Agilent Technologies 5975C TAD VL MSD Operating manual

Agilent Technologies
Agilent 5975 Series
MSD
Troubleshooting and
Maintenance Manual

2 5975 Series MSD Troubleshooting and Maintenance Manual
Notices
© Agilent Technologies, Inc. 2012
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
G3170-90037
Edition
Fourth edition, January 2012
Replaces G3170-90021
Printed in USA
Agilent Technologies, Inc.
5301 Stevens Creek Boulevard
Santa Clara, CA 95052
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The material contained in this docu-
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ject to being changed, without notice,
in future editions. Further, to the max-
imum extent permitted by applicable
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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.

5975 Series MSD Troubleshooting and Maintenance Manual 3
Contents
1 Introduction
5975 Series MSD Version 10
Abbreviations Used 11
The 5975 Series MSD 13
MSD Hardware Description 15
Electron Ionization (EI) systems 16
Chemical Ionization (CI) systems 16
Changing modes 17
Important Safety Warnings 18
Hydrogen Safety 20
Safety and Regulatory Certifications 25
Cleaning/Recycling the Product 28
Moving or Storing the MSD 28
2 General Troubleshooting
Troubleshooting Tips and Tricks 30
General Symptoms 31
Chromatographic Symptoms 33
Mass Spectral Symptoms 38
Pressure Symptoms 42
Temperature Symptoms 45
Error Messages 47
Air Leaks 53
Contamination 54

4 5975 Series MSD Troubleshooting and Maintenance Manual
3 CI Troubleshooting
Common CI-Specific Problems 58
Troubleshooting Tips and Tricks 59
Air Leaks 60
Pressure-Related Symptoms 64
Signal-Related Symptoms 68
Tuning-Related Symptoms 77
4 General Maintenance
Before Starting 84
Maintaining the Vacuum System 89
To Remove the MSD Covers 90
To Connect the Micro-Ion Vacuum Gauge 92
To Move or Store the MSD 94
To Check and Add Foreline Pump Oil 96
To Drain the Foreline Pump 98
To Refill the Foreline Pump 100
To Check the Diffusion Pump Fluid 101
To Separate the MSD from the GC 103
To Reconnect the MSD to the 7890A GC/7820A/6890 GC 105
To Reconnect the MSD to the 6850 GC 106
To Refill the EI Calibration Vial 109
To Purge the Calibration Valves 111
To Remove the EI Calibration and Vent Valve Assembly 112
To Reinstall the EI Calibration and Vent Valve Assembly 113
To Replace the Fan for the High Vacuum Pump 114

5975 Series MSD Troubleshooting and Maintenance Manual 5
To Remove the Micro-Ion Vacuum Gauge 116
To Reinstall a Micro-Ion Vacuum Gauge 117
To Lubricate the Side Plate O-Ring 118
To Lubricate the Vent Valve O-Ring 120
To Remove the Diffusion Pump 122
To Replace the Diffusion Pump Fluid 124
To Reinstall the Diffusion Pump 127
To Remove the Foreline Gauge 129
To Reinstall the Foreline Gauge 130
Maintaining the Analyzer 131
Maintaining the GC/MSD Interface 153
Maintaining the Electronics 157
5 CI Maintenance
To Clean the CI Ion Source 164
To Minimize Foreline Pump Damage from Ammonia (Standard
Pump) 166
To Replace the Methane/Isobutane Gas Purifier 167
To Clean the Reagent Gas Supply Lines 168
To Refill the CI Calibrant Vial 169
6 Vacuum System
Overview 172
Vacuum System Components 173
Common Vacuum System Problems 174
Foreline Pump 175
High Vacuum Pump 178

6 5975 Series MSD Troubleshooting and Maintenance Manual
Diffusion pump system 178
Turbo pump system 178
Analyzer Chamber 179
Diffusion pump version 179
Turbo pump version 179
Side Plate 180
Vacuum Seals 182
Foreline Gauge 184
Diffusion Pump and Fan 185
Turbo Pump and Fan 191
Calibration Valves and Vent Valve 192
Micro-Ion Vacuum Gauge 195
7 Analyzer
Overview 198
EI Ion Source 200
CI Ion Source 202
Filaments 204
Other Source Elements 206
Quadrupole Mass Filter 208
Detector 211
Analyzer Heaters and Radiators 213
8 Electronics
Local Control Panel and Power Switch 217
Side Board 218
Electronics Module 219

5975 Series MSD Troubleshooting and Maintenance Manual 7
LAN/MS Control Card 223
Power Supplies 224
Back Panel and Connectors 225
Interfacing to External Devices 228
9 Parts
To Order Parts 232
Electronics 233
Local Control Panel 238
Vacuum System 240
Analyzer 250
EI GC/MSD Interface 259
Consumables and Maintenance Supplies 260
CI Parts 265
Index 271

8 5975 Series MSD Troubleshooting and Maintenance Manual

9
Agilent 5975 Series MSD
Troubleshooting and Maintenance Manual
Agilent Technologies
1
Introduction
5975 Series MSD Version 10
Abbreviations Used 11
The 5975 Series MSD 13
Physical description 13
Local control panel 13
Vacuum gauge 13
MSD Hardware Description 15
Important Safety Warnings 18
Many internal parts of the MSD carry dangerous voltages 18
Electrostatic discharge is a threat to MSD electronics 18
Many parts are dangerously hot 19
The oil pan under the standard foreline pump can be a fire hazard 19
Hydrogen Safety 20
Dangers unique to GC/MSD operation 21
Hydrogen accumulation in an MSD 21
Precautions 23
Safety and Regulatory Certifications 25
Information 25
Symbols 26
Electromagnetic compatibility 27
Sound emission declaration 27
Cleaning/Recycling the Product 28
Moving or Storing the MSD 28
This manual describes the troubleshooting and maintenance of the Agilent
Technologies 5975 Series Mass Selective Detector (MSD). It assumes
familiarity with the procedures and information detailed in the 5975 Series
MSD Operation Manual and with the Agilent MSD ChemStation software.

10 5975 Series MSD Troubleshooting and Maintenance Manual
1Introduction
5975 Series MSD Version
5975 Series MSDs are equipped with a diffusion pump or one of two
turbomolecular (turbo) pumps. The serial number label displays a product
number (Table 1) that indicates what kind of MSD you have.
Table 1 Available high vacuum pumps
Model name Product number Description Ionization modes
5975C TAD VL MSD G3170A Diffusion Pump MSD Electron impact (EI)
5975C TAD inert MSD
5975C TAD inert XL MSD
G3171A
G3172A
Standard Turbo MSD
Performance Turbo MSD
Electron impact (EI)
Electron impact (EI)
5975C TAD inert XL EI/CI
MSD
G3174A CI Performance Turbo Pump Electron impact (EI)
Negative chemical ionization (NCI)
Positive chemical ionization (PCI)
7820 VL MSD G3175A Diffusion Pump MSD Electron impact (EI)
7820 MSD G3176A Standard Turbo MSD Electron impact (EI)

Introduction 1
5975 Series MSD Troubleshooting and Maintenance Manual 11
Abbreviations Used
The abbreviations in Table 2are used in discussing this product. They are
collected here for convenience.
Table 2 Abbreviations
Abbreviation Definition
AC Alternating current
ALS Automatic liquid sampler
BFB Bromofluorobenzene (calibrant)
CI Chemical ionization
DC Direct current
DFTPP Decafluorotriphenylphosphine (calibrant)
DIP Direct insertion probe
DP Diffusion pump
EI Electron impact ionization
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 (on the MSD)
m/z Mass to charge ratio
MFC Mass flow controller
MSD Mass Selective Detector

12 5975 Series MSD Troubleshooting and Maintenance Manual
1Introduction
NCI Negative CI
OFN Octafluoronaphthalene (calibrant)
PCI Positive CI
PFDTD Perfluoro-5,8-dimethyl-3,6,9-trioxydodecane (calibrant)
PFHT 2,4,6-tris(perfluoroheptyl)-1,3,5-triazine (calibrant)
PFTBA Perfluorotributylamine (calibrant)
Quad Quadrupole mass filter
RF Radio frequency
RFPA Radio frequency power amplifier
Torr Unit of pressure, 1 mm Hg
Turbo Turbomolecular (pump)
Table 2 Abbreviations (continued)
Abbreviation Definition

Introduction 1
5975 Series MSD Troubleshooting and Maintenance Manual 13
The 5975 Series MSD
The 5975 Series MSD is a stand-alone capillary GC detector for use with
Agilent Gas Chromatographs (Table 3). The MSD features:
•Local Control Panel (LCP) for locally monitoring and operating the MSD
•One of three different high vacuum pumps
•Rotary vane foreline pump
•Independently MSD heated electron-ionization ion source
•Independently MSD heated hyperbolic quadrupole mass filter
•High-energy dynode (HED) electron multiplier detector
•Independently GC heated GC/MSD interface
•Chemical ionization (EI/PCI/NCI) modes available
Physical description
The 5975 Series MSD is a rectangular box, approximately 42 cm high, 26 cm
wide, and 65 cm deep. The weight is 25 kg for the diffusion pump mainframe,
26 kg for the standard turbo pump mainframe, and 29 kg for the performance
turbo pump mainframe. The attached foreline (roughing) pump weighs an
additional 11 kg (standard pump).
The basic components of the instrument are: the frame/cover assemblies, the
local control panel, the vacuum system, the GC interface, the electronics, and
the analyzer.
Local control panel
The local control panel allows local monitoring and operation of the MSD. You
can tune the MSD, run a method or a sequence, and monitor instrument
status.
Vacuum gauge
The 5975 Series MSD may be equipped with a Micro-Ion Vacuum Gauge. The
MSD ChemStation can be used to read the pressure (high vacuum) in the
vacuum manifold. Installation of the gauge controller is described in this
manual.

14 5975 Series MSD Troubleshooting and Maintenance Manual
1Introduction
The gauge is required for chemical ionization (CI) operation.
Table 3 5975 series MSD models and features
Model
Feature G3170A
G3175A
G3171A
G3176A
G3172A G3174A
High vacuum pump Diffusion Standard
turbo
Performance
turbo
Performance
turbo
Optimal He column flow mL/min 1 1 1 to 2 1 to 2
Maximum recommended gas flow
mL/min*
* Total gas flow into the MSD: column flow plus reagent gas flow (if applicable).
1.5 2.0 4.0 4
Maximum gas flow, mL/min†
† Expect degradation of spectral performance and sensitivity.
2 2.4 6.5 6.5
Max column id 0.25 mm
(30 m)
0.32 mm
(30 m)
0.53 mm
(30 m)
0.53 mm
(30 m)
CI capability No No No Yes
DIP‡capability (3rd party)
‡ Direct insertion probe.
Yes Yes Yes Yes

Introduction 1
5975 Series MSD Troubleshooting and Maintenance Manual 15
MSD Hardware Description
Figure 1is an overview of a typical GC/MSD system.
Figure 1 5975 Series GC/MSD system
ALS
7890A GC
CI gas flow module
Local control panel
5975 Series MSD
MSD power switch
GC power switch

16 5975 Series MSD Troubleshooting and Maintenance Manual
1Introduction
Electron Ionization (EI) systems
EI systems ionize sample molecules by bombarding them with electrons. The
ions, including fragments, are drawn into the quadrupole analyzer where they
are separated by their mass-to-charge (m/z) ratios and detected.
Chemical Ionization (CI) systems
CI systems use a reagent gas as an intermediate between the electrons and the
sample. CI is more gentle than direct electron bombardment.
The CI hardware allows the 5975 Series MSD to produce high-quality, classical
CI spectra, which include molecular adduct ions. A variety of reagent gases
can be used.
In this manual, the term “CI MSD” refers to the G3174A MSD and upgraded
G3172A MSDs. It also applies, unless otherwise specified, to the flow modules
for these instruments.
The 5975 Series CI system adds to the 5975 Series MSD:
•EI/CI GC/MSD interface
•CI ion source and interface tip seal
•Reagent gas flow control module
•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.
A high vacuum gauge controller (G3397A) is required for CI MSD and is
recommended for EI also.
The MSD CI system has been optimized to achieve the relatively high source
pressure required for CI while still maintaining high vacuum in the
quadrupole 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.

Introduction 1
5975 Series MSD Troubleshooting and Maintenance Manual 17
Changing modes
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.

18 5975 Series MSD Troubleshooting and Maintenance Manual
1Introduction
Important Safety Warnings
There are several important safety notices to always keep in mind when using
the MSD.
Many internal parts of the MSD carry dangerous voltages
If the MSD is connected to a power source, even if the power switch is off,
potentially dangerous voltages exist on:
•The wiring between the MSD power cord and the AC power supply, the AC
power supply itself, and 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 MSD electronics
The printed circuit boards in the MSD 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. Wear a grounded wrist strap any time you must remove the MSD
right side cover.
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, or 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
5975 Series MSD Troubleshooting and Maintenance Manual 19
Many parts are dangerously hot
Many parts of the GC/MSD operate at temperatures high enough to cause
serious burns. These parts include but are not limited to:
•The inlets
•The oven and its contents
•The detector
•The column nuts attaching the column to an inlet or detector
•The valve box
•The foreline pump
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 MSD.
WARNING Be careful when working behind the instrument. During cool-down cycles, the GC
emits hot exhaust which 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; wash your hands with mild soap and cold water after
handling the insulation.
WARNING Combustible materials (or flammable/non-flammable 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 5975 Series MSD Troubleshooting and Maintenance Manual
1Introduction
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.
Additional information can be found in the Hydrogen Safety Guide which is
included on the Agilent GC/GCMSD Hardware User Information & Instrument
Utilities DVD.
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 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.