Agilent Technologies 7200 User manual

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

Notices
© Agilent Technologies, Inc. 2012, 2014
No part of this manual may be reproduced in
any form or by any means (including elec-
tronic storage and retrieval or translation
into a foreign language) without prior agree-
ment and written consent from Agilent
Technologies, Inc. as governed by United
States and international copyright laws.
Manual Part Number
G3850-90008
Edition
First Edition, August 2014
Printed in USA
Agilent Technologies, Inc.
5301 Stevens Creek Blvd.
Santa Clara, CA 95051
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adhered to, could result in damage
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conditions are fully understood and
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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.

7200 Accurate-Mass QTOF 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 7200 Accurate-Mass QTOF Operation Manual
Hardware User Information
Accompanying your hardware and software is a comprehensive collection of
manuals, videos, user applications, and method development tools. These are
located on the:
To Install Your Hardware Library
Insert Disk 1 into your DVD drive and follow the prompts.
This can be installed by anyone who has authority to copy
information onto the receiving computer.
To Install Your Software Library
Insert the memory stick into a USB port and follow the prompts.
This can be installed by anyone who has authority to copy
information onto the receiving computer.
©2013 Agilent Technologies,Inc.
Allrights reserved.
Madein USA
Agilent Technologies
GC/GCMS Hardware User Manuals and Videos
S1
Disk2/3
Toinstall:
1.Insert disk into DVD drive
2.Follow the instructions on the screen.
3.If autoplay is not enabled, double-click
"index_xx.html"on the DVD
where xx is:
enfor English
chfor中文
jpfor 日本語
VersionB.01.05
January,2013
©2013 Agilent Technologies,Inc.
Allrights reserved.
Madein USA
Agilent Technologies
GC/GCMS Hardware User Manuals and Videos
S1
Disk2/3
Toinstall:
1.Insert disk into DVD drive
2.Follow the instructions on the screen.
3.If autoplay is not enabled, double-click
"index_xx.html"on the DVD
where xx is:
enfor English
chfor中文
jpfor 日本語
VersionB.01.05
January,2013
•Agilent GC and GC/MS User Manuals and Tools DVD set
•Agilent GC/MS Software Information and Manuals memory stick
See the Agilent 7200 Accurate Mass Q-TOF GC/MS System Quick Start
document (G6845-90014) for more details on how to install this information
on your computer.

7200 Accurate-Mass QTOF Operation Manual 5
Contents
1 Introduction
Abbreviations Used 10
The 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS
System 12
Hardware Description 14
Important Safety Warnings 15
Safety and Regulatory Certifications 18
Intended Use 21
Cleaning/Recycling the Product 21
Liquid Spills 21
Moving or Storing the MS 21
2 Installing GC Columns
Columns 24
To Install a Capillary Column in a Split/Splitless Inlet 26
To Condition a Capillary Column 29
To Install a Capillary Column in the GC/MS Interface 30
3 Operating in Electron Impact (EI) Mode
Operating the MS from the Data System 34
The GC/MS Interface 35
Before You Turn On the MS 37
Pumping Down 38

6 7200 Accurate-Mass QTOF Operation Manual
Controlling Temperatures 38
Controlling Column Flow 38
Controlling Collision Cell Flow 39
Venting the MS 39
Typical Vacuum Pressures in EI Mode 40
To Set Monitors for Temperature and Vacuum Status 41
To Set the MS Analyzer Temperature 43
To Set the GC/MS Interface Temperature from the MassHunter Workstation 45
To Calibrate the Column 46
To Configure the Collision Cell Gas 48
To Set the Collision Cell Gas Flow Rate 49
To Autotune the MS for EI Mode 50
To Remove the Upper RIS Cover 52
To Open the Analyzer Cover for Access to the Analyzer Sideplate 53
To Pump Down the MS 54
To Vent the MS 56
4 Operating in Chemical Ionization (CI) Mode
Setting Up Your MS to Operate in CI Mode 58
The GC/MS Interface 59
Operating the CI MS 61
High Vacuum Pressure in CI Mode 62
Other Reagent Gases 63
CI Autotune 65
The Flow Control Module 66
To Switch from the EI Mode to CI Mode 67

7200 Accurate-Mass QTOF Operation Manual 7
To Operate the Reagent Gas Flow Control Module 69
To Set a Reagent Gas Flow 71
To Perform a CI Autotune 72
5 Using the Removable Ion Source
The Removable Ion Source 76
To Change the Ion Source 78
To Install the RIS Probe Extraction Tool 80
To Remove the Source from the Analyzer Chamber 82
To Change the Ion Source on the RIS Probe Extraction Tool 84
To Install the Ion Source in the Analyzer Chamber 86
To Remove the RIS Probe Extraction Tool from the Instrument 87
6 General Maintenance
Before Starting 90
Maintaining the Vacuum System 94
Maintaining the Analyzer 95
To Disassemble the EI Ion Source 97
To Assemble the EI Ion Source 99
To Disassemble the CI Ion Source 101
To Assemble the CI Ion Source 103
To Clean the Ion Source 105
To Remove a Filament 109
To Install a Filament 111

8 7200 Accurate-Mass QTOF Operation Manual

9
Agilent 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS System
Operation Manual
Agilent Technologies
1
Introduction
Abbreviations Used 10
The 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS System 12
Hardware Description 14
Important Safety Warnings 15
Safety and Regulatory Certifications 18
Intended Use 21
Cleaning/Recycling the Product 21
Liquid Spills 21
Moving or Storing the MS 21
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 7200 Accurate-Mass QTOF Operation Manual
1Introduction
Abbreviations Used
The abbreviations in Table 1 are 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)
PFET 2,4,6-tris (Pentafluoroethyl)-1,3,5-triazine

Introduction 1
7200 Accurate-Mass QTOF Operation Manual 11
PFTBA Perfluorotributylamine (calibrant)
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 7200 Accurate-Mass QTOF Operation Manual
1Introduction
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 7890 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
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 mainframe is 152 kg. The attached foreline
(roughing) pump weighs an additional 21.5 kg.
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.

Introduction 1
7200 Accurate-Mass QTOF Operation Manual 13
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 G3851BA 7200 Accurate-Mass Q-TOF GC/MS comes standard with both an
EI source and a CI source.
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 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 (RIS). 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.

14 7200 Accurate-Mass QTOF Operation Manual
1Introduction
Hardware Description
Figure 1 is an overview of a typical Agilent 7200 Accurate-Mass Q-TOF GC/MS
system.
Figure 1 7200 Q-TOF GC/MS System
Flight tube
Q-TOF
ALS
7890 GC
MS power
switch
Lower RIS
cover
Upper RIS
cover
GC power
switch Drawer
Oven door
latch

Introduction 1
7200 Accurate-Mass QTOF Operation Manual 15
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)
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.
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.

16 7200 Accurate-Mass QTOF Operation Manual
1Introduction
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
•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.
WARNING
The use of hydrogen gas is specifically prohibited with this product.
WARNING
You MUST ensure 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
over-tighten 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.

Introduction 1
7200 Accurate-Mass QTOF Operation Manual 17
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.
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, and do not leave absorbent material such as paper towels in it.

18 7200 Accurate-Mass QTOF Operation Manual
1Introduction
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.
Refer servicing to qualified service personnel. Substituting parts or
performing any unauthorized modification to the instrument may result in a
safety hazard.

Introduction 1
7200 Accurate-Mass QTOF Operation Manual 19
Symbols
Warnings in the manual or on the instrument must be observed during all
phases of operation, service, and repair of this instrument. Failure to comply
with these precautions violates safety standards of design and the intended
use of the instrument. Agilent Technologies assumes no liability for the
customer’s failure to comply with these requirements.
See accompanying instructions for more information.
Indicates a hot surface.
Indicates hazardous voltages.
Indicates earth (ground) terminal.
Indicates potential explosion hazard.
Indicates radioactivity hazard.
Indicates electrostatic discharge hazard.
Indicates that you must not discard this
electrical/electronic product in domestic household
waste.
or

20 7200 Accurate-Mass QTOF Operation Manual
1Introduction
Electromagnetic compatibility
This device complies with the requirements of CISPR 11. Operation is subject
to the following two conditions:
•This device may not cause harmful interference.
•This device must accept any interference received, including interference
that may cause undesired operation.
If this equipment does cause harmful interference to radio or television
reception, which can be determined by turning the equipment off and on, the
user is encouraged to try one or more of the following measures:
•Relocate the radio or antenna.
•Move the device away from the radio or television.
•Plug the device into a different electrical outlet, so that the device and the
radio or television are on separate electrical circuits.
•Ensure that all peripheral devices are also certified.
•Ensure that appropriate cables are used to connect the device to peripheral
equipment.
•Consult your equipment dealer, Agilent Technologies, or an experienced
technician for assistance.
Changes or modifications not expressly approved by Agilent Technologies
could void the user’s authority to operate the equipment.
Sound emission declaration
Sound pressure
Sound pressure Lp < 70 dB according to EN 27779:1991 and
EN ISO 3744:1995.
Schalldruckpegel
Schalldruckpegel LP < 70 dB nach EN 27779:1991 und EN ISO 3744:1995.