Agilent Technologies 7250 User manual

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
Printed in USA
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Software Revision
This guide applies to the Agilent Mass-
Hunter Workstation Software -- Data Acqui-
sition 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superseded.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.