Agilent Technologies 7200 Operating manual

Agilent Technologies
Agilent 7200
Accurate-Mass/Q-TOF
GC/MS System
Troubleshooting and
Maintenance Manual

2 Troubleshooting and Maintenance Manual
Notices
© Agilent Technologies, Inc. 2012, 2014
No part of this manual may be reproduced in
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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
G3850-90009
Edition
First Edition, August 2014
Printed in USA
Agilent Technologies, Inc.
5301 Stevens Creek Boulevard
Santa Clara, CA 95051
Warranty
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ject to being changed, without notice,
in future editions. Further, to the max-
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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 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS
System 10
7200 Accurate-Mass Q-TOF GC/MS Description 12
Side Panel AC Power Connectors 13
Back Panel Connectors 14
Interfacing Start Events to External Devices 15
Remote control processor 15
Remote start signals 15
System ready 15
Start run input 16
Important Safety Warnings 17
Safety and Regulatory Certifications 20
Intended Use 23
Cleaning/Recycling the Product 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 36
Temperature Symptoms 38

4 Troubleshooting and Maintenance Manual
Common Types of Errors 40
Air Leaks 45
Contamination 46
3 CI Troubleshooting
Common CI-Specific Problems 50
Troubleshooting Tips and Tricks 51
Air Leaks 52
Pressure-Related Symptoms 55
Signal-Related Symptoms 58
Tuning-Related Symptoms 64
The CI ion source is dirty 65
Air leak 65
4 General Maintenance
Before Starting 68
Scheduled maintenance 68
Tools, spare parts, and supplies 69
High voltage precautions 69
Dangerous temperatures 69
Chemical residue 70
Electrostatic discharge 71
To Refill the EI Calibration Vial 72
Materials needed 72
Refill 72
To Refill the IRM Vial 74
Materials needed 74
Procedure 74
To Connect the GC Nitrogen Gas Source to the Collision Cell 76

Troubleshooting and Maintenance Manual 5
Materials needed 76
Procedure 76
To Replace the Seals in the RIS Probe 77
Materials needed 77
Procedure 77
To Separate the GC from the MS 79
Materials needed 79
Procedure 79
To Position the GC Next to the MS 82
Procedure 82
To Move or Store the MS 83
Materials needed 83
Procedure 83
To Access the Left Side Lifting Handle 86
Materials needed 86
Procedure 87
5 CI Maintenance
To Minimize Foreline Pump Damage from Ammonia 90
To Replace the Methane/Isobutane Gas Purifier 91
To Clean the Reagent Gas Supply Lines 92
To Refill the CI Calibration Vial 93
Materials needed 93
Refill 93
6VacuumSystem
Overview 96
Maintaining the Vacuum System 97
Periodic maintenance 97
Other procedures 97

6 Troubleshooting and Maintenance Manual
Vacuum System Components 97
Common Vacuum System Problems 98
Foreline Pump 99
To check the oil mist filter 99
To check the foreline pump fluid level 100
To add foreline pump fluid 100
To replace the foreline pump fluid 101
Side Plate 104
Vacuum Seals 104
Calibration Valves 105
EI Calibration Valve 105
CI Calibration Valve 106
IRM Calibration Valves 107
7ReplacementParts
To Order Parts 110
Electronics 111
Vacuum System 116
Analyzer 121
RIS Manifold 130
GC/MS Interface 132
Consumables and Maintenance Supplies 133

7
Agilent 7200 Accurate-Mass Q-TOF GC/MS System
Troubleshooting and Maintenance Manual
Agilent Technologies
1
Introduction
Abbreviations Used 8
The 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS System 10
7200 Accurate-Mass Q-TOF GC/MS Description 12
Side Panel AC Power Connectors 13
Interfacing Start Events to External Devices 15
Important Safety Warnings 17
Safety and Regulatory Certifications 20
Intended Use 23
Cleaning/Recycling the Product 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.

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
DC Direct current
DFTPP Decafluorotriphenylphosphine (calibrant)
DIP Direct insertion probe
EI Electron impact
EPC Electronic pneumatic control
eV Electron volt
GC Gas chromatograph
id Inside diameter
IRM Internal Reference Mass
LAN Local Area Network
m/z Mass to charge ratio
MFC Mass flow controller
MS Mass spectrometer
MS1 Front quadrupole
NCI Negative chemical ionization
OFN Octafluoronaphthalene (sample)

Introduction 1
Troubleshooting and Maintenance Manual 9
PCI Positive chemical ionization
PFDTD Perfluoro-5,8-dimethyl-3,6,9-trioxydodecane (calibrant)
PFET 2,4,6-tris (Pentafluoroethyl)-1,3,5-triazine
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

10 Troubleshooting and Maintenance 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 bayonet and cooling chamber, which
allows quick change from EI to CI 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
•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 source removal
Physical description
The 7200 Q-TOF GC/MS is approximately 48 cm high, 71 cm wide, and 89 cm
deep. The flight tube extends 84 cm up over the top of the instrument. The RIS
probe handle, when attached, extends 48 cm from the front of the instrument.
The weight of the instrument is 152 kg for the turbo pump mainframe. The
attached foreline (roughing) pump weighs an additional 22.2 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 collision cell, the detector, and the analyzer.

Introduction 1
Troubleshooting and Maintenance Manual 11
Vacuum gauge
The 7200 Q-TOF GC/MS is equipped with four ion vacuum gauges:
•RIS vacuum chamber
•Vacuum manifold chamber
•TOF vacuum manifold chamber
•Turbomolecular vacuum pumps exhaust
The MassHunter Workstation can be used to read the pressure (high vacuum)
in the vacuum manifold, at 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 and CI removable ion source (RIS).
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, quadrupole, and TOF tube. 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 interface has special plumbing for reagent gas. A retractable insulating
seal fits onto the tip of the interface and is used for both EI and CI.
Switching back and forth between CI and EI sources takes less than 30
minutes with the new removable ion source. The RIS allows the instrument to
remain close to pressure, and provides a cooling chamber with N2 purge for
rapid source cooling without venting the machine. This saves hours in cycle
time over the traditional unit.

12 Troubleshooting and Maintenance Manual
1Introduction
7200 Accurate-Mass Q-TOF GC/MS Description
Figure 1 is an overview of a typical 7200 Accurate-Mass Q-TOF GC/MS system.
Figure 1 7200 Q-TOF GC/MS System
7200 Series MS
MS power
switch
7890 GC
GC power switch

Introduction 1
Troubleshooting and Maintenance Manual 13
Side Panel AC Power Connectors
Foreline pump power receptacle (top)
The foreline pump power cord receptacle located on the left side of the MS
provides AC power for the foreline pump. If the power switch is off, no power
is supplied to the foreline pump.
Main power cord receptacle (bottom)
The AC power cord located on the left side of the MS brings in all electrical
power for the MS. The power cord can be detached from the MS.
Figure 2 Side panel power supply (left) and back panel connections (right)

14 Troubleshooting and Maintenance Manual
1Introduction
Back Panel Connectors
Remote start connector
The remote start connector is the external connector for the remote start
circuitry on the LAN/MS control card. It receives remote start signals from the
GC.
LAN (I/O) connector
The LAN cable from the data system is connected to the LAN communications
connector. It carries all data communication between the PC and the MS.
Figure 3 Side panel power supply (left) and back panel connections (right)

Introduction 1
Troubleshooting and Maintenance Manual 15
Interfacing Start Events to External Devices
Remote control processor
The remote control processor on the LAN/MS control card synchronizes
start-run signals with GCs and other devices. The functions of the remote
control processor are extended to the remote start (Remote) connector
(Figure 4) on the back panel of the MS. The remote start cable connects the GC
and the MS. An optional cable can extend these events to another instrument.
Remote start signals
It is often necessary to communicate with external devices (for example, a
purge-and-trap) during a run. Typically, these communications are requests to
send a system-ready signal. They also include:
•Receive a start run signal from an external device
•Program the timing of events during a run
System ready
When interfacing to an external device, it is often desirable to send a
system-ready signal to the device. In the case of a multi-sample Tekmar
purge-and-trap, each sample is purged onto a trap where it waits for a ready
signal. On receipt of the ready signal, the desorption cycle begins. When a
specific temperature is reached, the purge-and-trap closes a contact to
indicate the run has started.
Figure 4 Remote start connector
Start Ground
Ready

16 Troubleshooting and Maintenance Manual
1Introduction
The ready pin on the remote start connector on the GC is held low at all times
except when the GC, MS, and data system are all ready. On system ready, a
logic high of 5 VDC is present between that pin and any ground. This same
high can be detected between the ready and ground pins on the remote start
connector on the MS.
Start run input
The best way to generate a start run signal is to use the remote start connector
on the GC. Since remote start cables are made for most common devices, this
is often the simplest way. A general-purpose remote start cable (Y-Remote
Start/Stop, NON APG p/n G1530-61200), is also available that terminates in
spade lugs. Care must be taken to ensure that the system is actually ready
before the start run signal is sent.
If necessary, the remote start connector on the back of the MS can be used to
send the start run signal. A contact closure between the start and ground pins
will start the run if the system is ready.

Introduction 1
Troubleshooting and Maintenance Manual 17
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.

18 Troubleshooting and Maintenance Manual
1Introduction
Precautions to take to prevent an explosion
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
•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.
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.

Introduction 1
Troubleshooting and Maintenance Manual 19
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.

20 Troubleshooting and Maintenance 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.