Agilent 7000E/7010C GC/MS Triple Quadrupole

Concepts Guide
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In This Guide...
The Concepts Guide presents “The Big Picture” behind the operation of the
Agilent 7000/7010 Series Triple Quadrupole GC/MS Systems by helping you
understand how the hardware and software work.

1 “Overview”
Learn how 7000/7010 Series Triple Quads help you do your job.

2 “Inner Workings – Triple Quadrupole MS vs. Single Quadrupole MS”

Learn the concepts you need to understand how 7000/7010 Series Triple Quads
work.

3 “Triple Quad and Sensitivity”

Learn how 7000/7010 Series Triple Quads achieve high sensitivity.

4 “Agilent MassHunter Workstation Software – Instrument Control for

the Triple Quad”
Learn concepts behind the design of the Agilent MassHunter Workstation
Software – Instrument Control for Triple Quadrupole program.

Agilent 7000/7010 Series Triple Quadrupole GC/MS System Concepts Guide 3

4 Agilent 7000/7010 Series Triple Quadrupole GC/MS System Concepts Guide
Contents
In This Guide... 3

1 Overview
System Description 8
Help for applications 8
Help for acquisition 9
Help for data analysis 11

2 Inner Workings – Triple Quadrupole MS vs. Single Quadrupole MS

Single Quadrupole MS Operation 14
Design for a single quadrupole mass spectrometer 14
How a single quadrupole mass spectrometer works 15
Triple Quadrupole MS Operation 20
Design of the 7000/7010 Series Triple Quads 20
Innovative enhancements in the 7000/7010 Series Triple
Quads 21
How a triple quadrupole mass spectrometer works 22

3 Triple Quad and Sensitivity

How the 7000/7010 Series Triple Quads Improve
Sensitivity 26
Sensitivity 26
Chemical noise reduction with MRM 28
Sensitivity and reproducibility of the 7000/7010 Series Triple
Quads 30
How Each Component Works to Improve Sensitivity 35
GC capillary flow backflush technology 35
Ion sources 35
Electron impact ion sources 35
Chemical ionization ion source 37
Quad mass filters 38

Agilent 7000E/7010C GCMS Triple Quadrupole Concepts Guide 5

 Pre- and post-filters 38
Collision cell 39
Detector 43
Pumping system 44

4 Agilent MassHunter Workstation Software – Instrument Control for the

Triple Quad
Description 46
Tuning 47
Acquisition 48

6 Agilent 7000E/7010C GCMS Triple Quadrupole Concepts Guide

1 Overview
System Description 8
Help for applications 8
Help for acquisition 9
Help for data analysis 11

This chapter provides an overview of the Agilent 7000/7010 Series Triple

Quadrupole GC/MS components and how they help get the job done.

Agilent 7000E/7010C GCMS Triple Quadrupole Concepts Guide 7

1 Overview
System Description

System Description
An Agilent 7000/7010 Series Triple Quadrupole MS is a standalone triple
quadrupole mass spectrometer for use with the Agilent 8890 and 9000 gas
chromatographs. The 7000/7010 Series Triple Quads feature:
• One split flow turbomolecular vacuum pump
• Rotary vane or optional dry scroll foreline pump
• Independently MS-heated electron-ionization ion source
• Two independently MS-heated hyperbolic quadrupole mass filters
• Single hexapole collision cell
• High-energy dynode (HED) electron multiplier detector
• Independently GC-heated GC/MS interface
This configuration has advantages for many applications. The data is interpreted
through the use of the MassHunter Workstation software, which provides
quantitative and qualitative analyses of the data obtained.
The 7000/7010 Series Triple Quads are the only triple quadrupole GC/MS
combinations that incorporates a hexapole collision cell, blanketed with a
combination of nitrogen and helium gas, to improve the ion fragmentation prior
to final filtration, detection, and quantification.

Help for applications

The 7000/7010 Series Triple Quad GC/MS combinations can quantify trace
organic compounds in complex matrices. The following applications use this
type of quantification:
• Food safety studies
• Environmental studies
• Drug discovery
• Toxicology
• Forensics

8 Agilent 7000E/7010C GCMS Triple Quadrupole Concepts Guide

1 Overview
Help for acquisition

Paired with Agilent 8890, 9000, or 7890 GCs, the 7000/7010 Series Triple Quads
deliver sensitive, reproducible analyses of target compounds in complex
matrices. This provides the following:
• Femtogram-level limits of detection and quantification
• Selective quantification of target compounds in high chemical background
samples
• Improved signal-to-noise ratios (S/N) in complex matrices
• Ability to meet stricter regulations regarding sample analytical limits for
certain applications
• Simplified operation with Agilent’s instrument control and data analysis
software
The 7000/7010 Series Triple Quads offer the high sensitivity in GC/MS/MS
analyses that is required by many commercial and regulatory applications.

Help for acquisition

The MassHunter Workstation Instrument Control software allows you to
perform the following tasks from a single window:

Prepare the instrument

• Start and stop the instruments from the software
• Download settings to the GC and the Triple Quad in real time to control the
instrument
• Optimize MS parameters automatically or manually through Agilent tuning
programs and print an Autotune report
• Monitor the actual conditions of the instrument
• View the real-time plot for chromatograms and instrument parameters (both
GC and MS) and print a real-time plot report
• View the centroid line spectrum of a peak or the mass range profile spectrum
of a peak in real time

Agilent 7000E/7010C GCMS Triple Quadrupole Concepts Guide 9

1 Overview
Help for acquisition

Set up acquisition methods

• Enter and save parameter values for the GC and the Triple Quad to an
acquisition method
• Select and label the total ion chromatograms or extracted ion
chromatograms that you want to appear in the real-time plot
• Set up time segments for each scan type and analysis where parameters
change with the time segment or with the scans within the time segment
• Print an acquisition method report

Acquire data
• Enter sample information and pre- or post-programs (scripts) and run single
samples interactively
• Enter and automatically run both individual samples and samples organized
in a sequence of samples
• Set up pre- and post-scripts to run between samples in a sequence
• Set up and run a sequence to optimize MS acquisition parameters
• Print a sequence report
• View system events, including start and stop times, run events, and errors
• Print an event log report
To learn how to get started with the Agilent Triple Quadrupole GC/MS, see the
7000E/7010C Series Triple Quad GC/MS Quick Start Guide.
To learn more about how to use the Agilent Triple Quadrupole GC/MS with real
samples and data, see the 7000E/7010C Series Triple Quad GC/MS
Familiarization Guide.
To learn how to do individual tasks with the GC/MS, see the online help.
To learn more about your Agilent GC, see the Agilent user documentation for
your specific GC model.

10 Agilent 7000E/7010C GCMS Triple Quadrupole Concepts Guide

1 Overview
Help for data analysis

Help for data analysis

Quantitative analysis program
Agilent has designed the quantitative analysis program to help quantify very low
amounts of material. The program has the following unique features:
• Imports information directly from the acquisition method
• Provides a curve-fit assistant to test all fits and statistics on curve quality
• Integrates with an automated, parameter-free integrator that uses a novel
algorithm, optimized for triple quadrupole data
• Presents a batch results window to help you review and operate on an entire
batch of data at once
• Automatically detects outliers
• Provides preconfigured templates for basic reporting and provides the
capability to create custom reports in Microsoft Excel
Please refer to the Agilent MassHunter Workstation Software – Quantitative
Analysis Familiarization Guide or the online help for the quantitative analysis
program.

Qualitative analysis program

For fast method development, this software is used to quickly review the
qualitative aspects of the data, such as the optimum precursor to product ion
transitions.
Agilent designed the qualitative analysis program to present large amounts of
data for review in one central location. With the program you can do these
operations for any type of mass spectrometer data that you open:
• Extract chromatograms
• View and extract peak spectra
• Subtract background
• Integrate the chromatogram
• Find compounds
You can also set up methods to automatically do the tasks in the list, as well as
others, when you open the data files.
Refer to the Agilent MassHunter Workstation Software – Qualitative Analysis
Familiarization Guide or the online Help for the qualitative analysis program.

Agilent 7000E/7010C GCMS Triple Quadrupole Concepts Guide 11

1 Overview
Help for data analysis

12 Agilent 7000E/7010C GCMS Triple Quadrupole Concepts Guide

2 Inner Workings – Triple
Quadrupole MS vs. Single
Quadrupole MS
Single Quadrupole MS Operation 14
Design for a single quadrupole mass spectrometer 14
How a single quadrupole mass spectrometer works 15

Triple Quadrupole MS Operation 20

Design of the 7000/7010 Series Triple Quads 20
Innovative enhancements in the 7000/7010 Series Triple Quads 21
How a triple quadrupole mass spectrometer works 22

This chapter explains the inner workings of the 7000/7010 Series Triple Quads.
The foundation for understanding the operation of a triple quadrupole mass
spectrometer is the operation of a single quadrupole mass spectrometer.
Therefore, an explanation of the workings of a single quadrupole mass
spectrometer is presented first.

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2 Inner Workings – Triple Quadrupole MS vs. Single Quadrupole MS
Single Quadrupole MS Operation

Single Quadrupole MS Operation

This section first reviews the fundamental aspects of the single quadrupole
mass spectrometer. Understanding the operation of a single quadrupole mass
spectrometer provides insight into the specific features of 7000/7010 Series
Triple Quads.

Design for a single quadrupole mass

spectrometer
Mass spectrometry is based on the analysis of ions moving through a vacuum.
The ionization of a sample occurs in the ion source that is shown, schematically,
on the left in Figure 1. In this case, the source used is an electron impact
ionization source, which ionizes the sample with a charged filament.
The ions are analyzed by a mass analyzer (mass filter) that controls the motion
of the ions as they travel to the detector to be converted into actual signals.

Figure 1. Schematic for single quadrupole mass spectrometer

The quadrupole mass analyzers consist of four parallel rods to which specific DC
(direct current) and RF (radio frequency) voltages are applied. These rods filter
out all ions except those of one or more particular mass-to-charge (m/z).
The RF is applied to all four rods, but the negative (–) rods are 180 degrees out of
phase with the positive (+) rods. The rods are labeled + and – in reference to the
DC voltages applied to them.
All ions that comprise the sample are generated at the source. However, when a
specific set of voltages is applied, only ions of the corresponding m/z value may
pass through the quadrupole to reach the detector. As the voltages are altered,
ions with other m/z values are allowed to pass through. A full MS scan is
obtained by increasing the DC and RF voltages applied to the four rods over an
expanded range of values.

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2 Inner Workings – Triple Quadrupole MS vs. Single Quadrupole MS
How a single quadrupole mass spectrometer works

How a single quadrupole mass spectrometer

works
A conceptual model can be used to explain the theory of a single quadrupole
mass spectrometer. See Figure 2.

External Ionization Source

Detector

Quadrupole Mass Filter

Figure 2. Conceptual model of a single quadrupole mass spectrometer

In the model:
• All of the ions contained in a sample are formed in the external ionization
source and collected in a funnel. The balls of different colors and sizes
represent different ions having different m/z values.
• The quadrupole mass analyzer is represented by a moving belt that serves to
filter the ions as they pass through openings of various sizes. The ions pass
from the funnel, through the filter, to the detector.
• The detector is represented by the collecting funnel below the filtering belt.
As the belt (the analyzer) moves, or the voltages on the rods are changed, ions
with different m/z values are filtered through the mass spectrometer.
As the analyzer moves from a small m/z value to increasingly larger values, a full
MS scan is created.
If the belt does not move, the detector continues to monitor the same single m/z
value over the entire scan period. This type of analysis is known as selected ion
monitoring, or SIM. It is the most sensitive operating mode for a single
quadrupole mass spectrometer.

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2 Inner Workings – Triple Quadrupole MS vs. Single Quadrupole MS
How a single quadrupole mass spectrometer works

The scan period is selected (fixed) by the user. The user may set the dwell time
to scan a specific mass range (for example, m/z 50 to 1,000) or to remain on one
selected ion (SIM) or to move to several selected ions during the scan period.
The quadrupole mass filter is not scanned over a range in the SIM mode. The
required RF and DC voltages are set to filter a single mass for a specified time
before moving to the setting for the next SIM.

Single quadrupole: SIM

To obtain the best sensitivity or quantitative measurement, the single quadrupole
is operated in SIM mode (Figure 3). The duty cycle is the measure of the
instrument’s time actually devoted to measuring signals. In SIM mode, the single
quadrupole analyzes the signal of a specific m/z ion almost all of the time. This
results in nearly 100 percent acquisition during the duty cycle.

Detector

Quadrupole Mass Analyzer

Figure 3. Single quadrupole: SIM

In this example:
1 All of the ions (+, –, and neutrals) are formed in the ionization source. The
Agilent ion sources consist of a series of lenses and a repeller assembly that
directs the ion beam into the analyzer.
2 Ion optics guide the ions to the quadrupole mass analyzer.
3 In the analyzer, only ions of a particular m/z value, represented in Figure 3 by
blue balls, are allowed to pass through to the detector.

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2 Inner Workings – Triple Quadrupole MS vs. Single Quadrupole MS
How a single quadrupole mass spectrometer works

4 The detector generates an electrical signal proportional to the number of ions

reaching it..
This system has several advantages:
• Provides the best sensitivity for quantitation
• Increases selectivity
• Improves chromatographic specificity

Single quadrupole: full MS scan

In a full MS scan, the quadrupole serves as a mass filter over time, and a scan is
carried out by stepping through increasing DC and RF voltages. This provides
filtering through the corresponding m/z values across a mass spectrum. See
Figure 4.

Detector

Quadrupole Mass Analyzer

Figure 4. Single quadrupole: full scan MS

The full scan MS mode is less sensitive because the duty cycle for each m/z
value is considerably less than 100 percent. The quadrupole mass analyzer
scans sequentially, passing each m/z value in the selected mass range to the
detector.

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2 Inner Workings – Triple Quadrupole MS vs. Single Quadrupole MS
How a single quadrupole mass spectrometer works

A full scan MS is still a useful mode of operation because it shows all of the ions
that are being formed in the ion source. This alerts analysts to other compounds
co-eluting with compounds of interest, and is helpful information for developing
SIM acquisitions.

What about fragment ions?

Full scans with a single quadrupole instrument can also be used to study
fragment ions. See Figure 5.

m/z 325 Analyte Precursor

m/z 325 Matrix Precursor

m/z 202 Matrix Precursor
m/z 184 Product Ion (?)
m/z 124 Product Ion (?)

Detector

Figure 5. Fragment ions with single quadrupole MS

The diagram shows that fragment ions, also known as product ions, are formed
by fragmenting or breaking apart precursor ions. Precursor ions formed in the
ion source travel through the mass analyzer without change, unless extra energy
is applied to their motion in a region where fragmentation can occur. If the ions
run into gas molecules and the translational energy is high enough, these
collisions convert the translational energy into molecular vibrations that can
cause the ions to fragment. This is called collision-induced dissociation (CID).
Fragmentation, or CID, can be carried out in a low-pressure region between the
ion source and the mass analyzer. The outlet of the ion source is under vacuum,
which is created by a two-stage vacuum pump. On the Agilent single quadrupole
mass spectrometer, the region between the ion source and the quadrupole
exhibits a gas pressure of about 10 to 20 × 10-5 Torr, which is well below
atmosphere pressure (760 Torr). Under normal operation, a voltage is applied

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2 Inner Workings – Triple Quadrupole MS vs. Single Quadrupole MS
How a single quadrupole mass spectrometer works

across this region to keep the ions passing through to continue on to the mass
analyzer. Even if these ions collide with the gas molecules in this region, they
usually do not have enough energy to fragment.
However, as the voltage is increased, the ions have more translational energy.
Then, if the ions run into gas molecules (Figure 6), CID can occur. Even though
this fragmentation does not occur where the ions are formed, this type of
fragmentation is still referenced as “in-source CID.”

Figure 6. Ion fragmentation caused by collision-induced dissociation

A triple quadrupole mass spectrometer can do MS/MS, with fragmentation

within its collision cell as described in the next section.

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2 Inner Workings – Triple Quadrupole MS vs. Single Quadrupole MS
Triple Quadrupole MS Operation

Triple Quadrupole MS Operation

The previous section regarding the operation of the single quadrupole mass
spectrometer helps to clarify the principles of the triple quadrupole mass
spectrometer.

Design of the 7000/7010 Series Triple Quads

The triple quadrupole mass spectrometer consists of an ion source, followed by
ion optics that transfer the ions to the first quadrupole. A diagram of the current
7000/7010 Series Triple Quads is shown in Figure 7.

Figure 7. 7000/7010 Series Triple Quad basic components

As in the single quadrupole MS, the analyzers consist of four parallel hyperbolic
rods through which selected ions are filtered. After passing through the first
quad, the filtered ions then enter a collision cell where they are fragmented. The
collision cell is typically called the second quadrupole, but in this case,
geometrically it is actually a hexapole filled with a combination of nitrogen and
helium.
The product ions formed in the collision cell are then sent to the third quadrupole
for a second filtering stage to enable isolation and examination of multiple
precursor to product ion transitions.

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2 Inner Workings – Triple Quadrupole MS vs. Single Quadrupole MS
Innovative enhancements in the 7000/7010 Series Triple Quads

Innovative enhancements in the 7000/7010

Series Triple Quads
Ions enter the MS from the GC. One of several enhancements to Agilent
7000/7010 Series Triple Quadrupole GC/MS systems is the backflush
technology that can be found in many Agilent GCs. Backflush technology
minimizes column bleed and provides better sample splitting. This results in less
sample dilution at low flows and a reduction in chemical noise with the
elimination of ghost peaks in the data.
After separation in the GC, the sample components are transferred to an
ionization source where ions are generated. The available electron impact (EI)
ion sources contain dual filaments, which can be tuned separately and selected
for use based upon their performance. The dual filament design allows the user
to continue running with one filament even if the other needs to be replaced or
cleaned.
Once the sample is ionized, a repeller directs the ions through a set of lenses and
into the first quadrupole analyzer, where they are filtered based on their
mass-to-charge ratio.
The ions passing through the first quadrupole analyzer are directed into an
improved collision cell, where they are fragmented. In the 7000/7010 Series
Triple Quads, the addition of a post-filter focuses the ion beam exiting the first
quadrupole, which ensures effective concentration of the ions.
The collision cell is actually a hexapole filled with a nitrogen and helium
combination gas stream. The innovative collision cell design features axial
acceleration for high-speed MS/MS analysis. The use of helium as a quench gas
in the collision cell reduces noise from helium neutrals as well as enhances the
efficiency of the fragmentation process. The addition of helium to the collision
cell gas stream provides stabilization to high-mass ions, allows more control
over the fragmentation process, and reduces neutral noise in the data.
Fragment ions formed in the collision cell are then sent through a prefilter, prior
to the third quadrupole. Similar to the post-filter on the first analyzer, the prefilter
focuses the ion beam into the quad. The third quadrupole provides a second
filtering stage.
Finally, the ions that pass through the third quadrupole are detected using a
high-energy detector. Additional improvement in sensitivity is achieved in the
7000/7010 Series Triple Quads through the triple axis high-energy dynode (HED).
The HED uses an off-axis configuration that pulls the charged ions away from
the neutrals, allowing the neutrals to be eliminated by the turbo pump.

Agilent 7000E/7010C GCMS Triple Quadrupole Concepts Guide 21

2 Inner Workings – Triple Quadrupole MS vs. Single Quadrupole MS
How a triple quadrupole mass spectrometer works

The split flow high-performance turbo pump provides vacuum and efficiently
eliminates carrier gas and un-ionized material to allow for accurate product
quantification.
Once through the HED, the ions are quantitated by an electron multiplier detector.
Gain normalized tuning of this detector provides consistent sensitivity over the
life of the electron multiplier.

How a triple quadrupole mass spectrometer

works
Triple quadrupoles provide the potential for MS/MS in several ways (see
Figure 8).

External
Ionization

Collision
Cell
Precursor
Quad
Filter Q1

Product
Quad Detector
Filter Q3

Figure 8. Conceptual model of a triple quadrupole mass spectrometer:

With MS1 (Q1) in SIM mode passing a single precursor m/z and MS2 (Q3)
in scan mode to analyze the product ions.

Representing the quadrupole mass analyzers as moving belts, a collision cell can
be placed between the belts to fragment the ions. The first belt can be fixed to
select which precursor ion travels to the collision cell. Different types of collision
cells can be used.

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2 Inner Workings – Triple Quadrupole MS vs. Single Quadrupole MS
How a triple quadrupole mass spectrometer works

The cell can be another quadrupole, a hexapole (six rods like the one used in the
7000/7010 Series Triple Quads), an octopole (eight rods), or even a transverse
wave guide.
Whichever geometry is used, an inert, nonreactive gas is required for use as the
collision gas. In addition, the voltages applied to the collision cell must be
different from those applied to the quadrupoles to accelerate the movement of
all of the ions so that their collision energy is sufficient to cause fragmentation.
In the example shown in Figure 8 on page 22, a precursor ion is selected using
the first quadrupole and is sent to the collision cell for fragmentation. The
fragments are then scanned through the third quadrupole, resulting in a
product-ion scan MS/MS. Since the fragment ions are pieces of the precursor,
they represent portions of the overall structure of the precursor molecule. They
are selected by the third quadrupole according to their m/z ratio in the same way
the precursor ions are chosen by the first quadrupole. In this manner, a triple
quad provides enhanced selectivity for accurate target compound analysis.
Full scan MS/MS (first belt remains steady, second belt moves) using a triple
quadrupole MS is not the most sensitive mode for the same reason that a full
scan MS using a single quadrupole is not the most sensitive mode. The most
sensitive mode of operation for the triple quadrupole MS instrument is to fix both
belts and only monitor a specific precursor ion and a specific product ion. This
mode is called selected reaction monitoring or SRM.
In normal operation, a triple quadrupole MS instrument involves running multiple
SRMs for the same precursor ions. This is called multiple reaction monitoring or
MRM.

Agilent 7000E/7010C GCMS Triple Quadrupole Concepts Guide 23

2 Inner Workings – Triple Quadrupole MS vs. Single Quadrupole MS
How a triple quadrupole mass spectrometer works

24 Agilent 7000E/7010C GCMS Triple Quadrupole Concepts Guide

3 Triple Quad and Sensitivity
How the 7000/7010 Series Triple Quads Improve Sensitivity 26
Sensitivity 26
Chemical noise reduction with MRM 28
Sensitivity and reproducibility of the 7000/7010 Series Triple Quads 30

How Each Component Works to Improve Sensitivity 35

GC capillary flow backflush technology 35
Ion sources 35
Quad mass filters 38
Pre- and post-filters 38
Collision cell 39
Detector 43
Pumping system 44

This chapter shows how the 7000/7010 Series Triple Quad reduces chemical and
electronic noise and how each component contributes to enhanced instrument
sensitivity.

Agilent 7000E/7010C GCMS Triple Quadrupole Concepts Guide 25

3 Triple Quad and Sensitivity
How the 7000/7010 Series Triple Quads Improve Sensitivity

How the 7000/7010 Series Triple Quads

Improve Sensitivity
Sensitivity is a performance standard for 7000/7010 Series Triple Quads. It is
expressed as the signal-to-noise ratio (S/N). Triple quadrupole mass
spectrometers exhibit multiple sources of noise, including interference from
chemical and cluster backgrounds and electronics.

Sensitivity
In the design of the 7000/7010 Series Triple Quads, sensitivity was addressed
within all stages of instrumentation, from the ion source to the detector. See
Figure 9.
3

1 2 4 5 4 6 7

8
Figure 9. Design elements that improve sensitivity

26 Agilent 7000E/7010C GCMS Triple Quadrupole Concepts Guide

3 Triple Quad and Sensitivity
Sensitivity

How the 7000/7010 Series Triple Quad instruments increase sensitivity

1 Sample enters the Triple Quad from the GC. Capillary flow backflush
technology produces better separation and reduce column bleed, providing a
cleaner sample.
2 Electron ionization ion sources incorporate dual filaments with tuning
capabilities to optimize ionization and filament use.
3 Front and rear analyzers use hyperbolic quadrupoles to optimize ion
transmission and spectral resolution.
4 RF quadrupole segments (pre- and post-filters) enhance ion transmission
into and out of the collision cell.
5 High-pressure collision cell with linear acceleration optimizes MS/MS
fragmentation while eliminating crosstalk, even at very low dwell times. A
small-diameter high-frequency hexapole assembly assists with capturing
and focusing fragmented ions. Helium quench gas assists in the
fragmentation process while reducing the neutral noise in the data.
6 Off-axis high-energy dynode detector with log amp signal compression
permits a high gain, long life, and low noise. This design allows neutrals to
pass without hitting the detector.
7 Multiplier has a long life since only electrons impact its surface, never ions.
Gain normalized tuning of the detector provides consistent sensitivity over
the life of the multiplier.
8 Vacuum system incorporating the use of a split flow turbomolecular pump
efficiently eliminates neutral materials prior to the detector.

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3 Triple Quad and Sensitivity
Chemical noise reduction with MRM

Chemical noise reduction with MRM

MRM can only be performed with a triple quadrupole MS. In this operation, the
front analyzer is run in SIM mode to monitor for a specific ion. After filtration in
the first quadrupole, it is expected that only ions with a single m/z ratio will pass
through (see Figure 10). After fragmentation in the collision cell, the third
quadrupole is also run in SIM for specific m/z values, to capture product ions
resulting from the precursor. The third graph in Figure 10 shows how the data
can be easily read for product identification and quantification.

Figure 10. Sensitivity with MRM

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3 Triple Quad and Sensitivity
Chemical noise reduction with MRM

The 7000/7010 Series Triple Quads pass through four transitional steps in
translating a signal in the MRM process (Figure 11).

Figure 11. Multiple reaction monitoring (MRM)

Step 1 The spectrum at the far left represents everything that is being ionized
at the ion source. A triple quad GC/MS reduces chemical noise for low-level
quantitation in a dirty matrix more than a single quad GC/MS does.

Step 2 This step is accomplished by first selecting the chemical of interest at

210 m/z from the coeluting interferences seen in the rest of the spectrum. The
second spectrum shows the result after passing through the first quadrupole, or
Q1 (MS1).

Step 3 After Q1 (MS1), fragment ions are generated in the collision cell. The
corresponding MS/MS spectrum is shown below the collision cell.

Step 4 Particular fragment ions can be selected to pass through the Q3 (MS2)
quadrupole. These are selected for quantitation and confirmation.

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3 Triple Quad and Sensitivity
Sensitivity and reproducibility of the 7000/7010 Series Triple Quads

The second stage of selectivity using the Q3 (MS2) quadrupole removes much of
the chemical background. Typically, the chance of an isobaric interference at the
same exact mass as the fragmentation ion is remote.

Sensitivity and reproducibility of the

7000/7010 Series Triple Quads
Sensitivity in MS data is affected by detection limits, sample dilution, and sample
contamination. Improvements in MS sensitivity are made through increased
signal strength and a reduction in chemical noise.
The sensitivity specifications for the 7000/7010 Series Triple Quads are at
femtogram to sub-femtogram levels, depending on the instrument model and
compound being measured. This is demonstrated at customer sites upon
installation. (See Figure ).

Analysis of 100 fg sample of OFN in MRM (272 222 m/z)

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3 Triple Quad and Sensitivity
Sensitivity and reproducibility of the 7000/7010 Series Triple Quads

Triple quad GC/MS analysis is useful for identifying quantities of target

compounds in complex matrices. The 7000/7010 Series Triple Quads provide
improved analysis in complex matrices. Figure 12 illustrates a chromatogram of
two PCB congeners (PCB 153 and PCB 138) injected at 400 fg each on column.
Quantitation transition is performed at 360  290 m/z, with the qualifier
transition measured at 360  325 m/z for simultaneous quantitation and
confirmation at the lowest detection limit. Resulting data produce strong signals
on a flat baseline.

Figure 12. Identifying target PCBs in complex matrices

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3 Triple Quad and Sensitivity
Sensitivity and reproducibility of the 7000/7010 Series Triple Quads

Another performance standard of 7000/7010 Series Triple Quads is high

sensitivity for contaminated samples. Figure 13 illustrates HCB analysis in diesel
fuel. Data from the single quad in SIM show a low signal-to-noise ratio (S/N), with
many peaks and chemical background noise. In the second graph, the sample
run in RMS mode results in a S/N of 86:1 with quantitative transition of
283.8213.9 m/z. This demonstrates high sensitivity in a “dirty” matrix.

Single MS:
SIM 283.8

MS/MS:
283.8—>213.9

Figure 13. HCB analysis by 7000/7010 Series Triple Quad in MRM mode

32 Agilent 7000E/7010C GCMS Triple Quadrupole Concepts Guide

3 Triple Quad and Sensitivity
Sensitivity and reproducibility of the 7000/7010 Series Triple Quads

The 7000/7010 Series Triple Quads produce clear data to help evaluate complex
samples at lower levels. Figure 14 illustrates a chromatogram of multiple PCB
congeners in mussel extract measured at 2 pg on-column. The resulting data
provide strong signals on a flat baseline for clear data interpretation.

Figure 14. Detection of multiple PCBs at low detection limits

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3 Triple Quad and Sensitivity
Sensitivity and reproducibility of the 7000/7010 Series Triple Quads

Reproducibility is an expression of how well the data agrees from test to test.
Figure 15 illustrates the GC/MS results when the organophosphorous
insecticide cyanophos, spiked into garlic at 0.5 ppb, is analyzed in MRM mode.
An overlay of five injections showing the quantitation transition of
243109 m/z demonstrates strong reproducibility.

Figure 15. Reproducibility in 7000/7010 Series Triple Quad data

34 Agilent 7000E/7010C GCMS Triple Quadrupole Concepts Guide

3 Triple Quad and Sensitivity
How Each Component Works to Improve Sensitivity

How Each Component Works to Improve

Sensitivity
This section describes in more detail how each of the components of the
7000/7010 Series Triple Quads contributes to reducing noise (Figure 9 on
page 26).

GC capillary flow backflush technology

Many Agilent GCs provide improved sample transmission through backflush
technology. Backflushing eliminates late eleuters from the column, reducing the
sample contamination and chemical noise that they create. This technology is
integral in the integrity and consistency of the MS data.

Ion sources
The 7000/7010 Series Triple Quads offer the same ionization methods as the
single quadrupole mass spectrometers: electron impact ionization (EI) and
chemical ionization (CI).

Electron impact ion sources

Electron impact is the standard ionization mode for 7000/7010 Series Triple
Quads. Sample components separated by the GC column enter the source
through the GC/MS interface. The sample components are ionized in the
ionization chamber.
A filament attached to the source body emits electrons into the ionization
chamber through the guidance of a magnetic field. These electrons interact with
sample molecules, ionizing and fragmenting them. The EI ion sources available
for the 7000/7010 Series Triple Quads (see Figure 16 on page 36 and Figure 19
on page 38 for the EI XTR) contain two filaments, which allows for a choice of
filament depending upon tuning results.
Once the sample has been ionized, the ions are directed by the repeller through a
stack of electrostatic lenses. The repeller contains a positive voltage, which
pushes positive ions into the lens stack. There the ions are concentrated into a
tight beam and pushed into the analyzer. Slots in the source body allow the

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3 Triple Quad and Sensitivity
Electron impact ion sources

vacuum system to pump away ions of carrier gas and un-ionized material as the
sample ions enter the quad, thereby reducing neutral noise and improving
sensitivity.

Filament assembly
Repeller

Source body

Lenses

Figure 16. EI high efficiency source (HES)

Lenses

Source body

Repeller

Filament

Filament

Figure 17. EI Extractor ion source (XTR)

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3 Triple Quad and Sensitivity
Chemical ionization ion source

Chemical ionization ion source

The 7000/7010 Triple Quads can be equipped with an optional chemical
ionization ion source (see Figure 18 on page 37). In chemical ionization, the
ionization chamber is flooded with large quantities of reagent gas. Electrons
from a filament ionize the highly abundant reagent gas molecules, which then, by
a variety of chemical reactions, ionize the sample molecules.
Chemical ionization is a “softer” ionization technique. It cause less fragmentation
than EI so CI spectra usually show a high abundance of the molecular ion. For
this reason, CI is often used to determine the molecular weights of sample
compounds.
Unlike EI sources, which generate only positive ions, the CI source can also be
operated so as to produce negative ions, making it useful for analyzing
compounds that do not analyze well or at all in positive ion mode. For a subset of
samples, negative CI can provide very high sensitivity.
The CI source available for the 7000/7010 Series Triple Quads can operate with a
variety of reagent gases, allowing the user to select the reagent gas that
produces the best sensitivity for a particular sample.
The CI source is superficially similar to the EI XTR source. The CI source,
however, has a single filament and much smaller orifices for the ion chamber. Its
lenses are also subtly different from, and not interchangeable with,
corresponding EI source parts.

Lenses

Drawout plate
Source body
Repeller

Filament

Dummy filament

Figure 18. CI ion source

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3 Triple Quad and Sensitivity
Quad mass filters

Quad mass filters

The quadrupoles consist of hyperbolic rods that optimize ion transmission and
spectral resolution. The quadrupole configuration tends to generate less ion loss
than circular rods. The gold-plated quartz material allows the analyzer to operate
at high temperatures and low vacuum, eliminating the contamination that occurs
with lower temperatures.

Pre- and post-filters

The end section of the Q1 (MS1) quadrupole assembly also consists of short
hyperbolic rods, but their RF voltages are only high enough to guide ions into the
collision cell. A similar set of rods on the exit side of the collision cell are part of
the Q3 (MS2) quadrupole. These short RF-only rods act as pre- and post-filters to
the quads to ensure optimum ion transmission into and out of the collision cell.
Quartz quadrupole rods Post-filter

Figure 19. Q1 (MS1) quadrupole assembly

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3 Triple Quad and Sensitivity
Collision cell

Collision cell
What is the collision cell?
The collision cell collects percursor ions selected by the first quadrupole mass
filter and fragments them. The resulting product ions are transmitted to the
second quadrupole mass filter. In the 7000/7010 Series Triple Quads, the
collision cell is a high-pressure hexapole assembly with its linear acceleration
adjusted to optimize MS/MS fragmentation while eliminating crosstalk even at
very low dwell times (Figure 20).

Front analyzer

Post-filter

Collision cell entrance Collision cell exit

Pre-filter Rear analyzer
Post-filter

Figure 20. Collision cell technology produces higher sensitivity and faster responses without memory or
cross-talk effects

The components that contribute to this higher sensitivity and faster response
are:
• Small diameter hexapole collision cell
• High frequency hexapole collision cell
• Linear axial acceleration
• High pressure collision cell
• High speed digital electronics

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3 Triple Quad and Sensitivity
Collision cell

The collision cell contains nitrogen and helium. Helium has been shown by
Agilent to provide more control over the fragmentation process, especially with
higher mass ions. It was added to the nitrogen stream to reduce neutral noise by
thermalizing metastables without letting them hit the detector. The helium is
then eliminated by the vacuum pump along with carrier gas and unfragmented
sample ions. The small diameter of the hexapole assembly assists in capturing
fragmented ions.

Why a hexapole?
The geometry of a hexapole provides advantages in two domains: ion focusing
and ion transmission (Figure 21).
• The first advantage is in ion focusing. Studies have shown that a quadrupole
provides better ion focusing than a hexapole and a hexapole provides better
ion focusing than an octopole. Therefore, ion focusing improves with a lower
number of poles in the filter.
• The second advantage involves ion transmission across a wide mass range,
or m/z bandwidth. In this case, the octopole is better than the hexapole,
which is better than the quadrupole.
The hexapole was chosen after extensive modeling, simulation, and
experimentation because it offered the best compromise between the focusing
of a quadrupole and the ion transmission of an octopole.

Figure 21. Broad mass range transmission and improved transmission efficiency using a hexapole

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3 Triple Quad and Sensitivity
Collision cell

Collision cell design

The collision cell hexapole consists of six resistively coated rods used to
generate a potential difference across the length of the collision cell (Figure 22).

Figure 22. Collision cell design

A potential difference is always present. This ensures that the precursor ions
coming from Q1 (MS1), or fragment ions generated in the collision cell, are
transmitted and not allowed to drift around at random.

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3 Triple Quad and Sensitivity
Collision cell

Sweeping out the ions in this manner avoids the issue of crosstalk, where
residual product ions from a previous MRM experiment can interfere with the
product ion spectrum of a subsequent MRM experiment (see Figure 23). A
collision energy voltage is applied over the accelerating linear voltage to generate
fragments or product ions.

Length of time for collision cell flushing

The low degree of crosstalk can be demonstrated by examining how long it takes
to evacuate ions from the collision cell (Figure 23).

0 V Collision Energy 5 V Applied Axial Potential

Figure 23. Collision cell clearing profile (500 pg Alprazolam, 20 ms dwell time)

The figure illustrates a sample analysis that is typically performed with an LC

triple quad MS. The model is useful to show that the higher the mass of the
compound moving through the triple quad, the longer it takes to evacuate the
collision cell. For example, m/z 922 takes about 600 µsec to evacuate the
collision cell using the linear potential, while m/z 118 only takes 350 µsec. This
also demonstrates a low degree of crosstalk since the Y axis is logarithmic,
showing complete clearance of the cell. This means that an inter-scan delay of
1 msec will be more than adequate to flush the collision cell of all ions.

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3 Triple Quad and Sensitivity
Detector

Detector
The detector assembly is unique to Agilent (Figure 24). It is a high-energy dynode
coupled with an electron multiplier.

Figure 24. Detector components

The high-energy dynode is located off-axis from the center of the rear quad
analyzer. This orientation reduces the possibility of neutral molecules impacting
the detector while at the same time attracting the ions with high voltages. When
the ion beam hits the dynode, the ions are converted to electrons before they
impact the multiplier. These electrons are attracted to the more positively
charged electron multiplier horn. The off-axis design of the detector allows
neutrals to pass through and be eliminated by the vacuum system without hitting
the detector.
The multiplier has a long lifetime since only electrons are allowed to impact it.
Ions never impact its surface. Gain normalized tuning provides consistent
sensitivity over the life of the electron multiplier. This also translates into
consistency from MS to MS, and lab to lab.

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3 Triple Quad and Sensitivity
Pumping system

Pumping system
A single split flow turbomolecular pump is used for the entire vacuum system.
Sufficient vacuum for the entire process is achieved by partitioning the turbo
pump to create multiple vacuum stages. The vacuum system removes
molecules of carrier gas and any un-ionized or unfragmented sample molecules
from the ion source outlet, the collision cell, and both analyzers. This pump is
backed by a single mechanical foreline (roughing) pump (Figure 25).

Figure 25. Split flow turbomolecular pump

44 Agilent 7000E/7010C GCMS Triple Quadrupole Concepts Guide

4 Agilent MassHunter Workstation
Software – Instrument Control
for the Triple Quad
Description 46
Tuning 47
Acquisition 48

This section will help you understand the design and operation of the Agilent
MassHunter Workstation Software for GC/MS Instrument Control for the
7000/7010 Series Triple Quads.

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4 Agilent MassHunter Workstation Software – Instrument Control for the Triple Quad
Description

Description
The Instrument Control program (Figure 26) has the following features:
• Showing the instrument at work through real-time plots
• Running multiple samples through the sequence table, a spreadsheet-like
interface
• Controlling and monitoring instrument settings
• Tuning the instrument
• Setting up acquisition parameters for the GC and the Triple Quad
• Monitoring the chromatogram and mass spectra as samples are analyzed
• Setting up sequences of samples

Figure 26. Instrument control

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4 Agilent MassHunter Workstation Software – Instrument Control for the Triple Quad
Tuning

Tuning
Autotune
An autotune taking about 8 minutes can be used when an extensive tune is
recommended (Figure 27). In this mode, everything is automatic. The tuning mix
is delivered by the calibrant delivery system (CDS), which is switched on
automatically during the tune.

Manual tune
A manual tune of user-defined ion masses with six corresponding profile masses
is available.

Figure 27. Autotune in progress

Tune reports
Tune reports are also available.

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4 Agilent MassHunter Workstation Software – Instrument Control for the Triple Quad
Acquisition

Acquisition
The 7000/7010 Series Triple Quad GC/MS systems can be controlled and
monitored from the Instrument Control panel, which is the window used for
accessing acquisition settings and sequence lists (Figure 28, Figure 29 on
page 49, and Figure 30 on page 50).
The real-time plot pane also can show the MS and GC results in real time.

Figure 28. MS acquisition settings

48 Agilent 7000E/7010C GCMS Triple Quadrupole Concepts Guide

4 Agilent MassHunter Workstation Software – Instrument Control for the Triple Quad
Acquisition

Figure 29. Sequence table

Agilent 7000E/7010C GCMS Triple Quadrupole Concepts Guide 49

4 Agilent MassHunter Workstation Software – Instrument Control for the Triple Quad
Acquisition

Figure 30. GC acquisition settings

50 Agilent 7000E/7010C GCMS Triple Quadrupole Concepts Guide

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First Edition, July 2022

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