAD TWC.
The TWC opens in a pane below the DAD spectrum.
You can also right-click inside the pane containing the DAD spectrum and then
select Show DAD TWC from the shortcut menu.

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Adjust the Threshold

The threshold is an invisible line drawn parallel to the x-axis of a graph that sets a limit below
which the software will not include peaks in a spectrum. The line has a handle, represented by a
blue triangle to the left of the y-axis. Click the blue triangle to view a dotted line that represents
the threshold. You can raise or lower the threshold; however, changing the threshold value does
not alter data. The software does not label any peaks in the region that lies beneath the
threshold.
1. Open a data file.
2. You can adjust the threshold in three ways:
• To raise the threshold, drag the blue triangle up the y-axis. To lower the
threshold, drag the blue triangle down.
• Click Explore > Set Threshold and then, in the Threshold Options dialog
that opens, type the threshold value.
• Click Explore > Threshold.
The graph updates to show the new threshold. Peak labeling and the peak list are
also updated.

Tip! To view the current threshold value, move the pointer over the
threshold handle.

Table 5-7 Right-Click Menu for Chromatogram Panes

Menu Function
List Data Lists the data points and integrates chromatograms.
Show Spectrum Generates a new pane.
Show Contour Plot Displays a color-coded plot of a data set, where the color represents
the intensity of the data at that point. Only certain MS modes are
supported.
Extract Ions Extracts a specific ion or set of ions from a selected pane and then
generates a new pane containing a chromatograph for the specific
ions.
Show Base Peak Generates a new pane containing a base peak chromatogram.
Chromatogram
Show ADC Data Generates a new pane containing the UV data trace, if acquired.
Spectral Arithmetic Opens the Spectral Arithmetic Wizard.
Wizard
Save to Text File Generates a text file of the pane, which can be opened in Excel or
other programs.
Save Explore History The Explore History File records changes to processing parameters,
also called Processing Options, when a .wiff file is processed in
Explore mode. The processing history is stored in a file with an .EPH
(Explore Processing History) extension.
Add Caption Adds a caption at the cursor point in the pane.
Add User Text Adds a text box at the position of the mouse cursor.

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Table 5-7 Right-Click Menu for Chromatogram Panes (Continued)

Menu Function
Set Subtract Range Sets the subtract range in the pane.
Clear Subtract Range Clears the subtract range in the pane.
Subtract Range Locked Locks or unlocks the subtract ranges. If the subtract ranges are not
locked then each subtract range can be moved independently. By
default, the subtract ranges are locked.
Delete Pane Deletes the selected pane.

Table 5-8 Right-Click Menu for Spectra Panes

Menu Function
List Data Lists the data points and integrates chromatograms.
Show TIC Generates a new pane containing the TIC.
Extract Ions Extracts a specific ion or set of ions from a selected pane and then
generates a new pane containing a chromatograph for the specific
ions.
Save to Text File Generates a text file of the pane, which can be opened in Excel or
other programs.
Save Explore History The Explore History File records changes to processing parameters,
also called Processing Options, when a .wiff file is processed in
Explore mode. The processing history is stored in a file with an .EPH
(Explore Processing History) extension.
Add Caption Adds a caption at the cursor point in the pane.
Add User Text Adds a text box at the position of the mouse cursor.
Show Last Scan Shows the scan prior to the selection.
Select Peaks For Label In this dialog, you can specify parameters to reduce peak labeling.
Delete Pane Deletes the selected pane.
Add a Record You may add records and compound-related data including spectra
to the library. You must have an active spectrum to perform this task.
Search Library Click to search the library without constraints or with previously
saved constraints.
Search With Constraints Click to search using the Search Constraints dialog.

Data Processing
You can process graphical data in a variety of ways. This section provides information and
procedures for using some of the most commonly used tools.

Work with Graphs in Panes

At some point you will want to compare data or examine the same data different ways. You may
want to keep your data for comparison purposes before performing processing operations such
as smoothing or subtraction.

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A window contains one or more panes, arranged in such a way that all the panes are fully visible
and they do not overlap.
Panes may be of variable or fixed size. Panes are automatically tiled within the window and are
arranged into column and row format. If you change the size of a window, the panes within the
window change in size to accommodate the resizing. You cannot resize a window to the point
where any of the panes would become smaller than its minimum size.
You can link two or more windows or panes containing similar data, for instance, spectra with
similar mass ranges. As you zoom in one pane or window, the other pane zooms simultaneously.
For example, you can link an XIC to the BPC from which it was extracted. Zooming in the BPC
also zooms the XIC, so that both chromatograms display the same magnification.
Table 5-9 Working with Graphs
To do this... use this menu option... ...or click this
icon
Copy a graph to a • Select the graph to copy, and then click Explore
new window > Duplicate Data > In New Window.

Rescale graph to its • Select the graph and then click Explore >
original size Home Graph.

Move a pane • Select the graph and then click Window > Move
Pane.
• Select the pane or window and then drag it to
the new position. This position can be within the
same window or within another window.
A four-headed arrow is shown when the cursor is
on the boundary of the active window or pane.
• If the pane is at the top or bottom of the
target pane, the pane moves above or
below that pane, respectively.
• If the pane is at the left or right of the target
pane, the pane moves to the left or right of
that pane, respectively.
• If the pane is at any other position, the pane
moves to the target row. The drop shadow
of the pane as you move it around indicates
its new position.
Link panes • With the two graphs displayed, click one to
make that pane active.
• Click Explore > Link, and then click the pane to
which you want to link.
Remove linking • Close one of the panes and then click Explore >
Remove Link

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Table 5-9 Working with Graphs (Continued)

To do this... use this menu option... ...or click this
icon
Delete a pane • Select the graph and then click Window >
Delete Pane.

Lock a pane • Select the graph and then click Window > Lock
Panes.

Hide a pane • Select the graph and then click Window > Hide
Pane.

Maximize a pane • Select the graph and then click Window >
Maximize Pane.

Tile panes • Select the graph and then click Window > Tile
all Panes.

Zoom in on a Graph
You can zoom in on part of a graph to view a particular peak or area in greater detail in both
spectra and chromatograms. You can zoom repeatedly to view smaller peaks.

Zoom on the Y-axis

1. Position the pointer to the left of the y-axis and then drag vertically away from your
starting point.
A box is drawn along the y-axis representing the new scale.

Note: Take care when zooming in on the baseline. If you go too low the
zoom-in box disappears.

2. Release the mouse button to redraw the graph to the new scale.

Zoom on the X-axis

1. Position the pointer under the x-axis to either side of the area that you want to
expand and then drag away from the starting point in a horizontal direction to expand
the area of interest.
2. Release the mouse button to redraw the graph to the new scale.

Tip! To return the graph to the original scale, double-click on either axis.
To restore the entire graph to original scale, click Explore > Home Graph.

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Label Graphs
You can customize the preset style for labels on graphs and chromatograms. You can select the
fonts to use for peak and axis labels, and the colors to use for your traces. You can add axis
labels and the type of label and precision for your peaks.

Add Captions to a Graph

You can use captions to label peaks of interest or significant points on the graph. When you place
a caption beside a peak, the caption stays with the peak when you zoom in or out. Captions also
stay with the original sample when you navigate between samples in a data file. A caption
contains one line of text, with a maximum of 128 characters.
1. On the spectrum, right-click, and then click Add Caption.
The Add Caption dialog opens.
2. In the Caption box, type the text.
3. To change the size and style of the caption, click Font.
4. To place the caption, click OK.

Tip! If you are not satisfied with the position of the caption, you can drag it
to a different position. The caption stays in the same place relative to the x-
and y-axes when you zoom in or out. To edit or delete the caption, right-
click the caption and then click the appropriate command.

Add Text to a Graph

You can use text to add multiple lines of information to a graph. Unlike captions, which are
associated with a specific peak and move with it as you zoom, text labels remain in their original
location as you zoom. They do not stay with the original sample when you navigate between
samples in a data file.
1. On the graph, right-click and then click Add User Text.
The Add User Text dialog opens.
2. In the User Text field, type the text.
3. If you want the text to be centered, select the Center Text check box.
4. If you want to change the size and style of the caption, click Font.
5. To insert the text, click OK.

Tip! If you are not satisfied with the position of the text, you can drag the
text to a different position. To edit or delete the text, right-click the text and
then choose the appropriate command.

Overlay and Sum Spectra or Chromatograms

You can visually compare two or more sets of data by overlaying graphs created by similar
methods. Each individual spectrum is distinguished by the color of its trace. For full scan data,
this allows you to visualize the differences between several sample spectra.

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After you have two or more graphs overlaid, you can sum the graphs to get a new trace. Each
point on the new trace is the sum of the points from the graphs. Summing several overlays of
similar data type can make subsequent processing operations easier and faster. For example,
you can overlay several XICs, sum them, and then smooth the summed overlay to remove noise.
Summing overlays is similar to generating a TIC with the benefit of being able to choose which
graphs to overlay. For example, if you were looking at ten experiments, the TIC will add all ten
experiments together. If you sum overlays, you have the option of adding only nine of the ten
overlaid graphs. You might want to do this if the data collected in the one experiment is just noise.

Overlay Graphs
If you choose one or more panes, then each XIC opens in a separate pane.

Tip! To overlay fewer than four graphs in the same pane, press Ctrl + right-click in
a pane and then click Appearance Options. In the Appearance Options dialog,
Multiple Graph Options tab, select Yes for the Overlay Multiple Panes fields for
Spectrum and Chromatogram.

1. Select the first pane that you want to overlay.

2. Click Explore > Overlay.
3. Click in the pane that you want to overlay.
The graphs are overlaid showing the two traces in different colors.

Tip! To view a color-coded list of the overlaid graphs, right-click the title
bar of the pane.

Cycle between Overlaid Graphs

1. Select a pane that contains overlaid graphs.
2. Click Explore > Cycle Overlays.
The view changes so that the next graph in the sequence is shown in the
foreground.

Sum Overlays
1. Overlay the graphs that you want to sum.
2. Click Explore > Sum Overlays.
The overlaid graphs are added together.
Table 5-10 Explore Toolbar Quick Reference: Overlaying Graphs
Icon Name Function
Home Graph Click to return the graph to the original scale.

Overlay Click to overlay graphs.

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Table 5-10 Explore Toolbar Quick Reference: Overlaying Graphs (Continued)

Icon Name Function
Cycle Overlays Click to cycle between overlaid graphs.

Sum Overlays Click to add the graphs together.

Perform Background Subtractions

Background subtraction reduces the amount of noise in a spectrum by subtracting either one or
two ranges that contain noise from a range that contains a peak. You can move the ranges
independently, or lock them and move them as a single entity within the graph. Locked
Background Subtraction is the preset setting. The software offers different methods of
background subtraction.
Background Subtract: You can use background subtract to isolate a peak of interest. You can
highlight and subtract up to two selected ranges from your peak. You can also lock your ranges
and move them within the graph to optimize peak isolation, or to isolate another peak.
Background Subtract to File: You can use Background Subtract to File to save a new file that
has a defined noise region subtracted from each scan. When a range is selected in the TIC, all
the scans from that selection are internally averaged, and the resulting spectrum is subtracted
from all the scans. In some cases, the resulting file might look close to the original scan.

Perform a Background Subtraction from a Spectrum

1. Open a data file.
2. Select a background range.

3. Hold down the Shift key and then select another background range.

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4. To set the subtract range, click Explore > Background Subtract > Set Subtract
Range.
5. Select the peak of interest.
6. Click Explore > Background Subtract > Perform Background Subtract.
The background is subtracted from the peak and a new spectrum is generated.
7. To isolate another peak, drag the locked ranges in the chromatogram and repeat the
background subtract.

Tip! To clear the background subtract region, click Explore >

Background Subtract > Clear Subtract Range.

8. To save your background subtracted spectrum as a processed data file, click File >
Save.

Unlock the Ranges

The selected subtraction range is set to locked.
• Click Explore > Background Subtract > Subtract Range Locked.
The ranges are unlocked and you can move each one independently.

Perform a Background Subtraction to File

Use the Background Subtract to File function to save a new file that has a defined noise region
subtracted from each scan. You first select a representative background range in the TIC; all the
scans in that region are averaged internally, and the resulting spectrum is then subtracted from
all the scans. In some cases, the results might look like the original scan.
1. Open a data file.
2. Select the background range within the TIC and set it as background.
3. Click Explore > Background Subtract to File.

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Figure 5-4 Background Subtract to File Dialog

4. In the Output Project and Filename section, type the project and file names for the
resulting file.
5. Click Start Processing.
The progress bar displays the progress of the subtraction process. If you select the
Open the new file immediately in Analyst check box, when the subtraction is
complete, the file will appear.
6. If the check box is cleared, when the subtraction is complete, click Finish.
Table 5-11 Explore Toolbar Quick Reference: Background Subtract
Icon Name Function
Perform Background Click to perform a background subtract after you
Subtract have selected the background ranges.

Subtract Range Locked Click to lock the selected background ranges. If you
unlock the background ranges you can move each
range independently.
Background Subtract to File Click to save a new file that has a defined noise
region subtracted from each scan.

Spectral Arithmetic Wizard Click to use the Spectral Arithmetic Wizard to

perform arithmetic operations using two complete
chromatograms to create a new chromatogram,
which you can save as a new data file.

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Smoothing Algorithms
Smoothing a data set removes local variations that are most likely due to noise. You may apply
several smoothing cycles to the data, but you can undo only the most recent smooth. Smoothing
is not available for MI/MRM spectra. You can choose the smooth algorithm or the Gaussian
smoothing algorithm as your preset smoothing method.

Smooth Algorithm
When you smooth data, you set the point weighting values for three data points; the current point,
the preceding point, and the following data point. The smooth algorithm multiplies the data points
by the assigned weighting values, sums these values, and then divides the total by the sum of
the point weight values. It is a gentler smooth than the Gaussian algorithm, and it takes a long
time to smooth very noisy data.

Gaussian Smoothing Algorithm

Gaussian smoothing involves replacing each data point with the weighted average of a number
of data points on either side of it. The weighting for each new data point is calculated on the basis
of a Gaussian curve. It is a coarser smooth than the smooth algorithm, but it is good for
smoothing very noisy data.
You set two values when using the Gaussian smoothing method:
Gaussian filter width (% of minimal distance between points): This value shows the width
used to calculate the weighting of neighboring points. The width is described in terms of
percentages of the distance between two points in the scan, where the preset width of 100%
gives a distribution that is as wide as the distance between data points.
Limit of Gaussian filter (number of minimal distance between points): This value
corresponds to the limits of the Gaussian curve, shown in multiples of the distance between
points. For example, the preset value of 10 creates a Gaussian curve that truncates after ten data
point widths on either side of the center.

Smooth Data
You can choose the Analyst® software smoothing method or the Gaussian smoothing method.

Tip! To undo smoothing, click Edit > Undo. The software supports one level of undo.

Smooth Data using the Smooth Algorithm

1. Select a pane containing a chromatogram or spectrum.
2. Click Explore > Smooth.
The Smoothing Options dialog opens.

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3. In the Previous Point Weight field, type the weighting factor to be applied to the
previous data point.
4. In the Current Point Weight field, type the weighting factor to be applied to the
center data point.
5. In the Next Point Weight field, type the weighting factor to be applied to the
following data point.
6. To smooth the data, click OK.
The data set is smoothed, replacing the current data set in the pane.

Smooth Data using Gaussian Smoothing

1. Select a pane containing a chromatogram or spectrum.
2. Click Explore > Gaussian Smooth.
The Gaussian smooth options dialog opens.

3. In the Gaussian filter width field, type the width used to find the weighting of
neighboring points as a percentage of the distance between the two points.
4. In the Limit of gaussian filter field, type the limit of the Gaussian curve, given in
multiples of the distance between points.
5. To smooth the data, click OK.
The data set is smoothed, replacing the current data set in the pane.

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Table 5-12 Explore Toolbar Quick Reference: Smoothing Data

Icon Name Function
Smooth Click to smooth data using the smooth
algorithm.

Gaussian smooth Click to smooth data using Gaussian

smoothing.

Centroid Data
Centroiding converts peak distribution values into a single value of m/z and intensity that
represents the peak. Centroiding data collected in profile mode simplifies the data and reduces
the file size. Centroiding provides more accurate peak assignment and reduces the amount of
data, but it also removes the information about the peak shape.
The centroiding algorithm converts peaks to single values by using an intensity weighted average
to calculate the center of gravity of the peak. The output of the algorithm is a list of peaks with
parameters, as shown in Table 5-13 on page 80.
Table 5-13 Peak Parameters
Parameter Definition
Centroid Value The value of the centroided data in units of mass or time.
Intensity The intensity of each peak in cps.
Width The width of the centroided peak in amu.

Data is automatically centroided when added to a library or when a search is conducted.

1. Select a pane containing a spectrum.
Centroiding data changes the appearance of the existing graph. To compare the
result with the original data, make a copy of the graph before centroiding.
2. Click Explore > Centroid.
The data is centroided.
Figure 5-5 Analyte Centroid Location

Centroid Location

A1=A2

A1 A2

Time

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Table 5-14 Explore Toolbar Quick Reference: Centroiding Data

Icon Name Function
Centroid Click to centroid data.

Save and Open Processed Data Files

You can save processed data, such as specific layouts and captions, that can be re-opened in
Explore mode only. These files also contain relevant history information and are similar to data
files except they will contain only the data from the active pane in Explore. These files have the
.pdt extension and are stored in the Data folder in your current project.

Save a Processed Data File

1. Select the pane of data that you want to save.
2. Click File > Save Processed Data File.
The Save Processed Data File dialog opens.
3. In the File name field, type the name of the processed data file and then click Save.

Open a Processed Data File

1. In Explore mode, click File > Open Processed Data File.
The Load Processed Data File dialog opens.
2. Select a file and then click Open.

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Contour Plots
A Contour Plot is a color-coded plot of a complete data set that uses color to represent a third
dimension in the plot. In a Contour Plot of a TIC, the x-axis represents retention time or scan
number, the y-axis represents mass, and the color represents the intensity of the data at that
point. In a Contour Plot of a TWC for DAD data, the x-axis represents retention time or scan
number, the y-axis represents wavelength, and the color represents absorbance. Contour Plot is
a post-acquisition tool that does not function in a real-time scan acquisition.

Note: Contour Plot does not support MI or MRM scans, but it does support DAD
scans.

Work with Contour Plots

Color is the third axis in Contour Plot, and it represents either intensity or absorbance. You can
change the high and low intensity or absorbance values in Contour Plot using the control
triangles on the color bar above the Contour Plot. The percentage parameters at the top of the
Contour Plot pane indicate the values held by the low and high sliders. The actual values are
based on a percentage of the maximum intensity or absorbance within the selected area. The
value is shown in the top right corner of the Contour Plot pane.
The controls shown in Figure 5-6 on page 82 change the colors in a Contour Plot.
Figure 5-6 Buttons Controlling Contour Plot Colors

You can define the colors on a Contour Plot graph to provide better contrast and display data
specifications according to your needs. For example, setting the intensity/wavelength and
changing the color of the values for Below Low Data and Above High Data can eliminate
background noise in Contour Plot.
The Below Low Data and Above High Data buttons shrink and expand on the color bar if you
move the slider controls. When you change the contour plot colors, the new colors become the
preset colors for all subsequent graphs.

View a Contour Plot

You can view a Contour Plot only after acquisition. You can view a Contour Plot from TIC, XIC,
TWC, or XWC graphs. TICs and XICs are available for all .wiff data files. TWCs and XWCs are
available only for data acquired by a DAD.
1. In Explore mode, open a data file as a TIC, XIC, TWC, or XWC graph.
2. Highlight the range you want to view in the Contour Plot. If you do not make a
selection, you will view the entire range.
3. Click Explore > Show > Show Contour Plot.
A Contour Plot of the selected area is shown in a separate pane.

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Select an Area in a Contour Plot

You may wish to zoom in on a particular selection, or view the corresponding mass spectrum for
that selection.
• Do one of the following:
• To select a standard area within a box, drag the pointer to create a box around
an area in the Contour Plot.
• To make a vertical selection, press Ctrl and drag the pointer vertically.
• To make a horizontal selection, press the space bar and drag the pointer
horizontally.

Set the Intensity and Absorbance in a Contour Plot

• Do one of the following:
• To set the low intensity/absorbance value in Contour Plot, from the color bar
above the Contour Plot, drag the left triangular slider to the required position.
Contour Plot automatically adjusts the color of values below the setting to
indicate they are outside the range.
• To set the high intensity/absorbance value in Contour Plot, from the color bar
above the Contour Plot, drag the right triangular slider to the required position.
Contour Plot automatically adjusts the color of values above the setting to indicate
they are outside the range.

Change Colors in a Contour Plot

1. In the Contour Plot pane, click one of the color buttons.
The Color dialog opens.
2. Click a color, and then click OK.
The graph changes to reflect the color change.

Tip! By using the Define Custom Colors palette, you can create
customized colors for use in a Contour Plot.

Table 5-15 Right-Click Menu for Contour Plot Panes

Menu Function
Show DAD Spectrum Opens a new pane with the DAD spectrum.
Extract Wavelengths Extracts up to three wavelength ranges from a DAD spectrum to
(Use Range) display the XWC.
Extract Wavelengths Extracts wavelength ranges using the maximum wavelengths.
(Use Maximum)
Zoom to selection Zooms in on the selected area.
Add User Text Adds a text box at the position of the cursor.
Undo Zoom Returns the graph to the original scale
Delete Pane Deletes the selected pane

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Table 5-15 Right-Click Menu for Contour Plot Panes (Continued)

Menu Function
Show Cross-Hair Shows the Cross-Hair (nm/min)

Fragment Interpretation
The Fragment Interpretation Tool generates a list of theoretical fragment masses from single,
non-cyclic bond cleavage of a molecular structure. You create the molecular structure in a third-
party drawing program and then save it as a .mol file. Fragment Interpretation displays the
theoretical fragments in the fragment list and compares the fragment masses to peaks in the
mass spectrum. Peaks above the threshold intensity and within the user-defined mass tolerance
(maximum 2 amu) of fragment masses are considered matched and appear in bold text in the
fragment list.

Note: The Fragment Interpretation tool cannot be used with the following scan types:

• Precursor Ion
• Neutral Loss
• Q1 Multiple Ion
• Q3 Multiple Ion
• Multiple Reaction Monitoring (MRM)

Work with the Fragment Interpretation Tool

If you are viewing multiple spectrum panes, then the Fragment Interpretation tool connects to the
active spectrum. If the data file contains more than one sample, then the Fragment Interpretation
tool connects to the active spectrum.
The tool automatically calculates the single, non-cyclic bond cleavage fragments from a .mol file.
When the Fragment Interpretation tool is connected to a spectrum, theoretical fragments in bold
text, indicate a matching peak in the spectrum within the specified mass tolerance and intensity
threshold.
When you select a single, non-cyclic bond in the molecular structure, the Fragment Interpretation
tool highlights the two fragments created when the bond is cleaved, and displays matching peaks
in the connected spectrum.

Connect the Fragment Interpretation Tool to a Spectrum

If you have a spectrum open when you open the Fragment Interpretation tool, then the active
panel links to the open spectrum automatically.
1. Click Explore > Show > Show Fragment Interpretation Tool.
2. From the lower right corner of the Fragment Interpretation pane, click the connect
button.
The pointer changes to the connecting tool.

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3. Click the spectrum graph that you want to connect to the Fragment Interpretation
tool.
The connected graph indicator in the lower left corner contains the name of the
graph connected to the Fragment Interpretation pane. The connection is broken
when either the graph or Fragment Interpretation is closed. If the connected .wiff file
has more than one sample, the Fragment Interpretation pane updates automatically
as you scroll through the samples.

Match Fragments with Peaks

1. Click Explore > Show > Show Fragment Interpretation Tool.
2. With a .mol file in the Fragment Interpretation pane, select a cell in the Fragment
List that is shown in bold.
In the spectrum, the software highlights the matching spectral peak in the color
selected under the Options tab. In the molecular structure, the bond is highlighted.
3. If you click a row that has more than one matching fragment, the spectral peak that
is closest to its monoisotopic mass is highlighted in the mass spectrum in the color
specified in the Options tab.

Select a Bond in a Molecular Structure

1. Click Explore > Show > Show Fragment Interpretation Tool.
2. With a .mol file opened in the Fragment Interpretation pane, click a single, non-cyclic
bond in the molecular structure.
The two resulting fragments appear as highlights in the fragment list. The masses of
the two fragments appear on either side of the bond.
If a spectrum is connected, then the Fragment Interpretation tool displays any
matching peaks in the graph. If you select a fragment in the list and the fragment is
matched to a peak, then the Fragment Interpretation window zooms in on that peak.

View Isotopes
The Fragment Interpretation tool can display the theoretical isotopic distribution for a peak
matching a fragment in the fragment list.
1. Click Explore > Show > Show Fragment Interpretation Tool.
2. In the Fragment Interpretation pane, click the Options tab.
3. Select the Show Isotopes check box.
4. Click Apply.
5. From the Fragment List, select a fragment that matches a peak.
The isotopic distribution for matched peaks is shown in the spectrum.

Show Formula Differences for Fragments

You can show the formula and monoisotopic mass difference between two related hypothetical
fragments. The formula difference is shown when you select two peaks. The formula and
monoisotopic mass difference is shown when you select two fragments, or two single, non-cyclic
bonds.

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Show a Formula Difference in a Spectrum

1. Click a fragment peak.
2. Press Shift and then click another fragment peak.
If the formula difference is equal to a fragment from the fragment list, the fragment
highlights in the list. Otherwise, the formula difference between the peaks' matching
fragments is shown in a message box.

Show a Formula Difference in the Fragment List

1. Click the row number for one fragment.
2. Press Ctrl and then click another fragment.
The formula and monoisotopic mass difference is shown in a message box if the
fragments are related.

Show a Formula Difference in a Molecular Structure

1. Click a single, non-cyclic bond. The default fragment (of the two highlighted
fragments) is selected. If you want to select the other fragment of the cleaved bond,
Ctrl+click the bond.
2. Select a second non-cyclic bond. To select the default fragment, press Shift and
then click the bond. To select the other fragment of the cleaved bond, press
Ctrl+Shift+click the bond.
Fragment Interpretation calculates the formula and monoisotopic mass difference
between the fragment you selected in step 1 and the fragment selected in step 2, if
the fragments are related. The formula and monoisotopic mass difference is shown
in a message box.
Table 5-16 Explore Toolbar Quick Reference: Fragment Interpretation Tool
Icon Name Function
Show Fragment Click to open Fragment Interpretation tool,
Interpretation Tool which calculates the single, non-cyclic bond
cleavage fragments from a .mol file.

Library Databases
The Library Search feature compares unknown spectra to known MS spectra contained in the
library database and generates a list of possible matches.
With Library Search you can:
• Compare library contents against an unknown spectrum.
• Add records to the library.
• Edit existing records.
You can store library data in the following locations:
• MS Access on a local database
• MS SQL Server

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Connect to a Library Database

Before you can use the Library Search feature, you must find where the library data is stored and
connect your computer to that location. Library databases can be stored locally on your computer
or on a server and accessed over a network.

Switch between Existing Library Databases

You can connect to any databases that have aliases that are already set up.
1. Click Tools > Settings > Optimization Options.
The Optimization Options dialog opens.
2. Click the Library Manager tab.
Figure 5-7 Library Manager Tab

3. In the Available Libraries section, click the alias of the database to connect to and
then click Connect.
4. To allow other users to access the database, select the Available to all users of
this machine check box.

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5. Click OK.

Connect to a Local Library Database

1. Click Tools > Settings > Optimization Options.
The Optimization Options dialog opens.
2. Click the Library Manager tab.
3. In the Available Libraries section, click New.
Figure 5-8 Add Library Dialog

4. Type a name for the library.

5. In the Database Information section, select MS Access (local).
6. Type the database location.
7. In the Security Information section, if a user name and password are required to
access this database, then type your user name and password.
8. Click Save.

Connect to a Server Library Database

1. Click Tools > Settings > Optimization Options.

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The Optimization Options dialog opens.

2. Click the Library Manager tab.
3. In the Available Libraries section, click New.
4. Type a name for the library.
5. In the Database Information section, select MS SQL Server (server).
Figure 5-9 Add Library Dialog

6. Type the name of the database server.

7. Type the name of the database.
8. Do one of the following:
• If a specific user name and password are required to access this database,
then type your user name and password.
• If you want to use Windows security, then in the Security Information
section, select the Use Windows integrated security option.
9. Click Save.

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Work with Library Records

If you request the library contents without constraints, all records are listed. When you request
records from the library with constraints, only those records that match the constraints you
specified are listed. The number of records shown depends on the number of constraints you
select. If you select many restraints, few records appear.

View all Library Records

• Click Explore > Library Search > List.
The Librarian dialog opens with all records in the database.

Search Library Records with Constraints

1. Click Explore > Library Search > List With Constraints.
Figure 5-10 List Constraints Dialog

2. In the Field Name list, select a field on which you want to base a constraint.
3. In the Relation list, select the relation (operator) that applies to the field name.
4. In the Value field, type the value of the field name based on the relation.
5. To add the selected constraint to the Conditions list, click Add.
6. Continue adding constraints to the conditions list as required.

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7. Coupling distinct constraints within the Conditions list creates more specific
conditions that enhance your search.
• To group constraints, select the constraints and then click Group.
• To separate grouped constraints, click the group, and then click Ungroup.
8. To change the relationship between constraints, click the relationship, and then click
And or Or.
9. To exclude compounds containing a certain number of atoms of specific elements,
select or type the elements in the Elements Included table, and then type a
minimum and maximum number of atoms of the element.

Note: Element symbols are case-sensitive. For example, Hydrogen is H,

not h and Sodium is Na, not NA or na.

10. To exclude compounds containing certain elements, select or type the elements in
the Excluded table.
11. To search for compounds fitting your criteria, click List.
Records that match all the constraints appear in the Records table. Listing
constraints are saved.

Add a Record to the Library

1. Right-click an active spectrum, and then click Add a Record.
The spectrum will be centroided automatically if it has not been centroided already.
The Add a Record dialog opens with data from the spectrum.
2. On the Mass Spectral Information tab, type a name in the Compound Name field.
The compound name is mandatory and must uniquely identify the compound within
the library.
3. Edit any of the other fields. Many of the fields are filled in automatically from the data
associated with the spectrum.
4. Click the General Information tab, edit the fields as required, and then click OK.

Search for a Similar Spectrum

You can search the library for a spectrum (and its related compound information) that matches
(or is similar to) an active spectrum. Searches can be performed with or without constraints.
When you search with constraints, only those records that match all the criteria appear. The
results appear in a ranked list; the first item on the list is the best fit to the active spectrum.
Entries lower in the list do not match as well.
The more constraints you select, the more precise the list becomes and fewer, more relevant
matches appear. Once you define a set of constraints they will apply to all subsequent searches,
unless you edit them.
Only peaks above the threshold are used in the search. When selecting search constraints, you
can also add or subtract peaks from the active spectrum. For example, if you think a peak is
actually a background or noise spike, you would not want to use it for the search because it could
produce inaccurate results.

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When you search without constraints you see a much larger list of suggested spectra because
the library makes fewer specific matches to the spectral data.

Search for a Similar Spectrum

1. Right-click on an active spectrum and then click Search With Constraints.
The software will centroid the spectrum automatically if you have not already done
so.
Figure 5-11 Search Constraints Dialog

2. In the Maximum Number of Match field, type the maximum number of compounds
you want returned by the search.
3. In the Preselect Constraints section, select the check boxes for the constraints to
apply.
4. For each constraint selected, in the Preset Tolerance section, type the tolerance.
5. If required, select a method of sorting records from the Result Sorted by list.
6. If required, type text in the Comment Contains field.
7. If required, type text in the Keyword Contains field.

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8. To apply peak constraints by adding and removing peaks, click Peak Constraints.
The Peaks Included table opens.
9. To add peaks to the list you want to search against, click Add and then type the m/z
and the corresponding intensity in the empty cell.
10. To remove peaks so they will not be included in the search, select the peaks that you
do not want to search against and then click Remove.
11. Click Search to save the constraints and begin the search.

View a Compound from the Search Results

If several spectra match the unknown spectrum, you can view other spectra and compare them
to the unknown.
1. In the Search Results dialog, in the list of compounds, select the row number of the
compound.
2. Click the spectrum pane of one of the known compounds.
The spectrum of the selected compound opens.
Table 5-17 Tips
To do this... ... do this
Library searches: To group Select the conditions to group and then click Group. This
conditions function behaves like parentheses in formulas.
Library searches: To search Right-click an active spectrum, and then click Search Library.
without using constraints The Search Results dialog opens.
Table-specific queries: To Right-click anywhere in the Results Table and then click Query >
view the entire table again Show All. You can also apply the query again or edit the query.
Peak Integration: To review To review all peaks, make sure that all samples are listed in the
peaks Results Table.
The Peak Review window contains the peaks listed in the
Results table. If some samples are hidden in the table (for
example, if you applied a query), then they are also hidden in
peak review.
Peak Integration: To move to Right-click anywhere in the Peak Review pane and then click
the first peak in the batch Show First Page. To move to the last peak in the batch, right-
click anywhere in the Peak Review pane and then click Show
Last Page.
To examine calibration Right-click anywhere in the curve, click Active Plot, and select
curves the curve to be plotted on top.
Sample statistic review: To Select the Display the Data Set(s) check box, and then, in the
review an individual peak Data Point column, double-click the data point that represents
the peak. The software displays the Peak Review window with
the peak you chose.
Results Tables: To return the Right-click on the Results Table and click Sort > Sort By Index.
Results Table to its original
order

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Table 5-17 Tips

To do this... ... do this
Acquisition Methods: To Right-click the file information pane and then click Save
create an acquisition method Acquisition Method.
from the file information pane

Table 5-18 Explore Quick Reference: Chromatograms and Spectrum

Icon Name Function
Open File Click to open files.

Show Next Sample Click to navigate to the next sample.

Show Previous Sample Click to navigate to the previous sample.

GoTo Sample Click to open the Select Sample dialog.

List Data Click to view the data in tables.

Show TIC Click to generate a TIC from a spectrum.

Extract Using Dialog Click to extract ions by selecting masses.

Show Base Peak Click to generate a BPC.

Chromatogram

Show Spectrum Click to generate a spectrum from a TIC.

Copy Graph to new Window Click to copy the active graph to a new window.

Baseline Subtract Click to open the Baseline Subtract dialog.

Threshold Click to adjust the threshold.

Noise Filter Click to use the Noise Filter Options dialog to define
the minimum width of a peak. Signals below this
minimum width are regarded as noise.
Show ADC Click to view ADC data.

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Table 5-18 Explore Quick Reference: Chromatograms and Spectrum (Continued)

Icon Name Function
Show File Info Click to show the experimental conditions you used
to collect your data.

Add arrows Click to add arrows to the x-axis of the active graph.

Remove all arrows Click to remove arrows from the x-axis of the active
graph.

Offset Graph Click to compensate for slight differences in the time

during which the ADC data and the mass
spectrometer data were recorded. This is useful
when overlaying graphs for comparison.
Force Peak Labels Click to label all the peaks.

Expand Selection By Click to set the expansion factor for a portion of a

graph that you want to view in greater detail.

Clear ranges Click to return the expanded selection to normal

view.

Set Selection Click to type start and stop points for a selection.
This provides more accurate selection than is
possible by highlighting the region using the cursor.
Normalize to Max Click to scale a graph to maximum, so that the most
intense peak is scaled is to full scale, whether or not
it is visible.
Show History Click to view a summary of data processing
operations performed on a particular file, such as
smoothing, subtraction, calibration, and noise
filtering.
Open Compound Database Click to open the compound database.

Set Threshold Click to adjust the threshold.

Show Contour Plot Click to display selected data as either a spectrum

graph or an XIC. Additionally, for data acquired by a
DAD, a contour plot can display selected data as
either a DAD spectrum or an XWC.
Show DAD TWC Click to generate a TWC of the DAD.

Show DAD Click to generate a DAD.

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Table 5-18 Explore Quick Reference: Chromatograms and Spectrum (Continued)

Icon Name Function
Extract Wavelength Click to extract up to three wavelength ranges from a
DAD spectrum to view the XWC.

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6
In this section, you will use the sample files found in the Example folder to learn how to select
samples for quantitation, how to choose preset queries and create table-specific queries, and
how to analyze the acquired data.

Quantitative Analysis
Quantitative analysis is used to find the concentration of a particular substance in a sample. By
analyzing an unknown sample and comparing it to other samples containing the same substance
with known concentrations (standards), the Analyst® software can calculate the concentration of
the unknown sample. The process involves creating a calibration curve using the standards and
then calculating the concentration for the unknown sample. The calculated concentrations of
each sample are then available in a Results Table.

About Quantitation Methods

A quantitation method is a set of parameters used to generate peaks in a sample. The
quantitation method can include parameters used to locate and integrate peaks, generate
standard curves, and calculate unknown concentrations.
You can create a quantitation method before data acquisition and then apply it to the quantitative
data automatically upon completion of the batch. Alternatively, a quantitation method can be
created and applied post-acquisition.
You can use three tools to create a quantitation method: the Quantitation Wizard, the Build
Quantitation Method, and Quick Quant.

Build Quantitation Method

If you use the Build Quantitation Method you will not generate a Quantitation Results Table
although the method can subsequently be used in the Quantitation Wizard to create a Results
Table. The Build Quantitation Method can also be used to modify existing quantitation methods.
This is the most flexible way of creating a quantitation method.

Quantitation Wizard
If you use the Quantitation Wizard, a Results Table is generated at the same time as the
quantitation method. Alternatively, you can use a pre-existing quantitation method to create
quantitate different sets of data. This is the most common way of creating a quantitation method.

Quick Quant
Quick Quant is part of the Batch Editor. You can use Quick Quant to add compound
concentrations prior to data acquisition. Because you have not yet acquired a sample, you
cannot choose a representative sample or review any peaks. With this process, you are only
defining the method components.
If you have a previously saved quantitation method that you would like to use, you can select it
from the Quantitation menu in your batch. For instructions on creating a batch, refer to Create
and Submit a Batch on page 42.

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About Results Tables

Results Tables summarize the calculated concentration of an analyte in each unknown sample
based on the calibration curve. They also include the calibration curves as well as statistics for
the results. You can customize the Results Table and view the Results Tables in layouts.
Using the software, you can export the data from a Results Table to a .txt file for use in other
applications, such as Microsoft Excel. You can also export data in the table or just the data in the
visible columns.

Create Quantitation Methods and Generate Results Tables

For the following procedures, you will use previously acquired sample data that is installed with
the Analyst software.
PK Data contains the batches Mix_Batch1 and Mix_Batch2. These sample batches are used to
demonstrate the usefulness of metric plots to isolate problematic samples. The ions scanned
were reserpine (609.4/195.0), minoxidil (210.2/164.2), tolbutamide (271.3/91.1) and
rescinnamine (635.4/221.2), which is the internal standard. Batch 1 contains no errors in terms of
sample preparation, whereas Batch 2 contains a QC sample where the internal standard was
added twice (sample QC2).

Create a Method using the Quantitation Method Editor

1. Make sure that you have the Example folder selected.
2. On the Navigation bar, under Quantitate, double-click Build Quantitation Method.
The Select Sample dialog opens.
3. In the Data Files list, navigate to Triple Quad > Mix_Batch_2.
The samples in the selected data file appear in the Samples list.
4. In the Samples list, select the samples and then click OK.
5. In the Internal Standards table, do the following:
• In the Name column, select resinamine from the list.
• In the Q1/Q3 column, from the list of masses, select 635.400/221.185 for each
standard.

Note: If the Compound ID field was populated for the samples and internal
standards in the acquisition method, then in the Internal Standards table,
when you select a value in Q1/Q3 field, the Name field is automatically
populated.

6. In the Analytes table, do the following:

• In the Name column, select reserpine.
• In the Internal Standard column, from the list, select the internal standard to
be associated with each analyte.
• In the Q1/Q3 column, from the list of masses, select 609.400/195.039.
• If required, you can add one or more of the other compounds for a more
complex analysis.

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Note: If the Compound ID field was populated for the samples and internal
standards in the acquisition method, then in the Analytes table, the Name
field and Q1/Q3 field are populated.

7. Click the Integration tab.

8. In general, the preset integration parameters are suitable for most peaks. However, if
the integration is not suitable, you can change the algorithm. Click the Show or Hide
Parameters icon to show the additional integration algorithms available.
9. Click the Calibration tab. The preset parameters are suitable for these samples.
10. Save the quantitation method as TutorialQuantMethod.qmf.
The new method can now be used when you create a batch in the Batch Editor or
when you can use the Quantitation Wizard to generate a Results Table.

Note: The quantitation method can only be used in the current project
unless you copy it to another project. To do this, click Tools > Project >
Copy Data. A new project must be created and selected to be available for
use.

Use the Quantitation Wizard to Create a Results Table

1. On the Navigation bar, under Quantitate, double-click Quantitation Wizard.
The Create Quantitation Set - Select Samples page opens.
2. In the Available Data Files list, navigate to Triple Quad > Mix_Batch_2, add all the
samples, and then click Next.
The Create Quantitation Set - Select Settings & Query page opens.
3. In the Default Query section, click Select Existing: Query and then select
Accuracy 15%. Click Next.

Note: If you want to create a query at the same time, refer to Create a
Standard Query on page 100.

The Create Quantitation Set - Select Method page opens.

4. Click Choose Existing Method, select TutorialQuantMethod.qmf, and then click
Finish.
The Results Table opens.

Tip! To add or remove samples in the Results Table, click Tools >
Results Table > Add/Remove Samples.

5. Save the Results Table.

Tip! You can create well-formatted reports from a Results Table using the
Reporter software. It is recommended that the user validate the results if a
Reporter template that contains a query is used. Refer to Reporter
Software on page 123.

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Create a Standard Query

You can create a query and a standard query numerous ways. The following is one example. For
more information on creating queries, refer to the Help.
It is recommended that the user validate any queries that are used to analyze data in a Results
Table.
1. On the Navigation bar, in Quantitate mode, double-click Quantitation Wizard.
2. On the Create Quantitation Set - Select Samples page, select samples and then
click Next.
3. On the Select Settings & Query page, in the Default Query section, select Create
New Standard Query and then type a query name.
Figure 6-1 Create Quantitation Set - Select Settings & Query Page

4. Click Next.

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Figure 6-2 Create Default Query Page

5. In the Maximum Allowed Accuracy Variation for QCs (%) table in the Max.
Variation column, type the maximum allowable percent of variation for each QC (for
example, 5 is ±5%) in the same row as the corresponding concentration. If the
concentrations were not specified during acquisition, they do not appear here. In that
case, you will have to type them in the Concentration column.
6. In the Maximum Allowed Accuracy Variation for Standards (%) table, in the Max.
Variation column, type the maximum allowable percent of variation for each
standard (for example, 10 is ±10%) in the same row as the corresponding
concentration. If the concentrations were not specified during acquisition, they do not
appear here. In that case, you will have to type them in the Concentration column.
7. Click Next.

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Figure 6-3 Create Quantitation Set - Select Method Page

8. Select or create a method.

9. Click Finish.
The query is applied as a standard query. The query results appear as a Pass or Fail
entry in the Standard Query Status column of the Results Table.

Define the Layout of Results Tables

Predefined views of the Results Table are available.
• Right-click in the Results Table and then click one of the following:
• To view the Full layout, click Full.
All the analytes are shown.
• To view the Summary layout, click Summary and then click a field name.
• To view the Analyte layout, click Analyte and then click a single analyte if
more than one analyte exists.
• To view the Analyte Group layout, click Analyte Group and then click an
analyte group.

Tip! A new analyte group must be created first. To do this, right-click in

the Results Table and then click Analyte Group > New.

The table is shown with the selected layout.

Tip! To go back to the full view, right-click and click Full.

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Sort Data in Results Tables

You can sort the data in a Results Table in the following ways:
• Quickly sort the table on one to three columns, using one of the Sort buttons. This
sort criteria cannot be saved.
• Create a table-specific sort to save the sort criteria with the current table. Table-
specific sorts allow you to sort the current table on one to three columns and save
the criterion for use with that table.
• Use a previously created preset sort. You can create and save a sort and later apply
it to a Results Table.

Tip! To save a sort or any other table setting, right-click in the table and
then click Table Settings > Export To New Table Settings. The sort and
other parameters can be used in the current project. To use the table
settings in a different project you must copy it to another project. Click
Tools > Project > Copy Data. A new project must be created and selected
to be available for use.

Sort a Results Table

1. Select up to three columns in the Results Table in the order that you want to sort
them.
2. Do one of the following:
• To sort in ascending order, click A-Z.
• To sort in descending order, click Z-A.

Sort a Results Table and Save the Sort Criteria

1. Right-click in the Results Table and then click Sort > New.

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Figure 6-4 Sort Dialog

2. In the Name field, type the name for the new sort.
3. For each sorting rule you want to set, in the Sort By section, do the following:
• In the Group list, select the type of column you want to sort on.
• In the Column list, select the column you want to sort on.
• Select the direction of the sort: Ascending or Descending.
4. Do one of the following:
• To perform the sort, save the sort criteria, and close the Sort dialog, click
Save/Execute.
• To perform the sort and close the Sort dialog without saving the sort criteria,
click Execute.

Save Default Sort Criteria for Future Results Tables

1. Click Tools > Settings > New Quantitation Results Table Settings.

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Figure 6-5 Table Settings Dialog

2. Expand the Table Settings folder and then double-click the Default folder.
3. From the expanded Default folder, select the Sorts folder, and then click New.
Figure 6-6 Sort dialog

4. In the Name field, type a name for the new sort.

5. For each sorting rule you want to set, in the Sort By section, do the following:
• In the Group list, select the type of column you want to sort on.
• In the Column list, select the column you want to sort on.
• Select the direction of the sort: Ascending or Descending.

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6. To save the criteria and close the Sort dialog, click OK.
7. To close the Table Settings dialog, click Done.

Sort a Results Table using Preset Sort Criteria

• Right-click in the Results Table, click Sort and then select the name of the sort that
you want to use.

Results Table Right-Click Menu

The following options are available if you right-click in the Results Table.
Figure 6-7 Results Table Right-Click Menu

Menu Function
Full Click to show all the columns.
Summary Click to show specific columns.
Analyte Click to show a specific analyte.
Analyte Group Click to create an analyte group.
Sample Type Click to show samples of a specific type or all samples.

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Menu Function
Add Formula Column Click to add a formula column.
Table Settings Click to edit or select a table setting.
Query Click to create or select a query.
Sort Click to create a sort or to sort by index.
Metric Plot Click to create a metric plot.
Delete Pane Click to delete the active pane.
Fill Down Click to fill the same data into the selected cells.
Add Custom Column Click to add a custom column.
Delete Custom Column Click to delete the selected custom column.

Peak Review and Manual Integration of Peaks

You can use peak review to survey the peaks that the software has identified, and then redefine
the peak or the start and end points where necessary.
After you have identified the analytes and internal standards that the software must find, the
software searches for the peaks in the samples. When the software identifies a peak, it displays
the chromatograms for each analyte and internal standard in the Create Quantitation Method:
Define Integration page of the Standard Wizard or on the Integration tab of the Full Method
Editor. At this point, you confirm the peaks that are found or modify the quantitation method to
better define your peaks.

Integrate Peaks Manually

During peak review, you may want to view a peak in its entirety—or you may want to examine the
baseline to find out how well the software found the start and end points of the peak. Use the
automatic zooming feature to help you do either.
To help the software find a peak, you can define the exact start and end points of the peak and
background manually. These changes will apply only to that individual peak unless you update
the global method.

Note: It is recommended that the user validate manually integrated results.

Review Peaks

Tip! To review an individual peak, right-click on a point on the curve and then click
Show Peak. The software opens the Peak Review window with the peak you chose.

1. Right-click in the Results Table, click Analyte and then select a sample.
2. Click Tools > Peak Review > Pane.

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The peaks are shown below the Results Table with only the peaks listed in the
Results Table.
3. Right-click in the pane and then click Options.
4. In the Peak Review Options dialog, in the Appearance section, change Num.
rows to 1 and Num. columns to 2.
5. In the Automatic Zooming section, click Zoom Y axis to: 100% of largest peak to
show the entire peak.
Figure 6-8 Peak Review Options

1 3

Item Definition
1 Number of rows
2 Number of columns
3 Zoom Y axis to 100% of largest peak

6. Click OK.
7. To move through the peaks, click the right-pointing arrow (for more information, refer
to Figure 6-9 on page 109.) Go to the second injection of standard 3. In this
example, you could integrate the peak closer to the baseline by selecting the
Specify Parameters option.

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Tip! To move to a specific peak in the Peak Review pane, select the
corresponding row in the Results Table.

Figure 6-9 Peak Review Pane

1 2 5

4
3

Item Description
1 Arrows: click to move through the peaks.
2 Show or Hide Parameters: click to show the integration parameters.
3 Integration parameters: click to change the parameters.
4 Noise Percentage: type a noise percent.
5 Apply: click to integrate the parameters.

8. Click Show or Hide Parameters twice, and then click Specify Parameters -MQ III.
9. Change the Noise Percent value and click Apply.
You will see the peak integrated closer to the baseline.
10. If the change does not improve the peak integration, then adjust the Noise Percent
parameter until you find the optimal value.
11. To update the algorithm for all peaks, right-click in the pane and then click Update
Method.

Note: The Update Method function will only update the algorithm values
for that specific analyte (or internal standard) and not all analytes.

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Figure 6-10 Update Method

Manually Integrate Peaks

Manually integrating peaks should be done last. You should manually integrate peaks only if you
have been unsuccessful in finding all the peaks after adjusting and updating the algorithm
parameters. This is done to limit person-to-person variability.

Note: Peaks that are manually integrated, or where the algorithm was changed for
only that peak, are identified as such in the Record Modified column of the Results
Table, as are the peaks that have algorithm parameter changes for a sample but not
updated to the entire analyte group.

1. In the Peak Review pane, click Manual Integration Mode.

Figure 6-11 Peak Review

Item Description
1 Manual Integration Mode

2. Zoom in on the lower 10% of the peak.

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Figure 6-12 Lower 10% of Peak

Item Description
1 Lower 10% of the peak

3. Position the cross-hair where you want to define the start of the peak and then drag
the cross-hair to where you want to define the end of the peak.
The software shades the area bounded by the base and sides of the peak. Peak
parameters are gray as they are no longer applicable because the peak was drawn
manually.
4. Do one of the following:
• To make this change permanent, click Accept.
• To discard your changes, clear the Manual Integration check box.

Tip! If you find that a peak was correct as originally selected, right-click
the peak and then click Revert to Method.

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Peak Review Right-Click Menu

The following options are available if you right-click in the Peak Review window or pane.
Figure 6-13 Peak Review Dialog

Menu Function
Options Click to open the Peak Review Options dialog.
Sample Annotation Click to open the Sample Annotation dialog.
Save Active to Text File Click to save the selected peak as a text file.
Show First Page Click to go to the first sample.
Show Last Page Click to go to the last sample.
Slide Show Peak Review Click to open the slide show.
Update Method Click to update the algorithm for all peaks.
Revert to Method Click to have a redefined peak reselected based on the current
quantitation method.
Delete Pane Click to delete the active pane.

Calibration Curves
A calibration curve is used to find the calculated concentration of samples, including QC (quality
control) samples. QC samples are added to a batch to estimate the data quality and accuracy of
standards in the batch. QC samples have known analyte concentrations but are treated as
unknowns so that the measured concentrations can be compared to the actual value.

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The calibration curve is generated by plotting the concentration of the standard versus its area or
height. If you are using an internal standard, the ratio of the standard concentration/internal
standard versus the ratio of the standard peak height or area to the internal standard peak height
or area is plotted. The area or height ratio of a sample is then applied to this curve to find the
concentration of the sample, as shown in the Results Table. A regression equation is generated
by this calibration curve according to the regression you specified. The regression equation is
used to calculate the concentration of the unknown samples.

Work with Calibration Curves

If you have a Results Table open, you can view the calibration curve and change the regression
options. If you have two or more Results Tables open, you can overlay their calibration curves. To
overlay curves, the method used to create the tables must be the same.

Show Calibration Curves

Plot a calibration curve to see the curve used for regression. If two or more curves are open, you
can overlay them. The Calculated Concentration field in the Results Table reflects any changes
resulting from the fit of the curve to the standard’s points

Note: This option is available only when a Results Table is open in the workspace.

1. With a Results Table open, click Tools > Calibration > Pane.
The Calibration Curve pane containing the calibration curve opens.
2. If you have more than one analyte you can view the calibration curve for another
analyte:
• From the Analyte list, select an analyte.
• From the next list, select Area or Height, if needed.
3. To change the regression options for the calibration curve, do the following:
• Click Regression.
Figure 6-14 Regression Options Dialog

• In the Fit list, select Linear.

• In the Weight list, select 1 / x.
• Click OK.

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The calibration curve is shown again. The Calculated Concentration field reflects any
changes resulting from the fit of the curve to the standard’s points. You can now
review individual peaks on the curve. You can also exclude points from the curve to
produce a better curve.
4. If necessary, repeat these steps, to create a more appropriate curve.
5. To save the changes, click Accept.

Overlay Calibration Curves

Note: If you want to examine the curve for one table more closely, right-click on the
curve and click Active Plot. Choose the curve to be plotted on top.

1. With two or more open Results Tables, view a calibration curve for one of the tables.
2. Right-click the calibration curve and then click Overlay.
Figure 6-15 Overlay Dialog

3. Select the tables to overlay with the current curve.

4. Click OK.
The software plots the curves for all selected tables on the same graph.

Calibration Curve Right-Click Menu

The following options are available if you right-click in the Calibration window or pane.

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Figure 6-16 Calibration Window

Menu Function
Exclude (Include) Right-click the point and then click Exclude to exclude the point
from the curve. Right-click the point and then click Include to
include the dropped point.
Exclude All Analytes Right-click a point and then click Exclude All Analytes to exclude
(Include All Analytes) all the analytes from the curve. Right-click a point and then click
Include All Analytes to include the points.
Show Peak Click to review an individual peak.
Overlay Click to overlay two graphs.
Active Plot Click to see which plot is active.
Legend Click to display the graph legend.
Log Scale X Axis* Click to use a log scale for the X axis.
Log Scale Y Axis* Click to use a log scale for the Y axis.
Delete Pane Click to delete the active pane.
Home Graph Click to rescale the graph to its original size
* A log scale arranges the data points in a more manageable view so that the effect of all
points can be monitored simultaneously. For this view, select Log Scale Y Axis versus
Log Scale X and not just the log of one axis.

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Sample Statistics
Use the Statistics window to view the statistics samples, typically for standards and QCs (quality
controls). The data from each available batch in the Results Table is shown in tabular form in the
grid and a row of data is shown for each standard or QC concentration.
It is recommended that the user include batch statistics in reports to be sure of the validity of the
results.

Review Sample Statistics

When you are viewing more than one Results Table, you can obtain statistical information on the
standards and QCs for additional batches in the Statistics window. This allows you to compare
results between batches and look for trends in the standards or QCs.

View the Statistics for Standards and QCs

1. With a Results Table open, click Tools > Statistics.
The Statistics window opens.
2. In the Statistics Metric list, select Concentration.
3. In the Analyte Name field, select an analyte.
4. In the Sample Type field, select Standard.
The results appear.
5. Look at the %CV and Accuracy columns.
The %CV shows you the coefficient of variance between the measurements of a
single parameter, for example the area. Accuracy shows you how close the plotted
point is to the interperlated value.
6. If required, select the Display Low/High values check box and then examine the
Low, High, and Mean for each row in the grid. Each row represents standards that
have the same concentration levels.
7. Choose another analyte.
The results appear on a per-analyte basis.
8. To check for Quality Control variations at the same concentration levels, select QC in
the Sample Type field.

Compare Results between Batches

The number of analytes and the analyte names must be the same for the data to be combined in
the Statistics pane.
1. Open the Results Tables that you want to compare.
2. Click Tools > Statistics.
The Statistics window opens.
3. Do one of the following:
• To arrange the results by Results Table, in the Conc. as Rows list, select
Group By Batch.

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• To arrange the results in order of concentration, in the Conc. as Rows list,

select Group By Concentration.
• To arrange the results in order of concentration, but without a row showing the
statistics for each group or batch, in the Conc. as Rows list, select Group By
Concentration (no All).
The software sorts the results. At the end of each batch or group, one or two
additional rows appear: All (statistics for all results tables in that group) and Average
(statistics on the statistics for that batch or group).

Metric Plots
A metric plot graphically shows the data in a Results Table column plotted against the x-axis or
the y-axis, or the data in two columns plotted against each other. This section describes how to
generate and work with metric plots.
A few predefined metric plots are also included:
• Int_Std_Response (to locate problem sample)
• Analyte_Area versus Height (to verify chromatography behavior)
• PK profile (conc. versus time point, to run after Sample query)

Generate Metric Plots

You can use metric plots to plot a given column, such as Analyte Peak Area, Accuracy, or
Calculated Concentration, from the Results Table. You can also plot two Results Table fields
against each other. You can then investigate points that appear outside the normal range. Metric
plots are often used with queries. For more information about queries, refer to the Help.
You can generate metric plots in the following ways:
• Use the Plot button to plot a column or columns of the current Results Table, but not
save the plotting criteria.
• Create a table-specific plot to save the plot criteria with the current table.
• Create a global plot to save the plotting criteria for use with future Results Tables.
You cannot see QC, unknown, blanks, double blanks, or solvents on the calibration curve, but
you can generate metric plots of them.

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Figure 6-17 Example of a Metric Plot

Item Description
1 Double blanks

Generate a Metric Temporary Plot

1. With a Results Table open, do one of the following:
• To plot the data on the y-axis with the x-axis as an index, click the heading of
the column for the data you want to plot.
• To plot the data from the first selected column on the x-axis and the second
selected column on the y-axis, select two columns by pressing the Ctrl key as
you click the column headings.
2. Above the Results Table, click the Metric Plot by Selection icon. Refer to Table 6-2
on page 121.
The metric plot opens.
3. Right-click in the plot pane and then click Data Legend to view an explanation of the
colors used by the plot.
4. Right-click in the plot pane and then click Point Legend to view an explanation of
the symbols used by the plot.

Generate a Metric Plot and Save the Plot Criteria

1. Open the Tutorial Results Table.rdb Results Table.
2. Right-click in the Results Table and then click Metric Plot > New.

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Figure 6-18 Metric Plot Dialog

3. In the Name field, type the name for the new plot criteria.
4. In the X-Axis section, in the Group list, to plot a field in the y-axis using the x-axis as
an index, select Index and leave the Column list blank.
5. If you want to plot two columns against each other, in the Y-axis section, in the
Group list, select Internal Standard, and then, in the Column list, select IS Peak
Area.
6. If required, in the Regression list, select the type of regression you want to use, and
then select the appropriate regression settings.
7. To generate the plot and save the plot criteria, click Save/Execute.
The metric plot opens. For more information, refer to Figure 6-17 on page 118.
8. Right-click in the plot pane and then click Data Legend to view an explanation of the
colors used by the plot.
9. Right-click in the plot pane and then click Point Legend to view an explanation of
the symbols used by the plot.
This set of criteria is now available for future plots of this Results Table when you
right-click in the Results Table. You can also edit the plotting criteria.
10. To view the problem sample, try plotting the concentration of the unknown against
time or plotting the area of the internal standard against the index.

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Save Default Plot Criteria for Future Results Tables

1. Right-click in the Results Table and then click Table Settings > Export To New
Table Settings.
This will export the table settings from the .rdb so that it can be reused in other
quantitation runs within the project.
2. To export table settings to another project, on the Tools menu click Project > Copy
Data.
Figure 6-19 Copy Data Dialog

Table 6-1 Integration Tab and Quantitation Wizard Icons

Icon Name Function
Set parameters from Click to use the peak that you selected.
Background Region

Select Peak Click to use the background that you selected.

Manual Integration Mode Click to manually integrate peaks.

Show or Hide Parameters Click to toggle the peak-finding parameters between

shown and hidden.

Show Active Graph Click to show the analyte chromatogram only.

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Table 6-1 Integration Tab and Quantitation Wizard Icons (Continued)

Icon Name Function
Show Both Analyte and IS Click to show the analyte and its associated
chromatogram (available only when an associated
internal standard exists).
Use Default View for Graph Click to return to the preset (view all data) view (if,
for example, you have zoomed in on a
chromatogram).

Table 6-2 Results Table Icons

Icon Name Function
Sort Ascending by Selection Click to sort the selected column by ascending
values.

Sort Descending by Click to sort the selected column by descending

Selection values.

Lock or Unlock Column Click to lock or unlock the selected column. You
cannot move a locked column.

Metric Plot by Selection Click to create a metric plot from the selected
column.

Show all Samples Click to show all the samples in the Results Table.

Delete Formula Column Click to delete formula columns.

Table 6-3 Icon Quick Reference: Quantitate Mode

Icon Name Function
Add/Remove Samples Click to add or remove samples from the Results
Table.

Export as Text Click to save the Results Table as a text file.

Modify Method Click to open a .wiff file.

Peak Review - Pane Click to review peaks in a pane.

Peak Review - Window Click to review peaks in a window.

Calibration - Pane Click to open the calibration curve in a pane.

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Table 6-3 Icon Quick Reference: Quantitate Mode (Continued)

Icon Name Function
Calibration - Window Click to open the calibration curve in a window.

Show First Peak Click to show the first peak in the pane or window.

Show Last Peak Click to show the last peak in the pane or window.

Show Audit Trail Click to show the audit trail for the Results Table.

Clear Audit Trail Click to clear the audit trail for the Results Table.

Statistics Click to open the Statistics window.

Report Generator Click to open the Reporter software.

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Reporter Software
7
The Reporter software extends the reporting functionality available in the Analyst® software.
It is recommended that the user validate the results if a Reporter template that contains a query
is used.

Analyst Software Reporter Overview

The Reporter software can be used to create custom reports with Microsoft Word and Excel
(2007, 2010, or 2013). The Reporter software has the following features:
• Provides a variety of reports that use the data available in a Results Table, in file
information, and in quantitative peak review windows.
• Uses Microsoft Word templates to provide the format information needed when
generating reports. These templates can be created or modified to provide
customized report formats. Refer to the Help if you want to create or edit templates
using the Report Template Editor.
• Contains a blank starting template that can be used in the Analyst software Reporter
editing environment to design report templates to meet most report requirement.
• Automates report generation through the use of the Autoquan Reporter batch script.
• Automatically prints, exports to Adobe Portable Document Format (pdf), and delivers
results by e-mail. This functionality requires the Save as PDF (Office 2007) addin
that is installed by the Analyst software.
• Attaches processing scripts to report templates to expand both the content and
automation level for various workflow requirements.
• Generates reports from custom software applications that use the available Analyst
software programming libraries.
Reporter software can be used in three ways:
• Within the Analyst software to manually generate a report or set of reports.
• By a batch script to automate report generation within a batch. You can generate
reports on a sample-by-sample basis, either during or after batch acquisition.
• By applications that do not use the Analyst software.

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Reporter Software

Reporter User Interface

Figure 7-1 User Interface

1 2 3
4

5 6

Item Option Description

1 File > Exit Exits the program and releases all resources.
2 Settings > Select Sets the language dictionary that will be used to replace
Output Language language tags within a report template. Templates that contain
language tags within them can be used to generate reports in any
language. The language tags are replaced with text from a
matching tag in the dictionary file for the selected language.
These dictionary files are contained in the folder: C:\Program
Files\AB SCIEX\AnalystReporter\Resources \Languages.
2 Settings > Select Browse to an spectral library. This library will be used for
Library matching and scoring MS/MS from Results Tables that contain
data from information dependent acquisition (IDA) triggered MS/
MS.
2 Settings > Select Sets the folder from which the available templates will be read. To
Template Folder return to the default template folder, select the Default option.
3 Help > About Shows information about the version of Reporter software
currently installed.

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Item Option Description

4 Current Output Displays the currently selected language dictionary used for
Language replacing language tags within a report template. The language
dictionary can be selected using Settings > Select Output
Language.
5 Current Spectral Displays the currently selected spectral library. The spectral
Library library can be selected using Settings > Select Library.
6 Available Displays a list of available report templates. Selecting a template
Templates and will show a description of the template. To change the folder
Description where available templates are read from, select Settings >
Select Template Folder > Browse.
7 Output Format The Reporter software supports several output formats. Only
formats that are compatible with the selected report template are
enabled.
• Word: Microsoft Word document (.docx) is produced. This
document can be viewed by Microsoft Word 2007 and
above.
• PDF: The PDF option creates a report directly in PDF
format.
• HTML: Microsoft Word is used to generate an HTML file.
Associated image files are stored in a folder with the same
name as the HTML file.
• Excel: A plain text file (.csv) is produced. Report templates
that contain values separated by commas can be opened
in Microsoft Excel, where each value will be displayed in a
separate cell. Only templates that are specifically marked
as text-compatible can be used for this output format.
• Text: A plain text document (.txt) is produced. Only
templates that have been specifically marked as text-
compatible can be used for this output format.
• Print Automatically: If selected, after the report has been
created it is printed to the selected printer. Select from any
available printer.

Generate Reports
The Reporter software extracts numerical data from the Results Table and sample and graphical
information from the .wiff file.
You can select a template in the Available Template field.

Tip! For reports that can be generated on a sample-by-sample basis, it may be more
efficient to generate the reports automatically using a batch script during acquisition to
avoid long processing times at the end of the acquisition. For more information about
batch scripts, refer to the Scripts User Guide.

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Reporter Software

1. Open a Results Table.

2. Under Companion Software, double-click Reporter 3.2.
3. In the Analyst Reporter dialog, in the Available Templates field, select a template.
4. Click an output format.
The Word option is pre-selected and the report is automatically saved in the current
project Results folder. If this option is not selected, then the report is created and
opened in Word or printed as selected, but the report is not saved. This lets you edit
the report in Word prior to saving the original report.
5. Select either one document containing all samples or multiple documents with one
sample in each.
6. Select the Print Automatically check box if you want your reports to print
automatically to a pre-selected printer.
The Default Printer set in Windows is used unless you select a different printer. The
Reporter tool retains the selected printer between operations. If the printer is set to a
.pdf printer driver, then you can use the Analyst Reporter to generate .pdf file
versions of the created reports automatically.
7. Click Create Report.
The screen shows various progress indicators as the tool opens the template and
populates it with data from the Results Table. Some reports may take seconds to
generate, others may take longer. A large data set with many MRM transitions or a
large number of graphics could result in reports of several hundred pages and could
take hours to generate.
Table 7-1 Icons in Quantitate Mode
Icon Name Function
Report Generator Click to open the Reporter software.

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Calibration Ions and Solutions
A
Table A-1 Tuning Frequency
Calibration Resolution Optimization
Scan Type Frequency Manual/ Frequency Manual/Automated
Automated
Q1 and Q3 3 to 6 months Both 3 to 6 months Both
LIT Every 2 weeks; Both 3 to 6 months Automated only
as required

Table A-2 Suggested Tuning Solutions for Quadrupole Systems

System Positive Negative
API 3000™ System 1× 10–5 M PPG (1:10) 3 × 10–4 NEG PPG
API 4000™ system 2 × 10–6 M PPG (1:50) 3 × 10–4 NEG PPG
API 5000™ system 2 × 10–7 M PPG (1:500) 3 × 10–5 NEG PPG (1:10)

Table A-3 Suggested Tuning Solutions for LIT Systems

Q1 and Q3 LIT
Instrument Positive Negative Positive and
Negative
4000 QTRAP system 2 × 10–6 M PPG (1:50) 3 × 10–4 NEG 1:100 Agilent mix
PPG

Table A-4 Q1 and Q3 PPG Positive Ion Scans

Instrument Masses
API 2000™ system 59.0 175.1 616.5 906.7 1254.9 1545.1 – –
API 3000™ system 59.0 175.1 616.5 906.7 1254.9 1545.1 2010.5 2242.6
API 4000 system 59.0 175.1 616.5 906.7 1254.9 1545.1 2010.5 2242.6
API 5000 system 59.0 175.1 616.5 906.7 1080.8 1196.9 – –
QTRAP system 59.0 175.1 616.5 906.7 1254.9 1545.1 – –
4000 QTRAP system 59.0 175.1 616.5 906.7 1254.9 1545.1 2010.5 2242.6

Table A-5 Q1 and Q3 PPG Negative Ion Scans

Instrument Masses
API 2000 system 45.0 585.4 933.6 1223.8 1572 – – –
API 3000 system 45.0 585.4 933.6 1165.8 1572.1 1863.3 2037.4 2211.6
API 4000 system 45.0 585.4 933.6 1223.8 1572.1 1863.3 2037.4 2211.6
API 5000 system 45.0 411.3 585.4 933.6 1223.8 – – –

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Table A-5 Q1 and Q3 PPG Negative Ion Scans (Continued)

Instrument Masses
QTRAP system 45.0 585.4 933.6 1223.8 1572.1 – – –
4000 QTRAP system 45.0 585.4 933.6 1223.8 1572.1 1863.3 2037.4 2211.6

Table A-6 Masses and Polarity for the 4000 QTRAP System (Agilent)
Instrument/ Masses
Polarity
LIT Positive 118.087 322.049 622.030 922.010 1521.972 2121.934 2721.895
LIT Negative 112.985 431.982 601.978 1033.988 1633.949 2234.911 –

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Parameters and Scan Types
B
This section describes the different parameters and scan types that you can use for your
analysis.

About Instrument Parameters

Source-dependent parameters, compound-dependent parameters, and detector parameters are
all configured in the Analyst® software and applied at specific points to the mass filter rail (ion
path). You should understand what each parameter controls and how it affects resolution,
intensity, and peak shape so that you can achieve optimal results during sample analysis. You
should also consider how changing the value of one parameter can affect another parameter
further along the ion path.

Source-Dependent Parameters
These parameters may change depending on the source you are using.
GS1 (Gas 1): The GS1 parameter controls the nebulizer gas. The nebulizer gas helps generate
small droplets of sample flow and affects spray stability and sensitivity.
GS2 (Gas 2): The GS2 parameter controls the auxiliary, or turbo, gas. It is used to help
evaporate the solvent to produce gas phase sample ions.
TEM (Temperature): The TEM parameter controls the temperature of the turbo gas in the
TurboIonSpray® probe or the temperature of the probe in the heated nebulizer (or APCI) probe.
CUR (Curtain Gas): The CUR parameter controls the gas flow of the Curtain Gas™ interface.
The Curtain Gas interface is located between the curtain plate and the orifice. It assists in solvent
evaporation and prevents solvent droplets from entering and contaminating the ion optics. The
gas flow should be maintained as high as possible without losing sensitivity.
IS (IonSpray Voltage): The IS parameter controls the voltage applied to the electrode that
ionizes the sample in the ion source. It depends on the polarity and it affects the spray stability
and the sensitivity. This parameter can be compound-dependent and should be optimized for
each compound.
IS (Ion Transfer Voltage): For the PhotoSpray® source, the IS parameter controls the voltage
that transfers the ions from the primary ionization region towards the curtain plate orifice.
NC (Needle Current): The NC parameter controls the current applied to the corona discharge
needle in the APCI probe, used in the Turbo V™ source. The discharge ionizes solvent
molecules, which in turn ionize the sample molecules.
ihe (Interface Heater): The ihe parameter switches the interface heater on and off. Heating the
interface helps maximize the ion signal and prevents contamination of the ion optics. This should
always stay on. The button controlling the interface heater reads ON when the interface heater is
on.
IHT (Interface Heater Temperature): The IHT parameter controls the temperature of the
NanoSpray® interface heater and is only available if the NanoSpray ion source and interface are
installed.

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Parameters and Scan Types

svp (Multi-source Selector): The svp parameter controls the selection of the DuoSpray™ ion
source probes: TurboIonSpray probe or APCI probe.

Compound-Dependent Parameters
The compound-dependent parameters consist mostly of voltages in the ion path. Optimal values
for compound-dependent parameters vary depending on the compound being analyzed.

Quadrupole- and LIT-Mode Scan Parameters

The following parameters are available for optimization if you are running a quadrupole mode
scan or an LIT-mode scan.
DP (Declustering Potential): The DP parameter controls the voltage on the orifice, which
controls the ability to decluster ions between the orifice and the skimmer (or for systems with a
QJet® Ion Guide, between the orifice and QJet Ion Guide). It is used to minimize the solvent
clusters that may remain on the sample ions after they enter the vacuum chamber, and, if
required, to fragment ions. The higher the voltage, the higher the energy imparted to the ions. If
the DP parameter is too high, unwanted fragmentation may occur.
EP (Entrance Potential): The EP parameter controls the potential difference between the
voltage on Q0 and ground. The entrance potential guides and focuses the ions through the high-
pressure Q0 region.
FP (Focusing Potential): (For API 2000™ and API 3000™ systems only.) The FP parameter
controls the voltage applied to the focusing ring lens. The focusing potential helps focus the ions
through the skimmer region of the mass spectrometer interface. It can induce fragmentation in
the interface area, similar to the declustering potential.
CEP (Collision Cell Entrance Potential): (For the API 2000 system only.) The CEP parameter
controls the collision cell entrance potential, which is the potential difference between Q0 and
IQ2. It focuses ions into Q2 (collision cell). CEP is used in Q1, MS/MS-type, and LIT scans. Note
that for Q3 scans, this voltage is called IQ2 and is preset to fixed mode.
CE (Collision Energy): The CE parameter controls the potential difference between Q0 and Q2
(collision cell). It is used only in MS/MS-type scans. This is the amount of energy that the
precursor ions receive as they are accelerated into the collision cell, where they collide with gas
molecules and fragment.
CAD (CAD Gas): The CAD parameter controls the pressure of collision gas in the collision cell
during Q3, MS/MS-type, and LIT scans. For Q3 scans, the collision gas helps to focus the ions as
they pass through the collision cell; the preset for the CAD parameter is in fixed mode. For MS/
MS-type scans, the collision gas aids in fragmenting the precursor ions. When the precursor ions
collide with the collision gas, they can dissociate to form product ions. For LIT scans, the collision
gas helps to focus and trap ions in the LIT.
CXP (Collision Cell Exit Potential): The CXP parameter controls the potential difference
between RO2 and IQ3 (for the API 2000 system and QTRAP system) or between RO2 and ST3
(for the API 3000 system, API 4000™ system, API 5000™ system, and 4000 QTRAP system). It
is only used in Q3 and MS/MS-type scans, where it transmits the ions into Q3.
IE1 (Ion Energy 1): The IE1 parameter controls the potential difference between Q0 and RO1.
Although this parameter does affect the sensitivity, it has a greater impact on peak shape, and it
is considered a resolution parameter. IE1 is used in Q1, MS/MS-type, and LIT scans. This
parameter should only be used by experienced users.

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IE3 (Ion Energy 3): The IE3 parameter controls the potential difference between RO2 and RO3.
Although this parameter does affect the sensitivity, it has a greater impact on peak shape, and it
is considered a resolution parameter. IE3 is used in Q3 and MS/MS-type scans. This parameter
should only be used by experienced users.

LIT Mode Scan Parameters

In addition to the compound-dependent parameters that are available on the Compound tab,
several parameters are available on the MS tab or the Advanced MS tab for LIT (linear ion trap)
mode scans that will affect your results. Because parameters on the MS tab or the Advanced MS
tab cannot be changed in real time, the best method of sample introduction for optimizing these
parameters is infusion. The acquisition must be stopped between each parameter change.
Q0 Trapping: The Q0 trapping parameter controls the storage of ions in the Q0 region. It is used
to increase sensitivity and duty cycle by trapping ions in the Q0 region while ions are being mass-
selectively ejected from the LIT. You must use fixed fill time with this parameter.
CES (Collision Energy Spread): The CES parameter, in conjunction with the Collision Energy
(CE), determines which three discreet collision energies will be applied to the precursor mass in
an Enhanced Product Ion (EPI) or MS/MS/MS (MS3) experiment when CES is used. By entering
a collision energy spread value, CES is automatically turned on.
TDF CE (Time Delayed Fragmentation Collision Energy): The TDF CE parameter controls the
potential difference between RO2 and RO3 for TDF (Time Delayed Fragmentation) scans. This is
the amount of energy that the precursor ions receive as they are accelerated into Q3, where they
collide with gas molecules and fragment.
Q3 Cool Time: The Q3 Cool Time parameter controls the amount of time that the precursor ions
are allowed to cool prior to collection of their product ions in TDF (Time Delayed Fragmentation)
scans.
Q3 Entry Barrier: The Q3 Entry Barrier parameter controls the potential difference between RO2
and RO3. It is used to transfer the ions from Q2 into the LIT.
AF2 (Excitation Energy): The AF2 parameter is the voltage of the auxiliary frequency (Aux RF)
applied to Q3 during MS/MS/MS scans. It is used to fragment the isolated second precursor ion.
MS/MS/MS Fragmentation Time: The MS/MS/MS Fragmentation Time parameter controls the
amount of time that the excitation energy is applied in MS/MS/MS scans. It is used in
combination with the excitation energy to fragment the isolated second precursor ion.
MCS (Multi-Charge Separation) Barrier: The MCS Barrier parameter controls the voltage used
when eliminating the singly-charged ions from the LIT in an EMC (Enhanced Multi-Charge) scan.
Q3 Empty Time: The Q3 Empty Time parameter controls the amount of time that singly-charged
ions are removed from the LIT in an EMC (Enhanced Multi-Charge) scan.
Fixed LIT Fill Time: The Fixed LIT Fill Time parameter controls the amount of time that the LIT
fills with ions.
DFT (Dynamic Fill Time): DFT will dynamically calculate the length of time that ions are
collected in the LIT based on the incoming ion signal. When DFT is turned on the signal is
optimized to either increase sensitivity or minimize space-charging.
EXB (Exit Barrier): The EXB parameter controls the voltage on the exit lens. It is used in LIT
scans to mass-selectively eject ions from the LIT. It affects the peak width, the peak shape, and
the intensity of the ion signal.

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AF3 (Trap RF Amplitude): The AF3 parameter controls the zero-to-peak voltage of the auxiliary
frequency (Aux RF) applied to Q3 when ejecting ions from the LIT. The AF3 parameter affects the
peak width, the peak shape, and the intensity of the ion signal.

Detector Parameters
The following parameters affect the detector.
CEM (CEM): The CEM parameter controls the voltage applied to the detector. The voltage
controls the detector response.
DF (Deflector): The DF parameter controls the voltage applied to the deflector. It is used to direct
ions into the detector. It is preset to be in fixed mode.

Scan Types
You can perform quadrupole-mode and LIT-mode scans either individually or in combination
when analyzing your sample.

Scan Techniques
MS: In MS scans, also referred to as single MS scans, ions are separated according to their
mass-to-charge ratio. A single MS scan may be used to find or confirm the molecular weight of a
compound. Single MS scans can also be referred to as survey scans. MS scans do not provide
any information as to the chemical make-up of the ions other than the mass. To obtain more
information about your ions, you need to perform MS/MS or MS/MS/MS.
MS/MS: MS/MS scans are used to help identify or confirm a molecular species. In MS/MS, a
precursor ion can be fragmented in one of two locations.
• For triple quadrupole instruments, fragmentation occurs in the collision cell.
• For LIT instruments, fragmentation can occur in the collision cell or the linear ion
trap.
If enough energy is used, the precursor ion fragments to produce characteristic product ions.
MS/MS/MS: The LIT instrument MS/MS/MS scans go one step further than MS/MS scans. A
fragment that is produced in the collision cell is fragmented further in the trap to give more
structural information about the molecular ion.

Quadrupole-Mode Scan Types

Triple quadrupole instruments have high-sensitivity MRM (Multiple Reaction Monitoring)
capabilities required for quantitation experiments. In addition, they have highly specific scan
types such as precursor ion and neutral loss scans which allow you to perform a more advanced
search on your samples’ components.
Q1 MS (Q1): A full scan using the first quadrupole (Q1). The ion intensity is returned for every
requested mass in the scan range.
Q1 Multiple Ions (Q1 MI): A zero width scan type using the first quadrupole (Q1). The ion
intensity is returned for the specified masses only.

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Q3 MS (Q3): A full scan using the third quadrupole (Q3). The ion intensity is returned for every
requested mass in the scan range.
Q3 Multiple Ions (Q3 MI): A zero width scan type using the third quadrupole (Q3). The ion
intensity is returned for the specified masses only.
MRM (MRM): Mode of operating a triple quadrupole instrument so that an ion of given mass in
Q1 must fragment or dissociate to give a product ion of specific mass in Q3 in order for a
response to be detected. Used primarily for quantitation.
Product Ion (MS2): MS/MS full scan where the first quadrupole (Q1) is fixed to transmit a
specific precursor ion and the third quadrupole (Q3) scans a defined mass range. Used to
identify all of the products of a particular precursor ion.
Precursor Ion (Prec): MS/MS scan where the third quadrupole (Q3) is fixed at a specified mass-
to-charge ratio to transmit a specific product ion and the first quadrupole (Q1) scans a mass
range. Used to confirm the presence of a precursor ion or more commonly used to identify
compounds sharing a common product ion.
Neutral Loss (NL): MS/MS scan where both the first quadrupole (Q1) and the third quadrupole
(Q3) scan a mass range, a fixed mass apart. A response is observed if the ion chosen by the first
analyzer fragments by losing the neutral loss (the fixed mass) specified. Used to confirm the
presence of a precursor ion or more commonly used to identify compounds sharing a common
neutral loss.

LIT (Linear Ion Trap)-Mode Scan Types

The LIT-mode scans use the third quadrupole, Q3, as a linear ion trap. Ions are trapped and
stored in the trap before being scanned out, giving increased sensitivity. In addition, MS/MS/MS
can be performed in the trap, providing more information about your sample.
Enhanced MS (EMS): Ions are scanned in Q1 to the linear ion trap where they are collected.
These ions are scanned out of Q3 to produce single MS type spectra.
Enhanced Multi-Charge (EMC): This scan is similar to the EMS scan except that before
scanning the ions out of the linear ion trap, there is a delay period in which low-charge state ions
(primarily singly-charged ions) are allowed to preferentially escape from the linear ion trap. When
the retained ions are scanned out, the multiply-charged ion population dominates the resulting
spectrum.
Enhanced Product Ion (EPI): Product ions are generated in the Q2 collision cell by the
precursor ions from Q1 colliding with the collision (CAD) gas in Q2. These characteristic product
ions are transmitted and collected in Q3. The ions are scanned out of the linear ion trap to
produce product ion spectra. Use the EPI scan mode to achieve good resolution and intensity.
Enhanced Resolution (ER): This scan is similar to the EMS scan except that a small 30 Da
mass around the precursor mass is scanned out of the linear ion trap at the slowest scan rate to
produce a narrow window of the best-resolved spectra.
MS/MS/MS (MS3): In MS/MS/MS, product ions are generated in the Q2 collision cell. These
product ions are transmitted and then collected in linear ion trap. The linear ion trap isolates a
specific product ion and removes all other ions from the trap. By applying a different voltage in
the trap, the selected product ion collides with the residual nitrogen in Q3, further fragmenting the
ion producing MSn fragments.
Time Delayed Frag (TDF): Product ions are generated and collected in the linear ion trap.
During the first part of the collection period, the lower mass ions are not collected in the linear ion
trap. During the second part of the collection period, all masses over the mass range of interest

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are collected. The resulting enhanced product ion spectra are simplified compared to EPI scan
type spectra. The nature of the spectra aids in the interpretation of the structure and
fragmentation pathways of the molecule of interest. This scan type is not applicable to the
QTRAP 4500, QTRAP 5500, and QTRAP 6500 LC/MS/MS systems.

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Index

automatic tuning, defined 21

A autosampler properties, setting 33
acquisition
starting 44 B
stopping 47 background subtract to file 75
acquisition methods background subtraction 75
adding experiments 38 backing up
adding or removing peripheral devices 32 API Instrument project 20
adding periods 39 instrument settings 22
changing 49 Base Peak Chromatogram
creating from file information pane 94 generating 66
MRM scans 30 purpose 62
Q1 MI scans 29 Batch Editor
Q1 MS scans 26 Auto Increment 44
ADC data, viewing 61 changing values in a table 49
adding Fill Down 44
adding sets and samples 42 Quantitation Methods 47
captions to graphs 73 right-click menu, features 50
experiments to acquisition methods 38 setting sample locations 45
periods to acquisition methods 39 batches
peripheral devices to acquisition methods adding sets and samples 42
32 changing values in a table 49
peripheral devices to hardware profiles 13 comparing 116
records to the Library Database 91 importing 48
samples to Results Tables 99 overview 41
text to graphs 73 submitting 44
adjusting BPC. See Base Peak Chromatogram
algorithm parameters 109
injection volume 44 C
peak width 21 calibrating, overview 21
performance 23 calibration curves
threshold 69 overview 112
AF2, defined 131 captions
AF3, defined 132 adding to graphs 73
algorithms See also text
adjusting parameters 109 CE, defined, Collision Energy, defined 130
types 78 CEM, defined 132
analog to digital converter properties, setting centroid, spectral data 26
37 centroiding data 80
Analyst smoothing algorithm 78 CEP, defined 130
analyte groups, creating 102 changing
analyzing data 57 acquisition methods 49
API Instrument project Batch Editor tables 49
overview 20 LC pump properties 33
Auto Increment, Batch Editor 44 changing. See adjusting

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Index

chromatograms analyzing 57
BPC 62 centroiding 80
DAD 62 chromatographic 57
generating XICs 63 comparing 73
overlaying 73 experimental conditions, viewing 59
overview 62 files, viewing 57
right-click menu features 69 generating XICs 64
TICs 62 obtaining quantitative data 61
TWC 62 opening file 58
types 62 opening files 81
XICs 62 opening processed data files 81
XWC 62 peak parameters 80
See also chromatographic data saving processed data files 81
chromatographic data smoothing 78
overview 57 sorting in Results Tables 103
Collision Cell Entrance Potential, defined 130 spectral 25, 57
colors stopping acquisition 47
Contour Plots 83 storing 43
column oven properties, setting 35 tables, viewing 60
comparing batches 116 TICs 63
Contour Plots Data List tab, described 57
colors 83 databases
intensity and absorbance, setting 83 Library 86
overview 82 Default project, overview 20
right-click menu features 83 deflector parameter, defined 132
selecting areas 83 deleting
viewing 82 panes 72
copying device status 50
graphs 71 DF, defined 132
subprojects 19 Diode Array Detector
copying experiments 38 properties, setting 36
creating purpose 62
acquisition methods 94 viewing 68
analyte groups 102 displaying
MRM scans 30 TICs 63
Q1 MI scan 29 See also viewing
Q1 MS scans 26 dwell time, defined 28
quantitation methods 98
Results Tables 98 E
standard queries 100 editing. See changing
subprojects 18 EMC scan, defined 133
criteria EMS scan, defined 133
saving metric plot criteria 120 Entrance Potential, defined 130
Curtain Gas, defined 129 EP, defined 130
EPI scan, defined 133
D ER scan, defined 133
DAD. See Diode Array Detector Example project, overview 20
data EXB, defined 131
acquiring 44 Excitation Energy, defined 131

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 Index

Exit Barrier, defined 131

experiments, copying 38 H
Extracted Ion Chromatograms hardware profiles
generating 63 adding peripheral devices 13
generation methods 64 overview 9
purpose 62 troubleshooting 14
Extracted Wavelength Chromatogram hiding panes 72
generating 67
purpose 62 I
IE1, defined 130
F IE3, defined 131
files importing batches 48
navigating between sample files 58 injection volume, changing 44
opening 58 instrument optimization, overview 21
viewing 57 instrument status 52
Fill Down, Batch Editor 44 integrated syringe pump properties, setting 34
Fixed LIT Fill Time, defined 131 Interface Heater Temperature, defined 129
Fragment Interpretation Tool Interface Heater, defined 129
connecting to a spectrum 84 Ion Energy 1, defined 130
matching fragments 85 Ion Energy 3, defined 131
overview 84 Ion Transfer Voltage, defined 129
fragments, formula and monoisotopic mass 85 IonSpray Voltage, defined 129
isotopes, viewing 85
G
Gas 1, defined 129 L
Gas 2, defined 129 labeling graphs 73
Gaussian smoothing algorithm 78 Library Database
generating adding records 91
BPCs 66 connecting 87
metric plots 118 records 90
reports 125 searching 91
TWCs 68 searching with constraints 93
XWCs 67 viewing compounds 93
graphs Library Search 86
adjusting threshold 69 linking panes 71
captions 73 locking panes 72
copying 71
current spectrum, instrument optimization M
23 manual integrating, peaks 107
cycle overlays 74 manual tuning, defined 21
labeling 73 maximizing panes 72
overlaying 73 MCS Barrier, defined 131
rescaling 71 methods. See quantitation methods or acquisi-
summing 74 tion methods
text 73 metric plots
unlocking ranges 76 generating 118
zooming in 72 overview 117
See also windows, panes modifying LC pump properties 33
molecular structure, formula difference 86

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Index

molecular structure, Fragment Interpretation integrating closer to the baseline 108

Tool 85 integration 93
monoisotopic mass of fragments 85 manual integration 107
moving panes 71 reviewing 93, 107
MRM scan, defined 133 periods, adding to acquisition methods 39
MRM scans, creating 30 peripheral device, status 52
MS scans, overview 132 peripheral devices
MS/MS scans, defined 132 adding to acquisition methods 32
MS/MS/MS Fragmentation Time, defined 131 adding to hardware profiles 13
MS3 scan, defined 133 polarity masses 128
Multi-Charge Separation Barrier, defined 131 Precursor Ion scan, defined 133
Product Ion scan, defined 133
N profile, spectral data 25
Nebulizer Current, defined 129 projects
Needle Current, defined 129 folder descriptions 15
Neutral Loss scan, defined 133 installed 20
noise, background subtraction 75 organization 15
overview 15
O subprojects, overview 16
opening
data files 58 Q
overlaying graphs 73 Q0 trapping, defined 131
Q1 MS scans
P creating 26
panes defined 132
defined 71 Q1 Multiple Ion scan
deleting 72 creating 29
hiding 72 defined 132
linking 71 Q3 Cool Time, defined 131
locking 72 Q3 Empty Time, defined 131
maximizing 72 Q3 Entry Barrier, defined 131
moving 71 Q3 scan, defined 133
tiling 72 Quantitation Methods
See also windows, graphs Batch Editor 47
parameters quantitation methods
adjusting algorithm parameters 109 creating 98
backing up 22 overview 97
restoring 22 updating 109
peak hopping, spectral data 25 Quantitation Wizard
Peak List tab, described 57 creating Results Tables 99
peak parameters 80 quantitative analysis, overview 97
peak review queries
integrating peaks 110 creating standard queries 100
overview 107 table-specific 93
right-click menu features 112, 114 queue
peaks overview 41
adjusting algorithm parameters 109 right-click menu, features 53
adjusting width 21 states 51
formula and monoisotopic mass 85 Queue Manager

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overview 50 Q1 MS 26
queue options searching
setting 41 Library Database 91
Queue Server, states 51 with constraints 93
selecting
R areas in Contour Plots 83
records sets
adding to the Library Database 91 adding samples 42
removing adding to a batch 42
peripheral devices from acquisition meth- setting
ods 32 analog to digital converter properties 37
reports, generating 125 autosampler properties 33
rescaling graphs 71 column oven properties 35
Reserpine Diode Array Detector properties 36
concentrations 26 integrated syringe pump properties 34
results summary, overview 23 queue options 41
Results Tables switching valve properties 35
calibration curves 113 smoothing data 78
creating 98 sorting
metric plots 117, 118 Results Tables 103
overview 98 saving criteria 104
Quantitation Wizard 99 spectra
Record Modified column 110 background subtraction 75
right-click menu features 106 comparing compounds 93
saving metric plot criteria 120 displaying TICs 63
saving sort criteria 104 formula and monoisotopic mass 86
sorting 103 Fragment Interpretation Tool 84
statistics 116 generating XICs 63
viewing specific layouts 102 overlaying 73
reviewing overview 62
peaks 93, 107 right-click menu features 70
sample statistics 116 searching Library Database 92
statistics 93 searching with constraints 93
spectral data
S overview 25, 57
sample queue, overview 41 spectra
samples See also spectral data
acquiring 44 standard queries, creating 100
adding to a batch 42 statistics
adding to Results Tables 99 comparing batches 116
data files 58 reviewing 93, 116
setting locations in the Batch Editor 45 storing data 43
starting acquisition 44 submitting, samples 44
stopping acquisition 47 subprojects
saving copying 19
metric plot criteria 120 creating 18
scan techniques 132 overview 16
scans summing graphs 74
Q1 MI 29 svp, described 129
switching valve properties, setting 35

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Index

defined 71
T See also panes, graphs
TDF CE, defined 131
TDF scan, defined 133 X
temperature, parameter 129 XIC. See Extracted Ion Chromatogram
text XWC. See Extracted Wavelength Chromato-
adding to graphs 73 gram
moving 73
See also captions
threshold, adjusting 69
TIC. See Total Ion Chromatogram
tiling panes 72
Time Delayed Fragmentation Collision Energy,
defined 131
Total Ion Chromatogram
displaying 63
purpose 62
Total Wavelength Chromatogram
generating 68
purpose 62
Trap RF Amplitude, defined 132
troubleshooting hardware profiles 14
tuning
instrument optimization 21
overview 21
tuning solutions 127
TWC. See Total Wavelength Chromatogram

U
unlocking ranges 76
updating quantitation methods 109

V
viewing
ADC data 61
Contour Plots 82
data 57
data in tables 60
device status 52
Diode Array Detector 68
experimental conditions 59
instrument status 52
isotopes 85
specific Results Tables layout 102
spectra 93
statistics 93

W
windows

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