Agilent Technologies 7200 User manual

Agilent Technologies
Agilent
7200 Accurate-Mass
Quadrupole
Time-of-Flight GC/MS
System
Operation Manual

Operation Manual
Notices
© Agilent Technologies, Inc. 2012
No part of this manual may be reproduced in
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tronic storage and retrieval or translation
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States and international copyright laws.
Manual Part Number
G3850-90005
Edition
First Edition, February 2012
Printed in USA
Agilent Technologies, Inc.
5301 Stevens Creek Blvd.
Santa Clara, CA 95051
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WARNING
A WARNING notice denotes a
hazard. It calls attention to an
operating procedure, practice, or
the like that, if not correctly per-
formed or adhered to, could result
in personal injury or death. Do not
proceed beyond a WARNING
notice until the indicated condi-
tions are fully understood and
met.

Operation Manual 3
About This Manual
This manual contains information for operating and
maintaining the Agilent 7200 Accurate-Mass Quadrupole
Time-of-Flight GC/MS system.
1 “Introduction”
Chapter 1 describes general information about the 7200 Q-TOF
GC/MS, including a hardware description, and general safety
warnings.
2 “Installing GC Columns”
Chapter 2 shows you how to prepare a capillary column for use
with the MS, install it in the GC oven, and connect it to the MS
using the GC/MS interface.
3 “Operating in Electron Impact (EI) Mode”
Chapter 3 describes routine operations in EI mode such as
setting temperatures, monitoring pressures, tuning, venting,
and pumpdown.
4 “Operating in Chemical Ionization (CI) Mode”
Chapter 4 describes additional tasks necessary to operate in CI
mode.
5 “Using the Removable Ion Source”
Chapter 5 shows you how to change the removable ion source.
6 “General Maintenance”
Chapter 6 describes general maintenance procedures for the
7200 Q-TOF GC/MS.

4 Operation Manual
Hardware User Information
Now your Agilent instrument documentation is in one place, at
your fingertips.
The hardware user information DVDs that ship with your
instrument provide an extensive collection of online help,
videos, and books for the Agilent 7890A GC, 7200 Q-TOF GC/MS,
7693 ALS, and the 7683B ALS. Included are localized versions of
the information you need most, such as:
• Getting Familiar documentation
• Safety and Regulatory guides
• Site Preparation checklists
• Installation information
• Operating guides
• Maintenance information
• Troubleshooting details

Operation Manual 5
Contents
1 Introduction
Abbreviations Used 10
The 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS
System 12
Hardware Description 15
Important Safety Warnings 16
Safety and Regulatory Certifications 20
Intended Use 23
Cleaning/Recycling the Product 23
Liquid Spills 23
Moving or Storing the MS 23
2 Installing GC Columns
Columns 26
To Prepare a Capillary Column for Installation 29
To Install a Capillary Column in a Split/Splitless Inlet 31
To Condition a Capillary Column 33
To Install a Capillary Column in the GC/MS Interface 35
To Prepare the Column Ends for a CFT Fitting 38
3 Operating in Electron Impact (EI) Mode
Operating the MS from the Data System 44
The GC/MS Interface 45
Before You Turn On the MS 47
Pumping Down 48

6 Operation Manual
Controlling Temperatures 48
Controlling Column Flow 48
Controlling Collision Cell Flow 49
Venting the MS 50
Typical Vacuum Pressures in EI Mode 51
To Set Monitors for Temperature and Vacuum Status 52
To Set the MS Analyzer Temperature 55
To Set the GC/MS Interface Temperature from the MassHunter
Workstation 57
To Calibrate the Column 58
To Configure the Collision Cell Gas 60
To Set the Collision Cell Gas Flow Rate 61
To Autotune the MS for EI Mode 62
To Remove the Upper RIS Cover 64
To Open the Analyzer Cover for Access to the Analyzer
Sideplate 65
To Pump Down the MS 66
To Vent the MS 69
4 Operating in Chemical Ionization (CI) Mode
Setting Up Your MS to Operate in CI Mode 72
The CI GC/MS Interface 73
Operating the CI MS 75
High Vacuum Pressure in CI Mode 76
Other Reagent Gases 78
CI Autotune 80

Operation Manual 7
The Flow Control Module 82
To Switch from the EI Mode to CI Mode 83
To Operate the Reagent Gas Flow Control Module 85
To Set a Reagent Gas Flow 87
To Perform a CI Autotune 88
5 Using the Removable Ion Source
The Removable Ion Source 92
To Change the Ion Source 94
To Install the RIS Probe Extraction Tool 97
To Remove the Source from the Analyzer Chamber 99
To Change the Ion Source on the RIS Probe Extraction Tool 101
To Install the Ion Source in the Analyzer Chamber 103
To Remove the RIS Probe Extraction Tool from the
Instrument 104
6 General Maintenance
Before Starting 106
Maintaining the Vacuum System 111
Maintaining the Analyzer 112
To Disassemble the EI Ion Source 114
To Assemble the EI Ion Source 116
To Disassemble the CI Ion Source 118
To Assemble the CI Ion Source 120
To Clean the Ion Source 122
To Remove a Filament 126
To Install a Filament 128

8 Operation Manual

9
Agilent Technologies
Agilent 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS System
Operation Manual
1
Introduction
Abbreviations Used 10
The 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS System 12
Hardware Description 15
Important Safety Warnings 16
Safety and Regulatory Certifications 20
Intended Use 23
Cleaning/Recycling the Product 23
Liquid Spills 23
Moving or Storing the MS 23
This section provides general information about the 7200
Accurate-Mass Quadrupole Time-of-Flight (Q-TOF) GC/MS
System, including a hardware description, and general safety
warnings.

10 Operation Manual
1 Introduction
Abbreviations Used
Abbreviations Used
The abbreviations in Table 1are used in discussing this
product. They are collected here for convenience.
Table 1 Abbreviations
Abbreviation Definition
AC Alternating current
ALS Automatic liquid sampler
BFB Bromofluorobenzene (calibrant)
CC Collision cell
CI Chemical ionization
DC Direct current
DFTPP Decafluorotriphenylphosphine (calibrant)
EI Electron impact
EPC Electronic pneumatic control
eV Electron volt
GC Gas chromatograph
id Inside diameter
LAN Local Area Network
m/z Mass to charge ratio
MFC Mass flow controller
MS Mass spectrometer
NCI Negative chemical ionization
OFN Octafluoronaphthalene (sample)
PCI Positive chemical ionization
PFDTD Perfluoro-5,8-dimethyl-3,6,9-trioxydodecane (calibrant)
PFTBA Perfluorotributylamine (calibrant)

Introduction 1
Abbreviations Used
Operation Manual 11
Q-TOF Quadrupole time-of-flight
Quad Quadrupole mass filter
RF Radio frequency
RFPA Radio frequency power amplifier
TOF Time-of-flight
Torr Unit of pressure, 1 mm Hg
Turbo Turbomolecular vacuum pump
Table 1 Abbreviations (continued)
Abbreviation Definition

12 Operation Manual
1 Introduction
The 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS System
The 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS
System
The 7200 Accurate-Mass Quadrupole Time-of-Flight (Q-TOF)
GC/MS System is a standalone capillary GC detector for use
with the Agilent 7890A Series gas chromatograph. The 7200
Q-TOF features:
•Three turbomolecular vacuum pumps
•Rotary vane foreline pump
•Independently MS-heated EI or CI ion source
•Removable ion source (RIS) probe with RIS bayonet and
cooling chamber, which allows quick change from EI to CI ion
source with minimal loss of vacuum in the instrument
•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
•Vacuum-insulated flight tube with dual-stage ion mirror
•Fast electronics, allowing fast sampling rates
•Analog to digital detector
•Independently GC-heated GC/MS interface with automatic
retraction during ion source removal
Physical description
The 7200 Q-TOF GC/MS is approximately 48 cm high, 71 cm
wide, and 89 cm deep excluding the flight tube and RIS handle.
The flight tube extends 84 cm up over the top of the instrument.
The RIS handle, when attached, extends 48 cm from the front of
the instrument.
The weight of the instrument is 152 kg for the mainframe. The
attached foreline (roughing) pump weighs an additional 11 kg.

Introduction 1
The 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS System
Operation Manual 13
The basic components of the instrument are: the frame/cover
assemblies, the vacuum system, the GC/MS interface, the
removable ion source, the flight tube electronics, the
quadrupole mass filter, the collision cell, and the detector.
Vacuum gauge
The 7200 Q-TOF GC/MS is equipped with four ion vacuum
gauges. The MassHunter Workstation can be used to read the
pressure (high vacuum) in the vacuum manifold, the
turbomolecular vacuum pump discharge, and the flight tube.
Ionization modes
The 7200 Accurate-Mass Q-TOF GC/MS can be purchased in two
different ionization configurations:
•G3850AA 7200 Q-TOF GC/MS EI RIS Bundle
•G3851AA 7200 Q-TOF GC/MS EI/CI RIS Bundle
An upgrade kit is available, which allows the user to bring an EI
system to an EI/CI system. This kit adds to the 7200 Q-TOF
GC/MS:
•CI ion source
•Reagent gas flow control module plus associated tubing and
cabeling
•Utilities panel update
•New ribs for cover support
•New routing for the IRM assembly
For the CI system, a methane/isobutane gas purifier is provided
and is required. It removes oxygen, water, hydrocarbons, and
sulfur compounds.
The MS CI system has been optimized to achieve the relatively
high ion source pressure required for CI while still maintaining
high vacuum in the collision cell, quadrupole, and TOF tube.
Special seals along the flow path of the reagent gas and very
small openings in the ion source keep the ion source gases in

14 Operation Manual
1 Introduction
The 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS System
the ionization volume long enough for the appropriate reactions
to occur. The interface has special plumbing for reagent gas. A
retractable insulating seal fits onto the tip of the interface and
is used for both CI and EI.
Switching back and forth between CI and EI ion sources takes
less than 30 minutes with the new removable ion source. The
RIS allows the instrument to remain under vacuum, and
provides a cooling chamber with N2 purge for rapid ion source
cooling without venting the machine. This saves hours in cycle
time over the traditional unit.

Introduction 1
Hardware Description
Operation Manual 15
Hardware Description
Figure 1is an overview of a typical Agilent 7200 Accurate-Mass
Q-TOF GC/MS system.
Figure 1 7200 Q-TOF GC/MS System
Flight tube
ALS tray
Q-TOF
ALS
7890 GC
MS power
switch
Lower RIS
cover
Upper RIS
cover
GC power
switch Tray
Oven door
latch

16 Operation Manual
1 Introduction
Important Safety Warnings
Important Safety Warnings
There are several important safety notices to always keep in
mind when using the instrument.
Many internal parts of these instruments carry dangerous
voltages
If the instrument is connected to a power source, even if the
power switch is off, potentially dangerous voltages exist on:
•The wiring between the instrument power cord and the AC
power supply
•The AC power supply itself
•The wiring from the AC power supply to the power switch
With the power switch on, potentially dangerous voltages also
exist on:
•All electronics boards in the instrument
•The internal wires and cables connected to these boards
•The wires for any heater (oven, detector, inlet, or valve box)
WARNING All these parts are shielded by covers. With the covers in place, it
should be difficult to accidentally make contact with dangerous
voltages. Unless specifically instructed to, never remove a cover
unless the detector, inlet, and oven are turned off.
WARNING If the power cord insulation is frayed or worn, the cord must be
replaced. Contact your Agilent service representative.

Introduction 1
Important Safety Warnings
Operation Manual 17
Electrostatic discharge is a threat to instrument electronics
The printed circuit boards in these instruments can be damaged
by electrostatic discharge. Do not touch any of the boards
unless it is absolutely necessary. If you must handle them, wear
a grounded wrist strap and take other antistatic precautions.
Precautions to take to prevent an explosion
Many parts are dangerously hot
Many parts of these instruments operate at temperatures high
enough to cause serious burns. These parts include, but are not
limited to the:
•Inlet
•Oven and its contents
•Valve box
•Column nuts attaching the column to an inlet, detector, or
MS interface
WARNING The use of hydrogen gas is specifically prohibited with this product.
WARNING You MUST make sure the top thumbscrew on the front analyzer side plate and the top
thumbscrew on the rear analyzer side plate are both fastened finger-tight. Do not
overtighten the thumbscrews; this can cause air leaks.
You MUST leave the collision cell chamber top plate shipping brackets fastened. Do
not remove the shipping brackets from the top plate for normal operation; they
secure the top plate in the event of an explosion.
WARNING Failure to secure your MS as described above greatly increases the chance of
personal injury in the event of an explosion.

18 Operation Manual
1 Introduction
Important Safety Warnings
•Foreline pump
•GC/MS transfer line
Always cool these areas of the system to room temperature
before working on them. They will cool faster if you first set the
temperature of the heated zone to room temperature. Turn the
zone off after it has reached the setpoint. If you must perform
maintenance on hot parts, use a wrench and wear gloves.
Whenever possible, cool the part of the instrument that you will
be maintaining before you begin working on it.
The oil pan under the standard foreline pump can be a fire
hazard
Oily rags, paper towels, and similar absorbents in the oil pan
could ignite and damage the pump and other parts of the MS.
WARNING Be careful when working behind the instrument. During cooldown
cycles, the GC emits hot exhaust that can cause burns.
WARNING The foreline pump can cause burns if touched when operating.
WARNING The insulation around the inlets, detectors, valve box, and the
insulation cups is made of refractory ceramic fibers. To avoid
inhaling fiber particles, we recommend the following safety
procedures: ventilate your work area; wear long sleeves, gloves,
safety glasses, and a disposable dust/mist respirator; dispose of
insulation in a sealed plastic bag in accordance with local
regulations; wash your hands with mild soap and cold water after
handling the insulation.

Introduction 1
Important Safety Warnings
Operation Manual 19
WARNING Combustible materials (or flammable/nonflammable wicking
material) placed under, over, or around the foreline (roughing) pump
constitutes a fire hazard. Keep the pan clean, but do not leave
absorbent material such as paper towels in it.

20 Operation Manual
1 Introduction
Safety and Regulatory Certifications
Safety and Regulatory Certifications
The 7200 Q-TOF GC/MS conforms to the following safety
standards:
•Canadian Standards Association (CSA): CAN/CSA-C22.2 No.
61010-1-04
•CSA/Nationally Recognized Test Laboratory (NRTL):
UL 61010–1
•International Electrotechnical Commission (IEC): 61010–1
•EuroNorm (EN): 61010–1
The 7200 Q-TOF GC/MS conforms to the following regulations
on Electromagnetic Compatibility (EMC) and Radio Frequency
Interference (RFI):
•CISPR 11/EN 55011: Group 1, Class A
•IEC/EN 61326-1
•AUS/NZ
This ISM device complies with Canadian ICES-001. Cet appareil
ISM est conforme a la norme NMB—001 du Canada.
The 7200 Q-TOF GC/MS is designed and manufactured under a
quality system registered to ISO 9001.
Information
The Agilent Technologies 7200 Accurate-Mass Q-TOF GC/MS
meets the following IEC (International Electrotechnical
Commission) classifications: Equipment Class I, Laboratory
Equipment, Installation Category II, and Pollution Degree 2.
This unit has been designed and tested in accordance with
recognized safety standards and is designed for use indoors. If
the instrument is used in a manner not specified by the
manufacturer, the protection provided by the instrument may
be impaired. Whenever the safety protection of the MS has been
compromised, disconnect the unit from all power sources and
secure the unit against unintended operation.