Agilent Technologies 7000 Triple Quadrupole GC/MS User manual

Agilent Technologies
Agilent 7000 Triple
Quadrupole GC/MS
System
Troubleshooting and
Maintenance Manual

2 Troubleshooting and Maintenance Manual
Notices
© Agilent Technologies, Inc. 2009
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
G7000-90037
Edition
Second edition, September 2009
Printed in USA
Agilent Technologies, Inc.
5301 Stevens Creek Boulevard
Santa Clara, CA 95051
Warranty
The material contained in this docu-
ment is provided “as is,” and is sub-
ject to being changed, without notice,
in future editions. Further, to the max-
imum extent permitted by applicable
law, Agilent disclaims all warranties,
either express or implied, with regard
to this manual and any information
contained herein, including but not
limited to the implied warranties of
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ticular purpose. Agilent shall not be
liable for errors or for incidental or
consequential damages in connec-
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arate agreement shall control.
Safety Notices
CAUTION
A CAUTION notice denotes a
hazard. It calls attention to an
operating procedure, practice, or
the like that, if not correctly
performed or adhered to, could
result in damage to the product or
loss of important data. Do not
proceed beyond a CAUTION notice
until the indicated conditions are
fully understood and met.
WARNING
A WARNING notice denotes a
hazard. It calls attention to an
operating procedure, practice, or
the like that, if not correctly
performed or adhered to, could
result in personal injury or death.
Do not proceed beyond a
WARNING notice until the
indicated conditions are fully
understood and met.

Troubleshooting and Maintenance Manual 3
Contents
1 Introduction
Abbreviations Used 8
The 7000 Series Triple Quad GC/MS 10
Triple Quad GC/MS Hardware Description 12
Important Safety Warnings 13
Hydrogen Safety 15
Safety and Regulatory Certifications 20
Intended Use 23
Cleaning/Recycling the Product 23
Liquid Spills 23
Moving or Storing the MS 23
2 General Troubleshooting
Troubleshooting Tips and Tricks 26
General Symptoms 27
Chromatographic Symptoms 29
Mass Spectra General Symptoms 34
Pressure Symptoms 38
Temperature Symptoms 40
Common Types of Errors 42
Air Leaks 47
Contamination 48

4 Troubleshooting and Maintenance Manual
3 CI Troubleshooting
Common CI-Specific Problems 52
Troubleshooting Tips and Tricks 53
Air Leaks 54
Pressure-Related Symptoms 58
Signal-Related Symptoms 62
Tuning-Related Symptoms 70
4 General Maintenance
Before Starting 76
Maintaining the Mainframe 80
Maintaining the Vacuum System 93
Maintaining the Analyzers and Collision Cell 107
Maintaining the GC/MS Interface 115
Maintaining the Electronics 119
5 CI Maintenance
To Minimize Foreline Pump Damage from Ammonia 124
To Replace the Methane/Isobutane Gas Purifier 125
To Clean the Reagent Gas Supply Lines 126
To Refill the CI Calibrant Vial 127
6VacuumSystem
Overview 130
Vacuum System Components 131
Common Vacuum System Problems 132
Foreline Pump 133

Troubleshooting and Maintenance Manual 5
Turbo Pump 135
Analyzer Chambers 135
Side Plates 136
Vacuum Seals 137
Foreline Gauge 139
Turbo Pump and Fan 140
Calibration Valve and Vent Valve 141
7 Analyzers and Collision Cell
Overview 146
EI Ion Source 148
CI Ion Source 150
Filaments 152
Other Source Elements 154
Quadrupole Mass Filters 156
Post- and Pre-Filters 159
Collision Cell 160
Detector 161
Analyzer Heaters and Radiators 163
8 Electronics
Power Switch 166
Ion Source Board 167
Quadrupole Boards 168
Collision Cell Board 169
Detector Board 170

6 Troubleshooting and Maintenance Manual
Electronics Module 171
Bus board 176
PLX card 176
LAN/MS Control Card (Smartcard 4) 176
Power Supplies 177
Back Panel Connectors 178
Interfacing to External Devices 180
9ReplacementParts
To Order Parts 184
Electronics 185
Local Control Panel 189
Vacuum System 190
Analyzer 195
EI GC/MS Interface 205
Consumables and Maintenance Supplies 206
Additional CI Parts 210

7
Agilent 7000 Series Triple Quadrupole GC/MS
Troubleshooting and Maintenance Manual
Agilent Technologies
1
Introduction
Abbreviations Used 8
The 7000 Series Triple Quad GC/MS 10
Triple Quad GC/MS Hardware Description 12
Important Safety Warnings 13
Hydrogen Safety 15
Safety and Regulatory Certifications 20
Intended Use 23
Cleaning/Recycling the Product 23
Liquid Spills 23
Moving or Storing the MS 23
This manual describes the troubleshooting and maintenance of the Agilent
Technologies 7000 Triple Quadrupole Mass Spectrometer (MS) system. It is
often referred to in this document as the 7000 Triple Quad GC/MS. This
manual assumes familiarity with the procedures and information detailed in
the Agilent 7000 Series Triple Quad GC/MS Operation Manual and with the
Agilent MassHunter Workstation software.
The 7000 Triple Quad GC/MS system consists of a 7890A gas chromatograph
(GC) and a 7000 triple quadrupole mass spectrometer (MS).
This section provides general information about the 7000 Series Triple Quad
GC/MS, including a hardware description, general safety warnings, and
hydrogen safety information.

8 Troubleshooting and Maintenance 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
CID Collision induced dissociation
DC Direct current
DFTPP Decafluorotriphenylphosphine (calibrant)
DIP Direct insertion probe
EI Electron impact
EM Electron multiplier (detector)
EMV Electron multiplier voltage
EPC Electronic pneumatic control
eV Electron volt
GC Gas chromatograph
HED High-energy dynode (refers to detector and its power supply)
id Inside diameter
LAN Local Area Network
LCP Local control panel
m/z Mass to charge ratio
MFC Mass flow controller

Introduction 1
Troubleshooting and Maintenance Manual 9
MRM Multiple reaction monitoring
MS Mass spectrometer
MS1 Front quadrupole
MS2 Rear quadrupole
NCI Negative chemical ionization
OFN Octafluoronaphthalene (sample)
PCI Positive chemical ionization
PFDTD Perfluoro-5,8-dimethyl-3,6,9-trioxydodecane (calibrant)
PFTBA Perfluorotributylamine (calibrant)
QQQ Triple quadrupole
Quad Quadrupole mass filter
RF Radio frequency
RFPA Radio frequency power amplifier
Torr Unit of pressure, 1 mm Hg
Turbo Split flow turbomolecular vacuum pump
Table 1 Abbreviations (continued)
Abbreviation Definition

10 Troubleshooting and Maintenance Manual
1Introduction
The 7000 Series Triple Quad GC/MS
The 7000 Series Triple Quad GC/MS is a standalone capillary GC detector for
use with the Agilent 7890A Series gas chromatograph. The Triple Quad MS
features:
•One split flow turbomolecular vacuum pump
•Rotary vane foreline pump
•Independently MS heated ion source
•Chemical and electron-ionization modes available (PCI/NCI/EI)
•Two independently MS heated hyperbolic quadrupole mass filters
•Single hexapole collision cell
•High-energy dynode (HED) electron multiplier detector
•Independently GC heated GC/MS interface
•Independently GC controlled collision cell gas flows
•High sensitivity electronic upgrades for the EI source and HED available
•Local control panel (LCP) for locally monitoring the MS
Physical description
The 7000 Series Triple Quad GC/MS is a rectangular box, approximately 47 cm
high, 35 cm wide, and 86 cm deep. The weight is 59 kg for the turbo pump
mainframe. The attached foreline (roughing) pump weighs an additional 11 kg.
The basic components of the instrument are: the frame/cover assemblies, the
vacuum system, the GC/MS interface, the ion source, the electronics, the
collision cell, the detector, and the front and rear analyzers.
Local control panel
The local control panel allows local monitoring of the MS instrument status.
Vacuum gauge
The 7000 Series Triple Quad GC/MS is equipped with two ion vacuum gauges.
The MassHunter Workstation can be used to read the pressure (high vacuum)
in the vacuum manifold and at the turbomolecular vacuum pump discharge.

Introduction 1
Troubleshooting and Maintenance Manual 11
In this manual, the term “CI MS” refers to the 7000 Series Triple Quad GC/MS
CI source system. It also applies, unless otherwise specified, to the flow
modules for these instruments.
The 7000 Series Triple Quad GC/MS CI source system upgrade kit adds to the
7000 Triple Quad MS:
•EI/CI GC/MS interface
•High sensitivity EI source
•CI ion source and interface tip seal
•Reagent gas flow control module
•HED with high sensitivity electronics
•Bipolar HED power supply for PCI and NCI operation
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 source
pressure required for CI while still maintaining high vacuum in the collision
cell, quadrupoles, and detector. Special seals along the flow path of the
reagent gas and very small openings in the ion source keep the source gases in
the ionization volume long enough for the appropriate reactions to occur.
The CI interface has special plumbing for reagent gas. A spring-loaded
insulating seal fits onto the tip of the interface.
Switching back and forth between CI and EI sources takes less than an hour,
although a 1- to 2-hour wait is required to purge the reagent gas lines and bake
out water and other contaminants. Switching from PCI to NCI requires about 2
hours for the ion source to cool.

12 Troubleshooting and Maintenance Manual
1Introduction
Triple Quad GC/MS Hardware Description
Figure 1 is an overview of a typical 7000 Triple Quad GC/MS system.
Figure 1 7000 Triple Quad MS
ALS
7000 Series Triple
Quad MS
Local control
panel
MS power
switch
7890A GC
Tray
GC power switch

Introduction 1
Troubleshooting and Maintenance Manual 13
Important Safety Warnings
There are several important safety notices to always keep in mind when using
the MS.
Many internal parts of the MS carry dangerous voltages
If the MS is connected to a power source, even if the power switch is off,
potentially dangerous voltages exist on:
•The wiring between the MS 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 MS electronics
The printed circuit boards in the MS 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.

14 Troubleshooting and Maintenance Manual
1Introduction
Many parts are dangerously hot
Many parts of the GC/MS 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
•Detectors
•Column nuts attaching the column to an inlet or detector
•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 cool-down cycles, the GC
emits hot exhaust that can cause burns.
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, but do not leave absorbent material such as paper towels in it.

Introduction 1
Troubleshooting and Maintenance Manual 15
Hydrogen Safety
Hydrogen is a commonly used GC carrier gas. Hydrogen is potentially
explosive and has other dangerous characteristics.
•Hydrogen is combustible over a wide range of concentrations. At
atmospheric pressure, hydrogen is combustible at concentrations from 4%
to 74.2% by volume.
•Hydrogen has the highest burning velocity of any gas.
•Hydrogen has a very low ignition energy.
•Hydrogen that is allowed to expand rapidly from high pressure can
self-ignite.
•Hydrogen burns with a nonluminous flame, which can be invisible under
bright light.
Dangers unique to GC/MS operation
Hydrogen presents a number of dangers. Some are general, others are unique
to GC or GC/MS operation. Dangers include, but are not limited to:
•Combustion of leaking hydrogen
•Combustion due to rapid expansion of hydrogen from a high-pressure
cylinder
WARNING
The use of hydrogen as a GC carrier gas is potentially dangerous.
WARNING
When using hydrogen (H2) as the carrier gas or fuel gas, be aware that hydrogen
gas can flow into the GC oven and create an explosion hazard. Therefore, be sure
that the hydrogen supply is turned off until all connections are made and ensure that
the inlet and detector column fittings are either connected to a column or capped at
all times when hydrogen gas is supplied to the instrument.
Hydrogen is flammable. Leaks, when confined in an enclosed space, may create a
fire or explosion hazard. In any application using hydrogen, leak test all
connections, lines, and valves before operating the instrument. Always turn off the
hydrogen supply at its source before working on the instrument.

16 Troubleshooting and Maintenance Manual
1Introduction
•Accumulation of hydrogen in the GC oven and subsequent combustion (See
your GC documentation and the label on the top edge of the GC oven door.)
•Accumulation of hydrogen in the MS and subsequent combustion
Hydrogen accumulation in an MS
All users should be aware of the mechanisms by which hydrogen can
accumulate (Table 2) and know what precautions to take if they are certain or
suspect that hydrogen has accumulated. Note that these mechanisms apply to
all mass spectrometers.
WARNING
The MS cannot detect leaks in inlet and/or detector gas streams. For this reason, it
is vital that column fittings should always be either connected to a column or have a
cap or plug installed.
Table 2 Hydrogen accumulation mechanisms
Mechanism Results
Mass spectrometer turned off A mass spectrometer can be shut down
deliberately. It can also be shut down accidentally
by an internal or external failure. A mass
spectrometer shutdown does not shut off the flow
of carrier gas. As a result, hydrogen may slowly
accumulate in the mass spectrometer.
Mass spectrometer automated shutoff
valves closed
The mass spectrometers are equipped with
automated shutoff valves for the calibration vial
and the reagent gases. Deliberate operator action
or various failures can cause the shutoff valves to
close. Shutoff valve closure does not shut off the
flow of carrier gas. As a result, hydrogen may
slowly accumulate in the mass spectrometer.

Introduction 1
Troubleshooting and Maintenance Manual 17
GC off A GC can be shut down deliberately. It can also be
shut down accidentally by an internal or external
failure. Different GCs react in different ways. If a
7890A GC equipped with Electronic Pressure
Control (EPC) is shut off, the EPC stops the flow of
carrier gas. If the carrier flow is not under EPC
control, the flow increases to its maximum. This
flow may be more than some mass spectrometers
can pump away, resulting in the accumulation of
hydrogen in the mass spectrometer. If the mass
spectrometer is shut off at the same time, the
accumulation can be fairly rapid.
Power failure If the power fails, both the GC and mass
spectrometer shut down. The flow of carrier gas,
however, is not necessarily shut down. As
described previously, in some GCs a power failure
may cause the carrier gas flow to be set to
maximum. As a result, hydrogen may accumulate in
the mass spectrometer.
Table 2 Hydrogen accumulation mechanisms (continued)
Mechanism Results
WARNING
Once hydrogen has accumulated in a mass spectrometer, extreme caution must be
used when removing it. Incorrect startup of a mass spectrometer filled with
hydrogen can cause an explosion.
WARNING
After a power failure, the mass spectrometer may start up and begin the pumpdown
process by itself. This does not guarantee that all hydrogen has been removed from
the system or that the explosion hazard has been removed.

18 Troubleshooting and Maintenance Manual
1Introduction
Precautions
Take the following precautions when operating a GC/MS system with
hydrogen carrier gas.
Equipment precautions
General laboratory precautions
•Avoid leaks in the carrier gas lines. Use leak-checking equipment to
periodically check for hydrogen leaks.
•Eliminate from your laboratory as many ignition sources as possible (for
example, open flames, devices that can spark and sources of static
electricity).
•Do not allow hydrogen from a high pressure cylinder to vent directly to
atmosphere (danger of self-ignition).
•Use a hydrogen generator instead of bottled hydrogen.
Operating precautions
•Turn off the hydrogen at its source every time you shut down the GC or MS.
•Do not use hydrogen as a collision cell gas.
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.
You must remove the plastic cover over the glass window on the front of the
analyzer. In the unlikely event of an explosion, this cover may dislodge.
WARNING
Failure to secure your MS as described above greatly increases the chance of
personal injury in the event of an explosion.

Introduction 1
Troubleshooting and Maintenance Manual 19
•Turn off the hydrogen at its source every time you vent the MS (do not heat
the capillary column without carrier gas flow).
•Turn off the hydrogen at its source every time shutoff valves in the MS are
closed (do not heat the capillary column without carrier gas flow).
•Turn off the hydrogen at its source if a power failure occurs.
•If a power failure occurs while the GC/MS system is unattended, even if the
system has restarted by itself:
1Immediately turn off the hydrogen at its source.
2Turn off the GC.
3Turn off the MS and allow it to cool for 1 hour.
4Eliminate all potential sources of ignition in the room.
5Open the vacuum manifold of the MS to atmosphere.
6Wait at least 10 minutes to allow any hydrogen to dissipate.
7Start up the GC and MS as normal.
When using hydrogen gas, check the system for leaks to prevent possible fire
and explosion hazards based on local Environmental Health and Safety (EHS)
requirements. Always check for leaks after changing a tank or servicing the
gas lines. Always make sure the vent line is vented into a fume hood.

20 Troubleshooting and Maintenance Manual
1Introduction
Safety and Regulatory Certifications
The 7000 Series Triple Quad GC/MS conforms to the following safety
standards:
•Canadian Standards Association (CSA): CAN/CSA-C222 No. 61010-1-04
•CSA/Nationally Recognized Test Laboratory (NRTL): UL 61010–1
•International Electrotechnical Commission (IEC): 61010–1
•EuroNorm (EN): 61010–1
The 7000 Triple Quad 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
•AUS/NZ
This ISM device complies with Canadian ICES-001. Cet appareil ISM est
conforme a la norme NMB—001 du Canada.
The 7000 Series Triple Quad GC/MS is designed and manufactured under a
quality system registered to ISO 9001.
Information
The Agilent Technologies 7000 Series Triple Quad 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.