Agilent Technologies 5977B Series Operating manual

Agilent Technologies
Agilent 5977B
Series MSD
Troubleshooting and
Maintenance Manual

2
Notices
© Agilent Technologies, Inc. 2016
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
G7077-90028
Edition
First edition, September 2016
Printed in USA
Agilent Technologies, Inc.
5301 Stevens Creek Boulevard
Santa Clara, CA 95052
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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.

5977B Series MSD Troubleshooting and Maintenance Manual 3
1 Introduction
5977B Series MSD Version 10
Abbreviations Used 11
The 5977B Series MSD 13
MSD Hardware Description 16
Electron Ionization (EI) systems 17
Chemical Ionization (CI) systems 17
Changing modes 18
Important Safety Warnings 19
Hydrogen Safety 22
Safety and Regulatory Certifications 28
Cleaning/Recycling the Product 31
Moving or Storing the MSD 31
To Replace the Primary Fuses 32
2 General Troubleshooting
Instrument State 36
Troubleshooting Tips and Tricks 37
General Symptoms 38
Chromatographic Symptoms 40
Mass Spectral Symptoms 45
Pressure Symptoms 49
Temperature Symptoms 52
Error Messages 54
Air Leaks 60
Contamination 61

4 5977B Series MSD Troubleshooting and Maintenance Manual
3 CI Troubleshooting
Common CI-Specific Problems 64
Troubleshooting Tips and Tricks 65
Air Leaks 66
Pressure-Related Symptoms 70
Signal-Related Symptoms 74
Tuning-Related Symptoms 83
4 General Maintenance
Before Starting 91
Maintaining the Vacuum System 96
To Separate the MSD from the 7890 GC 97
To Separate the MSD from the 9000 GC 99
To Reconnect the MSD to the 7890 GC 101
To Reconnect the MSD to the 9000 GC 102
To Move or Store the MSD when Connected to a 7890 GC 105
To Move or Store the MSD when Connected to a 9000 GC 107
To Check the Foreline Pump Fluid 109
To Drain the Foreline Pump 111
To Refill the Foreline Pump 112
To Change the Blue Oil Mist Filter on the Foreline Pump 113
To Install the Exhaust Filter on the IDP3 Dry Pump 114
To Change the Filter Cartridge on the IDP3 Dry Foreline Pump 115
To Check the DP Fluid 116
To Remove the DP 118

5977B Series MSD Troubleshooting and Maintenance Manual 5
To Replace the DP Fluid 120
To Install the DP 123
To Remove the Foreline Gauge 125
To Install the Foreline Gauge 127
To Refill the EI Calibration Vial 128
To Purge the Calibration Valves 130
To Remove the EI Calibration and Vent Valve Assembly 131
To Install the EI Calibration and Vent Valve Assembly 132
To Replace the Fan for the High Vacuum Pump 133
To Remove the Ion Vacuum Gauge 135
To Install an Ion Vacuum Gauge 136
To Lubricate the Side Plate O-Ring 137
To Lubricate the Vent Valve O-Ring 139
Maintaining the Electronics 141
To Adjust the Quad Frequency 143
To Replace the Primary Fuses 145
5 CI Maintenance
To Replace the Methane/Isobutane Gas Purifier 148
To Clean the Reagent Gas Supply Lines 149
To Refill the CI Calibrant Vial 150
6VacuumSystem
Overview 154
Vacuum System Components 155
Common Vacuum System Problems 156

6 5977B Series MSD Troubleshooting and Maintenance Manual
Foreline Pump 157
High Vacuum Pump 161
Diffusion pump system 161
Turbo pump system 161
Analyzer Chamber 162
Diffusion pump version 162
Turbo pump version 162
Side Plate 163
Vacuum Seals 166
Foreline Gauge 168
Diffusion Pump and Fan 169
Turbo Pump and Fan 175
Calibration Valves and Vent Valve 176
Micro-Ion Vacuum Gauge 179
7Analyzer
Overview 182
EI Ion Source 185
HES EI Ion Source 192
CI Ion Source 195
Filaments 199
Other Source Elements 201
Quadrupole Mass Filter 203
Detector 206
Analyzer Heaters and Radiators 208

5977B Series MSD Troubleshooting and Maintenance Manual 7
8 Electronics
GC Control Panel, Power Switch, and Front Panel LED 212
Side Board 214
Electronics Module 215
LAN/MS Control Card 219
Power Supplies 220
Back Panel and Connectors 221
High vacuum gauge connector 222
Interfacing to External Devices 224
9Parts
To Order Parts 228
Electronics 229
Vacuum System 230
Analyzer 238
Consumables and Maintenance Supplies 251

8 5977B Series MSD Troubleshooting and Maintenance Manual

9
Agilent 5977B Series MSD
Troubleshooting and Maintenance Manual
Agilent Technologies
1
Introduction
5977B Series MSD Version 10
Abbreviations Used 11
The 5977B Series MSD 13
Physical description 15
Front Panel LED 15
Vacuum gauge 15
MSD Hardware Description 16
Important Safety Warnings 19
Many internal parts of the MSD carry dangerous voltages 19
Electrostatic discharge is a threat to MSD electronics 19
Many parts are dangerously hot 20
The oil pan under the standard foreline pump can be a fire hazard 20
Hydrogen Safety 22
Dangers unique to GC/MSD operation 23
Hydrogen accumulation in an MSD 23
Precautions 26
Safety and Regulatory Certifications 28
Information 28
Symbols 29
Electromagnetic compatibility 30
Sound emission declaration 30
Cleaning/Recycling the Product 31
Moving or Storing the MSD 31
To Replace the Primary Fuses 32
This manual describes the troubleshooting and maintenance of the Agilent
Technologies 5977B Series Mass Selective Detector (MSD).It assumes
familiarity with the procedures and information detailed in the 5977B Series
MSD or 5975/77 Series for OpenLAB CDS Operation Manual, and with the
accompanying software.

10 5977B Series MSD Troubleshooting and Maintenance Manual
1Introduction
5977B Series MSD Version
The 5977B MSD is equipped with a turbomolecular (turbo) pump, and a choice
of four foreline pumps. A CI ion source includes a reagent flow control system,
a CI calibration system, and other required hardware features. The serial
number label displays a product number (Table 1) that indicates what type of
MSD you have.
Table 1 Available high vacuum pumps
Model name Product number Description Ionization mode/Type
5977B MSD Diff Pump G7080B Diffusion pump Electron ionization
(EI)/Stainless Steel
5977B MSD Turbo Pump G7081B Turbo pump Electron ionization
(EI)/Stainless Steel
5977B Inert+ EI MSD Turbo G7077B Turbo pump MSD Electron ionization
(EI)/Extractor
5977B Inert+ EI/CI MSD Turbo G7078B Turbo pump MSD Electron ionization 
(EI) /Extractor
Chemical ionization /PCI, NCI
5977B HES MSD G7079B Turbo pump Electron ionization (EI)/High
Efficiency