Agilent Technologies
Agilent
7250 Accurate-Mass
Quadrupole
Time-of-Flight GC/MS
System
Concepts Guide
2 Agilent 7250 Q-TOF GC/MS Concepts Guide
Notices
© Agilent Technologies, Inc. 2017
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Manual Part Number
G7250-90003
Edition
First Edition, July 2017
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Software Revision
This guide applies to the Agilent MassHunter Workstation Software -- Data Acquisition for 7250 Quadrupole Time-of-Flight
program version B.03.00 or higher until
superseded.
.
Agilent 7250 Q-TOF GC/MS Concepts Guide 3
In This Guide...
The Concepts Guide presents “The Big Picture” behind the
operation of the Agilent 7250 Accurate-Mass Quadrupole
Time-of-Flight GC/MS System by helping you understand how
the hardware and software work.
1 Overview
Learn how the 7250 Q-TOF GC/MS helps you do your job.
2 Theory and Inner Workings
Learn the concepts you need to understand how the 7250
Q-TOF works.
3 Agilent 7250 Accurate-Mass Q-TOF and Performance
Learn how the 7250 Q-TOF exceeds performance measures.
4 Agilent 7250 Q-TOF GC/MS Concepts Guide
Agilent 7250 Q-TOF GC/MS Concepts Guide 5
Contents
1 Overview
System Description 8
Q-TOF applications 9
Instrument control software 10
Data analysis software 12
Reference Documentation 14
2 Theory and Inner Workings
The 7250 Q-TOF Mass Spectrometer 16
Sample Ionization Technology 18
Electrion Impact Ionization 18
LE-EI Ion Source 18
Quadrupole Collision Cell MS/MS Technology 22
Quadrupole filtration 22
Quad mass filter 24
Ion fragmention and collision cell technology 26
Collision cell 26
Time-of-Flight MS Operation 30
Proprietary INVAR flight tube 31
Detector 32
Pumping system 34
3 Agilent 7250 Accurate-Mass Q-TOF Performance
How the 7250 Q-TOF Meets Performance Measures 36
Resolving Power 36
Mass Accuracy 36
Scan Speed 36
Sensitivity 37
Dynamic Range 37
6 Agilent 7250 Q-TOF GC/MS Concepts Guide
7250 Accurate-Mass Q-TOF Design 38
7
Agilent Technologies
Agilent 7250 Accurate-Mass Quadrupole Time-of-Flight GC/MS System
Concepts Guide
1
Overview
System Description 8
Q-TOF applications 9
Instrument control software 10
Data analysis software 12
This chapter provides an overview of the Agilent 7250
Accurate-Mass Quadrupole Time-of-Flight (Q-TOF) GC/MS
system, its applications, and its data analysis system.
8 Agilent 7250 Q-TOF GC/MS Concepts Guide
1 Overview
System Description
System Description
The Agilent 7250 Accurate-Mass Quadrupole Time-of-Flight
(Q-TOF) GC/MS is a stand-alone quadrupole time-of-flight mass
spectrometer for use with the Agilent 7890 Gas Chromatograph.
The 7250 Q-TOF features:
• A new independently MS-heated high efficiency, Low Energy
Electron Impact (LE-EI) ion source capable of operating in
standard (70 eV) or low energy (9 eV to 30 eV) modes
• Both 70 eV and 15 eV tune parameters are stored in the same
tune file allowing use of both modes in different time
segments for the same sample run
• Automated fast venting, that uses nitrogen to break vacuum
thereby reducing the influx of air into the analyzer, resulting
in lower stabilization times after pump down
• Independently MS-heated hyperbolic quadrupole mass filter,
which can be heated to high temperatures, minimizing the
contamination typical with low temperature analyses
• Single hexapole collision cell
• Ion-focusing slicer to improve resolution
• A new 50% longer vacuum-insulated flight tube provides
increased resolution and uses a dual-stage ion mirror for
improved mass accuracy
• A new faster pulser than on the 7200 Q-TOF that allows
extension of the mass range up to 3000 m/z
• A new 5 GS/s sampling rate with or without Transient-Level
Peak Picking (TLPP)
• Analog detector
• Independently GC-heated GC/MS interface
• Full RoHS compliance
• Three turbomolecular vacuum pumps
• Rotary vane foreline pump
• An optional isolated dry foreline pump
Overview 1
Q-TOF applications
Agilent 7250 Q-TOF GC/MS Concepts Guide 9
The 7250 Q-TOF incorporates a hexapole collision cell blanketed
with a nitrogen and helium gas mix, to improve the ion
fragmentation prior to detection quantification. It also includes
ion optics for focusing the ions prior to the flight tube and
detector.
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 7250 Q-TOF can operate in either MS (TOF) mode or MS/MS
mode. When operating in MS mode, the instrument can obtain
high resolution, accurate mass measurements, and fast full
spectrum acquisition. MS/MS mode provides high resolution,
accurate mass measurements, and fast full product ion spectra
with high sensitivity. These features make the 7250 Q-TOF a
good tool for solving complex analytical problems, resolving
structural elucidation of unknowns, and confirmation of
non-target compounds.
Q-TOF applications
The 7250 Q-TOF GC/MS combination can quantify trace organic
compounds in complex matrices. The following applications use
this type of quantification:
• Food safety and research
• Environmental contaminants studies
• Toxicology
• Forensics
• Metabolomics and Metabolomics
• Natural product research
• Human and animal doping studies
• Energy research and petrochemicals
• Homeland security
Paired with the Agilent 7890 GC, the 7250 Q-TOF delivers
sensitive, reproducible analyses of target compounds in
complex matrices. This provides the following:
10 Agilent 7250 Q-TOF GC/MS Concepts Guide
1 Overview
Instrument control software
• Femtogram-level limits of detection and quantification
• Selective quantification of target compounds in high
chemical background samples
• Improved signal-to-noise ratios in complex matrices
• Ability to meet stricter regulations on sample analytical
limits for certain applications
• Simplified operation with Agilent’s data analysis software
• Fast MS/MS operation
• Reproducible mass accuracy
The 7250 Q-TOF offers the improved sensitivity in GC/MS
analysis that is required by many commercial and regulatory
applications.
Instrument control software
The MassHunter WorkStation Instrument Control software
allows you to perform the following tasks from a single window:
Prepare the instrument
• Start and stop the instrument from the software
• Download settings to the GC and the Q-TOF in real time to
control the instrument
• Evaluate if the MS parameters are within the limits to
produce the specified mass accuracy and resolution with
a Checktune report
• Optimize MS parameters automatically (Autotune) or
manually through Agilent tuning programs and print a tune
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 centroided line spectrum of a peak or the mass
range profile spectrum of a peak in real time
Overview 1
Instrument control software
Agilent 7250 Q-TOF GC/MS Concepts Guide 11
Set up acquisition methods
• Enter and save the acquisition method parameter values for
the GC and the Q-TOF
• Select and label the total ion chromatograms (TIC) or
extracted ion chromatograms (EIC) 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 run both individual samples and automated
multiple samples organized in a sequence
• 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 and print an event log report
Please refer to the Agilent MassHunter Software Data
Acquisition Familiarization Guides, the online Help for the
Data Acquisition program, or the 7250 Hardware manuals that
can be found in the location specified in “Reference
Documentation" on page 14.
To learn how to get started with the Agilent 7250 Q-TOF GC/MS,
see the Quick Start Guide.
To learn more about how to use the Agilent 7250 Q-TOF GC/MS
with real samples and data, see the Agilent 7250 Q-TOF
Acquisition Familiarization Guide.
To learn how to do individual tasks with the GC/MS, see the
Online Help.
12 Agilent 7250 Q-TOF GC/MS Concepts Guide
1 Overview
Data analysis software
To learn more about an Agilent 7890 GC, see the Agilent 7890A
GC Documentation.
Data analysis software
Quantitative analysis program
Agilent has designed the MassHunter Quantitative Analysis
program to help quantify very low amounts of material with the
following unique features:
• Imports information directly from the acquisition method
• Provides a curve-fit assistant to test all fits and statistics on
the calibration curve quality
• Integrates signals with an automated, parameter-free
integrator that uses a novel algorithm, optimized for Q-TOF
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
enables the capability to create custom reports in Microsoft
Excel
Please refer to the Agilent MassHunter Software Quantitative
Analysis Familiarization Guides or the online Help for the
Quantitative Analysis program that can be found in the location
specified in “Reference Documentation" on page 14.
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 MassHunter 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
Overview 1
Data analysis software
Agilent 7250 Q-TOF GC/MS Concepts Guide 13
• 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.
Please refer to the Agilent MassHunter Software Qualitative
Analysis Familiarization Guides, Training Videos, or the
online Help for the Qualitative Analysis program that can be
found in the location specified in “Reference
Documentation" on page 14.
14 Agilent 7250 Q-TOF GC/MS Concepts Guide
1 Overview
Reference Documentation
Reference Documentation
Available on the 7250 Q-TOF installation of the MassHunter
Software User Information. This documentation application is
delivered to you as part of your MassHunter Software.
• MassHunter Familiarization Guides for GC/MS for an
introduction to data Acquisition WorkStation, Qualitative
Analysis, and Quantitative Analysis program features.
• Qualitative Analysis Training Videos for those seeking visual
and audio lessons presenting a comprehensive use of the
MassHunter Qualitative Analysis Navigator and MassHunter
Qualitative Workflows.
• On-line Help for detailed information on how Data Acquisition
WorkStation, Qualitative Analysis, and Quantitative Analysis
works.
• Demo data files and libraries that allow you to perform all the
analysis steps demonstrated in various familiarization guides.
• Quick Start Guide explains what documentation is included in
the applications and what information is on each document.
Available on the 7250 Q-TOF installation of the User Manuals and
Tools DVD. This documentation application is delivered to you with
your 7250 Q-TOF instrument.
• Concepts Guide to learn more about how the 7250 Q-TOF GC/MS
System works.
• Quick Start Guide explains what documentation is included in
the applications and what information is on each document.
• Hardware manuals to learn how to operate and perform
maintenance on the 7250 Q-TOF.
15
Agilent Technologies
Agilent 7250 Accurate-Mass Quadrupole Time-of-Flight GC/MS System
Concepts Guide
2
Theory and Inner Workings
The 7250 Q-TOF Mass Spectrometer 16
Sample Ionization Technology 18
Electrion Impact Ionization 18
LE-EI Ion Source 18
Quadrupole Collision Cell MS/MS Technology 22
Quadrupole filtration 22
Quad mass filter 24
Ion fragmention and collision cell technology 26
Collision cell 26
Time-of-Flight MS Operation 30
Proprietary INVAR flight tube 31
Detector 32
Pumping system 34
This chapter explains the inner workings of the 7250 Q-TOF
GC/MS.
16 Agilent 7250 Q-TOF GC/MS Concepts Guide
2 Theory and Inner Workings
The 7250 Q-TOF Mass Spectrometer
The 7250 Q-TOF Mass Spectrometer
The Agilent 7250 Q-TOF is an orthogonal time-of-flight mass
spectrometer. It performs MS/MS using a quadrupole and a
hexapole, or collision cell, prior to a flight tube and detector.
The sample is first ionized by the electron impact ion source.
After ionization, the ions pass through the quadrupole analyzer,
which consists of four parallel hyperbolic rods through which
selected ions are filtered, based on their mass to charge ratio
(m/z). A diagram of the current 7250 Q-TOF mass spec is shown
in Figure 1.
The ions passing through the quad are then directed to the
collision cell, where the entering precursor ions are further
fragmented. The collision cell is a hexapole filled with a
nitrogen and helium gas mix, and is designed for axial
acceleration, which helps with high speed MS/MS analysis. The
Figure 1 The 7250 Q-TOF diagram
Theory and Inner Workings 2
The 7250 Q-TOF Mass Spectrometer
Agilent 7250 Q-TOF GC/MS Concepts Guide 17
fragmented ions, or product ions are sent through a slicer,
which helps to focus the ion stream before they are sent through
a flight tube to the detector.
The acceleration pulse applied to send the ions up the flight
tube is orthogonal to the direction that the ions are leaving the
mass analyzer. This geometry minimizes the effect of the
entrance velocity on the flight time, leading to higher
resolution. Once the ions reach the end of the flight tube, they
bounce off a reflector, or dual-stage ion mirror and travel in a
reverse path back down to the bottom of the tube. The analog
detector is located at the bottom of the flight tube.
The detector sends an analog voltage, proportional to the ion
intensity as a function of time, to the 7250 data acquisition
system. Here the analog signal is digitized and converted by an
embedded microcomputer to a mass spectrum. This converted
data is sent to the MassHunter software for data collection and
analysis.
18 Agilent 7250 Q-TOF GC/MS Concepts Guide
2 Theory and Inner Workings
Sample Ionization Technology
Sample Ionization Technology
In GC/MS, before the sample can be analyzed, it must be ionized
in the ion source. There are two primary methods of ionization
in GC/MS: electron impact (EI) ionization, and chemical
ionization (CI). The 7250 Q-TOF at this time supports only an EI
source.
Electrion Impact Ionization
In electron impact ionization mode, the sample stream enters
an EI ion source from the GC/MS interface. Electrons emitted
from a filament located in the ionization chamber, are guided by
a magnetic field axially along with the ion beam. The
high-energy electrons interact with the sample molecules,
ionizing and fragmenting them. The positive voltage on the
repeller pushes the positive ions into the lens stack, where they
pass through several electrostatic lenses. These lenses
concentrate the ions into a tight beam, which is directed into
the quadrupole mass filter.
The 7250 Q-TOF ion source has two modes of ionization, 70 eV
for classical fragment libraries and 15 eV for low energy
ionization.
LE-EI Ion Source
The 7250 Q-TOF uses the an improved version of the new high
efficiency ionization source (HES) first used in the Agilent
single and triple quadrupole mass spectrometers.
Agilent’s HES technology provides a greater than 10 to 20 fold
increase in ion creation relative to sources that ionize
compounds in a orthogonal plane to the ion beam.
Sample ions enter the source through the GC/MS interface. The
sample is ionized in the ionization chamber which is made up of
the source body, repeller, and filament block containing the
filament and a focusing lens.
Theory and Inner Workings 2
LE-EI Ion Source
Agilent 7250 Q-TOF GC/MS Concepts Guide 19
A filament attached to the filament block emits electrons into
the ionization chamber through the guidance of a strong
magnetic field. These electrons interact with sample molecules,
ionizing and fragmenting them. The long-lifetime, low-current
filament in the EI ionization source of the 7250 Q-TOF is
designed for easy replacement.
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
vacuum system to pump away ions of carrier gas and unionized
material as the sample ions enter the quad, thereby reducing
neutral noise and improving sensitivity.
Source Body
The cylindrical ion source body holds the lens stack, and along
with the repeller and the filament block, forms the ionization
chamber. The ionization chamber is the space where the sample
molecules are ionized. Slots in the source body help the vacuum
system pump away carrier gas and unionized molecules.
Filament
The filament is located on the filament block. The filament
carries an adjustable AC emission current. The emission
current heats the filament causing it to emit electrons, which
ionize the sample molecules. In addition, the filament has an
adjustable DC bias voltage. The calibration of this voltage and
the electron extractor lens voltage establishes the energy of the
electrons. The filament shuts off automatically if there is a
general instrument shutdown. The high efficiency of the 7250
ion source requires less emission current to produce a desired
ion abundance.
Filament Emission current
The filament emission current (Emission) has a typical
operating range between 0.5 µA and 20 µA, with the maximum
emission current at 40 µA.
20 Agilent 7250 Q-TOF GC/MS Concepts Guide
2 Theory and Inner Workings
LE-EI Ion Source
Electron energy
The electron energy is the amount of energy on the ionizing
electrons. It is determined by the bias voltage; 70 VDC bias on
the filament causes emitted electrons to possess 70 eV (electron
volts). This value is adjustable from 70 to 200 eV, but for
classical operation, set this parameter to 70 eV. For low energy
EI this value is typically set from 12 eV to 15 eV.
Magnet
A strong magnetic field directs the electrons emitted by the
filament into and across the ionization chamber. The magnet
assembly uses permanent magnets with a charge of 800 gauss in
the center of the field.
Repeller
The repeller forms one wall of the ionization chamber. A
positive charge on the repeller pushes positively charged ions
out of the source through a series of lenses. The repeller voltage
is typically set by autotune.
Extractor lens assembly
The extractor lens assembly forms another wall of the
ionization chamber. The ion beam passes through a hole in the
extractor lens. The assembly has longitudinal slots, that align
with the slots in the source body, to allow carrier gas and
unionized molecules to be pulled away by the vacuum system.
Theory and Inner Workings 2
LE-EI Ion Source
Agilent 7250 Q-TOF GC/MS Concepts Guide 21
Ion focus
The voltage on the ion focus his has an operational range from
-50 to –200 VDC.
In general:
• Increasing the ion focus voltage improves sensitivity at lower
masses.
• Decreasing the ion focus voltage improves sensitivity at
higher masses.
• Incorrect ion focus adjustment results in poor high mass
response.
Entrance lens
The entrance lens is at the end of the ion source, prior to the
entrance of the quadrupole mass filter. This lens minimizes the
fringing fields of the quadrupole, which discriminate against
high-mass ions. There is a permanent +4.4 volt voltage added to
the entrance lens. The total voltage applied to the entrance lens
is the sum of the entrance lens offset and entrance lens gain and
the +4.4 volt permanent offset. Entrance lens voltage = +4.4 VDC
+ offset + (gain × mass)
22 Agilent 7250 Q-TOF GC/MS Concepts Guide
2 Theory and Inner Workings
Quadrupole Collision Cell MS/MS Technology
Quadrupole Collision Cell MS/MS Technology
Quadrupole filtration
Understanding the operation of a single quadrupole provides
insight into some of the features of a 7250 Q-TOF GC/MS
system. This section reviews the fundamentals of a single
quadrupole mass spectrometer.
Mass spectrometry is based on the analysis of ions moving
through a vacuum.
As described in the previous section, the ionization of a sample
occurs in the ion source. The ions are filtered by a mass
analyzer that controls the motion of the ions as they travel out
of the analyzer. In the case of a single quadrupole MS, the ions
will travel to the detector to be converted into analog signals
(Figure 2). In Q-TOF MS, an additional component (collision
cell) is employed downstream of the quadrupole to enable ion
fragmentation prior to the time-of-flight detection.
The quadrupole mass analyzer consists of four parallel rods to
which specific DC and RF voltages are applied. These rods filter
out all ions except those of one or more particular m/z, or mass
to charge ratio value as determined by the voltages applied.
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.
Figure 2 Schematic for single quadrupole mass spectrometer
Theory and Inner Workings 2
Quadrupole filtration
Agilent 7250 Q-TOF GC/MS Concepts Guide 23
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 a detector, in this case, the flight tube. As the voltages
are increased to other values, 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.
A conceptual model can be used to explain the theory of a single
quadrupole mass spectrometer. See Figure 3.
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, and are fragmented and focused before
they are sent to the flight tube.
Figure 3 Conceptual model of a single quadrupole mass spectrometer
24 Agilent 7250 Q-TOF GC/MS Concepts Guide
2 Theory and Inner Workings
Quad mass filter
• The collecting funnel below the filtering belt represents the
focusing electronics prior to the flight tube.
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.
The scan period is selected (fixed) by the user. The user may set
the scan to a specific mass range (for example, m/z 50 to 1000)
or to dwell on one selected ion (SIM) or to dwell on several
selected ions during the scan period. The quadrupole mass
filter is not scanned over a range in the SIM mode. The required
RF/DC voltages are set to filter a single mass for a specified
dwell time before moving to the setting for the next SIM.
The ions that pass through the quadrupole can either be
measured by a detector, or sent through additional filtering
methods for MS/MS analysis.
Quad mass filter
The quadrupole consist of hyperbolic rods that optimize ion
transmission. 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-filter
The end section of the 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
Theory and Inner Workings 2
Quad mass filter
Agilent 7250 Q-TOF GC/MS Concepts Guide 25
is found on the exit side of the collision cell. These short
RF-only rods act as filters to ensure optimum ion transmission
in and out of the collision cell.
Figure 4 Quadrupole assembly
Pre-filter
Quartz quadrupole rods
26 Agilent 7250 Q-TOF GC/MS Concepts Guide
2 Theory and Inner Workings
Ion fragmention and collision cell technology
Ion fragmention and collision cell technology
As charged ions move through the analyzer chamber, they can
collide with each other and with the gas molecules present
throughout the region. When the voltages increase along their
path, ions have more translational energy, which causes
fragmentation as they collide.
Because fragmentation patterns provide information about the
original ions, a collision cell can be used to purposely fragment
the ions that pass through the analyzer. These ions are called
precursor ions, and their fragments are called product ions. The
quadrupole can be tuned to select which precursor ion travels
to the collision cell. Analysis of their product ions by the
detector provides a means of chemical (Analyte) identification
of the precursor molecule.
Different types of collision cells can be used. The cell can be
another quadrupole, a hexapole (six rods like the one used in
the 7250 Q-TOF), 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 quadrupole to accelerate the movement of
all of the ions so that their collision energy is sufficient to cause
fragmentation.
In the collision cell, a potential difference along the length of
the cell ensures that the precursor ions coming from the
quadrupole or fragment ions generated in the collision cell are
transmitted and not allowed to drift around at random, which
helps to focus the ion stream before it is sent to the flight tube.
Collision cell
The collision collects parents of precursor ions and ion
fragments, thermalizes the ion beam, and focuses the beam into
the flight tube. 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.
Theory and Inner Workings 2
Collision cell
Agilent 7250 Q-TOF GC/MS Concepts Guide 27
The collision cell contains a nitrogen and helium gas mix, which
is eliminated by the vacuum pump along with carrier gas and
fragmented sample ions. The small diameter of the hexapole
assembly assists in colliding fragmented ions.
Why a hexapole?
The geometry of a hexapole provides compromise to competing
performance issues:
• Ion focusing improves with a lower number of poles in the
filter. Studies have shown that a quadrupole provides better
ion focusing than a hexapole and a hexapole provides better
ion focusing than an octopole.
• Ion transmission improves with a higher number of poles in
the filter 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 is chosen after extensive modeling, simulation
and experimentation because it offers the best compromise
between the focusing of a quadrupole and the ion transmission
of an octopole.
Collision cell design
The collision cell hexapole consists of six resistively coated
rods. A 5V potential difference established across the length of
the collision cell (Figure 5) ensures that the precursor ions
coming from the quadrupole, and the fragment ions generated
in the collision cell, are transmitted and not allowed to drift
around at random.
An additional voltage is superimposed to establish an
appropriate collision energy for fragmentation.
28 Agilent 7250 Q-TOF GC/MS Concepts Guide
2 Theory and Inner Workings
Collision cell
Length of time for collision cell flushing
A low degree of crosstalk can be demonstrated by examining
how long it takes to evacuate ions from the collision cell. (See
Figure 6)
Figure 5 Collision cell design
Figure 6 Collision cell clearing profile (500 pg Alprazolam, 20 ms dwell
time)
0 V Collision Energy
5 V Applied Axial Potential
Theory and Inner Workings 2
Collision cell
Agilent 7250 Q-TOF GC/MS Concepts Guide 29
The figure shows that the higher the mass 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 the
low degree of crosstalk since the Y axis is logarithmic, showing
complete clearance of the cell. This means that an inter-scan
delay of 5 msec will be more than adequate to flush the collision
cell of all ions.
30 Agilent 7250 Q-TOF GC/MS Concepts Guide
2 Theory and Inner Workings
Time-of-Flight MS Operation
Time-of-Flight MS Operation
The previous section discusses the theory behind ion separation
using quadrupole mass spectrometry, and fragmentation with a
collision cell. In quadrupole time-of-flight (Q-TOF) mass
spectrometry, these methods are used for preliminary ion
separation prior to detection at the end of the flight tube.
Time-of-flight mass spectrometry measures the time it takes for
ions to travel a known distance, and using this time value,
determines the mass to charge ratio of the ions.
Ions are accelerated through a flight tube by an electric field.
This acceleration results in an ion having the same kinetic
energy as any other ion that has the same charge. The velocity
of the ion depends on the mass-to-charge ratio. The time that it
subsequently takes for the particle to reach a detector at a
known distance can be measured. This time will depend on the
mass-to-charge ratio of the particle (heavier particles reach
lower speeds). From this time and the known experimental
parameters, one can find the mass-to-charge ratio of the ion
using the following relationships:
KE = 1/2 m v
2
v = d/t
t = m
1/2 *
d/(2KE)
1/2
Where KE = Kinetic Energy, v = velocity, m = mass, d is the
distance traveled by the ion, and t is the time it takes for the ion
to travel the distance d.
We can assume that the d/2KE term of the above equation
remains constant. Therefore, the mass of the particle can be
determined by measuring the time the particle takes to travel
the flight tube.
Consider the Q-TOF model in Figure 1 on page 16. Ions that
have been selected in the quadrupole, and fragmented in the
collision cell are sent to the flight tube, where they are sent in
an orthogonal direction up the tube. This means that they are
sent in a direction perpendicular to their flight through the
Theory and Inner Workings 2
Proprietary INVAR flight tube
Agilent 7250 Q-TOF GC/MS Concepts Guide 31
quadrupole and collision cell. The orthogonal direction
minimizes the effects of ion generation and transmission on
mass measurement and provides a uniform initial condition
(approximately zero transverse velocity) for the ions being
launched down the flight tube.
The nearly parallel beam of ions passes through a slicer, which
is a narrow slit that further discriminates the ion beam and
constrain initial conditions for the ions prior to launch down
the flight tube by the time-of-flight ion pulser. The ion pulser is
a stack of plates, each one (except the bottom-most plate) with a
center hole. The ions pass into this stack from the side just
above the bottom-most plate. To start the flight of the ions to
the detector, a high voltage (HV) pulse is applied to the back
plate. The applied pulse repels the ions and accelerates them
through the stack of pulser plates, acting as a rapid- fire ion
gun.
The charged plates of the pulser send the charged ions through
the flight tube, which is about 1.5 meters in length. Changes in
temperature and humidity can alter pulse electronics. In
addition, any collision of an ion with residual gas slows the ion
on its path to the detector and affects the accuracy of the mass
calculation. Therefore, the flight tube should be maintained at
constant temperature and vacuum.
Proprietary INVAR flight tube
The 7250 Q-TOF flight tube is about 1.5 meters in length, 50%
greater than the 7200 Q-TOF and maintains vacuum pressure of
about 10-7 Torr. It is vacuum insulated throughout the length of
the tube. This eliminates the ion scatter that can occur at higher
pressures, and the temperature fluctuations that can change the
flight distance of the ions. In addition, changes in temperature
and humidity can change flight distance. The insulated flight
tube helps minimize these effects, and increase measurement
accuracy.
32 Agilent 7250 Q-TOF GC/MS Concepts Guide
2 Theory and Inner Workings
Detector
The dual stage ion “mirror” at the end of the flight tube reflects
the ions that arrive near the end of the flight tube towards the
detector. As it reflects, it refocuses the ions and minimizes the
kinetic energy variations in arrival time. Ions with higher
kinetic energies will penetrate further into the mirror, traveling
a greater distance, helping them to reach the detector
simultaneously. This corrects the variability in measurement
and results in higher resolving power. Since the ions entered the
ion pulser with a certain amount of forward momentum
orthogonal to the flight direction in the flight tube, when they
reflect off the mirror, they never return to the ion pulser, but
reach the ion detector, as shown in Figure 1 on page 16.
Detector
The detector records the ion intensity as a function of time for
ions arriving at the detector. Fast electronics allow high
sampling rates, and many data points within a given mass
spectrum.
At the surface of the ion detector is a microchannel plate
(MCP), which is a very thin plate containing a set of
microscopic tubes that pass from the front surface to the rear of
the plate. When an ion hits the front surface of the MCP, an
electron escapes and begins the process of electrical signal
amplification. As freed electrons collide with the walls of the
microscopic tubes, an ever-increasing cascade of electrons
travels to the rear of the plate. Roughly 10 times more electrons
exit the MCP than incoming ions contact the surface.
These electrons are then focused onto a scintillator, which,
when struck by electrons, produces photons. The photons from
the scintillator are focused through two small lenses onto a
photocathode in a photomultiplier tube (PMT). The
photocathode converts photons back to electrons, and the
electrons are subsequently multiplied by secondary emission in
the dynode stage of the PMT. The electrical signal emanating
from the PMT is read by the data acquisition system.
Theory and Inner Workings 2
Detector
Agilent 7250 Q-TOF GC/MS Concepts Guide 33
One benefit of converting from electrical current to photons and
then back again to electrons is that the high DC bias voltage
required at the MCP (typically -7000 V) can be electrically
isolated from the data acquisition system, which typically
remains at ground bias potential.
Figure 7 The process of conversion of electrons to photons by the
scintillator
34 Agilent 7250 Q-TOF GC/MS Concepts Guide
2 Theory and Inner Workings
Pumping system
Pumping system
The vacuum system is a five-stage pumping system created by
one split flow and two additional turbo-molecular pumps and a
single roughing (mechanical) pump (Figure 8). The vacuum
system removes particles of carrier gas and any unionized
molecules from the ion source outlet, the collision cell and the
analyzer. In addition, it creates the constant low pressures
necessary to focus the ions and propel them through the
1-meter flight tube with minimal ion scatter.
Vacuum quality affects mass accuracy, resolution, and overall
data quality, because ion collisions with residual gas can alter
the flight time of the ion as well as produce unwanted
fragmentation. Accurate mass calculation depends upon
accurate flight times. Therefore, the background gas pressure in
the flight tube is very low and very consistent.
Figure 8 Vacuum system
35
Agilent Technologies
Agilent 7250 Accurate-Mass Quadrupole Time-of-Flight GC/MS System
Concepts Guide
3
Agilent 7250 Accurate-Mass Q-TOF
Performance
How the 7250 Q-TOF Meets Performance Measures 36
Resolving Power 36
Scan Speed 36
Mass Accuracy 36
Sensitivity 37
Dynamic Range 37
7250 Accurate-Mass Q-TOF Design 38
This chapter shows how the Agilent 7250 Accurate-Mass Q-TOF
GC/MS reduces chemical and electronic noise and how each
component contributes to enhanced instrument performance.
36 Agilent 7250 Q-TOF GC/MS Concepts Guide
3 Agilent 7250 Accurate-Mass Q-TOF Performance
How the 7250 Q-TOF Meets Performance Measures
How the 7250 Q-TOF Meets Performance Measures
There are several performance standards for the 7250 Q-TOF
GC/MS. The most important are:
• Resolving Power
• Mass Accuracy
• Scan Speed
• Sensitivity
• Dynamic Range
Resolving Power
Resolving power in mass spectrometry refers to the ability to
distinguish between two peaks of slightly different mass to
charge ratios (m/z) in a mass spectrum. High resolving power
enables improved mass measurement accuracy and charge state
identification of multiple charged ions, which leads to better
compound identification. The vacuum-insulated flight tube and
dual stage ion mirror in the 7250 Q-TOF GC/MS provides
consistently high resolution.
Mass Accuracy
Mass accuracy is the ability with which the analyzer can
accurately provide m/z information. In mass spectrometry, this
is a function of stability and resolution. This performance
standard is important because accurate mass detection reduces
the risk of effort invested on the wrong molecule. The high
sampling rate and multiple ion event data provided by the
5 G Hz data acquisition system lead to highly accurate mass
identification.
Scan Speed
The scan rate of a mass spectrometer refers to how fast it
samples the ion beam, that is, how many individual transients
Agilent 7250 Accurate-Mass Q-TOF Performance 3
Sensitivity
Agilent 7250 Q-TOF GC/MS Concepts Guide 37
are compiled to produce a composite mass spectrum. Similarly,
the spectral data acquisition rate (typically 1 Hz - 50 Hz or
greater) sets the number of composite mass spectra acquired in
a given interval of time. This is important for chromatography
applications where at least one composite mass spectrum must
be acquired in a time period less than the elution time of the
chromatographic peak. Ideally, a minimum of 10 mass spectra
are acquired for a single chromatographic peak. The fast
electronics of the 7250 Q-TOF provides a maximum data
acquisition rate of about 50 Hz. The number of transients used
to compile a composite spectrum is dependent upon the mass
range selected. Using a standard mass range of 20 - 1200 m/z,
approximately 10,000 transients per second are acquired, i.e.
approximately 10,000 transients at a spectral acquisition rate of
1 Hz and 200 transients at a spectral acquisition rate of 50 Hz.
Each transient collected can contain up to 100,000 data points.
The ability to acquire a mass spectrum comprised of many
rapidly acquired individual data collection transients enhances
data integrity by improved ion statistics.
Mentioned above, the number of acquired transients used to
construct a mass spectrum is related to mass range for a given
experiment. The mass (m/z) ranges available on the 7250 are:
• Standard 20-1200 m/z acquiring 9591 Transients/Spectrum
• Low 20-650 m/z acquiring 13091 Transients/Spectrum
• Extended 20-3000 m/z acquiring 6132 Transients/Spectrum
Sensitivity
Sensitivity in MS data is affected by many factors that include
spectral acquisition rate, mass range, 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 of the 7250 LE-EI
ion source is nearly an order-of-magnitude greater than the
previous generation Agilent 7200 EI source, based on m/z 272 of
OFN. In addition, the high separation, focusing and
38 Agilent 7250 Q-TOF GC/MS Concepts Guide
3 Agilent 7250 Accurate-Mass Q-TOF Performance
Dynamic Range
fragmentation levels achieved by the quadrupole and collision
cells, as well as the elimination of contaminants prior to the
flight tube by the slicer and pumping systems help to contribute
to the high data integrity of the 7250 Q-TOF GC/MS.
Dynamic Range
Dynamic range is a measure of the detection range of a detector
and data acquisition system and describes the range of signal
intensities over which accurate masses can be determined. It is
the ratio of the largest to smallest detectable signal. The 7250
Q-TOF data acquisition system has an improved dynamic range,
when compared to the 7200 Q-TOF.
Agilent 7250 Accurate-Mass Q-TOF Performance 3
7250 Accurate-Mass Q-TOF Design
Agilent 7250 Q-TOF GC/MS Concepts Guide 39
7250 Accurate-Mass Q-TOF Design
In the design of the 7250 Q-TOF GC/MS, the performance
measures were addressed within all stages of instrumentation,
from the ion source to the detector.
Figure 9 7250 Q-TOF performance
1
7
3
4
5
6
2
8
40 Agilent 7250 Q-TOF GC/MS Concepts Guide
3 Agilent 7250 Accurate-Mass Q-TOF Performance
7250 Accurate-Mass Q-TOF Design
1 LE-EI ion source includes repeller, ion volume, high
sensitivity extraction lens and filament.
2 Analyzer uses hyperbolic quadrupoles to optimize ion
transmission and spectral resolution.
3 ADC electronics provide high sampling rates, improving
resolution, mass accuracy, and sensitivity for low abundance
samples.
4 Dual stage ion mirror improves second-order time focusing in
the flight tube by extending the ion flight time provides high
mass resolution.
5 Proprietary INVAR flight tube is 50% longer than previous
model. It is vacuum-insulated and eliminates thermal mass
drift from temperature changes, providing high mass
accuracy and resolution.
6 Analog detector and high speed data acquisition system
provides simultaneous high resolution and wide linear
dynamic range.
7 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.
8 Vacuum system incorporating the use of three
turbomolecular pumps efficiently eliminates neutral
materials prior to the detector
Agilent Technologies, Inc. 2017
First Edition, July 2017
*G7250-90003*
G7250-90003
www.agilent.com
Agilent Technologies
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