Agilent Technologies 5975T LTM GC/MSD Operating manual

Agilent Technologies
Agilent 5975T 
LTM GC/MSD
Troubleshooting and
Maintenance Guide

Notices
© Agilent Technologies, Inc. 2010
No part of this manual may be reproduced
in any form or by any means (including
electronic storage and retrieval or transla-
tion into a foreign language) without prior
agreement and written consent from Agi-
lent Technologies, Inc. as governed by
United States and international copyright
laws.
Manual Part Number
G4360-90008
Edition
First edition, December 2010
Printed in USA
Agilent Technologies, Inc.
5301 Stevens Creek Boulevard 
Santa Clara, CA 95052
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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 Guide 3
Contents
1 Introduction
Overview 12
Hardware Description 14
Electron Ionization (EI) systems 14
Abbreviations Used 15
Important Safety Warnings 17
Hydrogen Safety 19
Safety and Regulatory Certifications 23
Cleaning/Recycling the Product 26
Liquid Spillage 26
Moving or Storing the GC/MSD 26
2 Concepts and General Tasks
Troubleshooting Tips and Tricks 28
Rule 1: “Look for what has been changed.” 28
Rule 2: “If complex isn't working, go back to simple.” 28
Rule 3: “Divide and conquer.” 28
Concepts 29
How to troubleshoot using this manual 29
Configurable Items to Always Keep Current 30
Column configuration 30
Automatic Liquid Sampler configuration 30
Gas configuration 30
Information to Obtain Before Calling Agilent for Service 31
3 Chromatographic Symptoms
Chromatographic Symptoms 34
Retention Times Not Repeatable 35
Peak Areas Not Repeatable 36
Poor repeatability 36

4 Troubleshooting and Maintenance Guide
Contamination or Carryover 37
Isolate the source 37
Check possible causes—all inlet and detector combinations 37
Larger Peaks Than Expected 38
Peaks Not Displayed/No Peaks 39
No peaks 39
Low Boiler Peaks Present/High Boiler Peaks are Missing 41
Baseline Rise During LTM Column Temperature Program 42
Baseline is rising 42
Baseline is high 42
Baseline is falling 42
Baseline wanders 43
Poor Peak Resolution 44
Peak Tailing 45
Peaks are tailing 45
Peak Boiling Point or Molecular Weight Discrimination Poor 46
For any inlet operating in split mode 46
For any inlet operating in splitless mode 46
Sample Decomposition in Inlet/Missing Peaks 47
Peak Fronting 48
Peaks are fronting 48
Peaks have flat tops 48
Peaks have split tops 49
Noisy Signal, Including Wander, Drift, and Baseline Spikes 50
Noisy baseline 50
Baseline wander and drift 51
Baseline spiking 51
Retention times for all peaks drift – shorter 52
Retention times for all peaks drift – longer 52
Poor sensitivity 53
Low Peak Area or Height (Low Sensitivity) 54
Mass Spectral Symptoms 55
No peaks 55
Isotopes are missing or isotope ratios are incorrect 55
High background 55
High abundances at m/z 18, 28, 32, and 44 or at m/z 14 and 16 55
Mass assignments are incorrect 56
Peaks have precursors 56
Peak widths are inconsistent 56

Troubleshooting and Maintenance Guide 5
Relative abundance of m/z 502 is less than 3% 56
Spectra look different from those acquired with other MSDs 57
High mass sensitivity is poor 57
Pressure Symptoms 59
Foreline pressure is too high 59
Analyzer chamber pressure is too high (EI operation) 59
Foreline pressure is too low 60
Analyzer chamber pressure is too low 60
Gauge controller displays 9.9+9 and then goes blank 60
Power indicator on the gauge controller does not light 60
Temperature Symptoms 61
Ion source will not heat up 61
Mass filter (quad) heater will not heat up 61
GC/MSD interface will not heat up 62
Inlet will not heat up 62
LTM column module will not heat up 62
Heated guard column enclosure will not heat up 63
Analyzer Error Messages 64
Difficulty in mass filter electronics 64
Difficulty with the electron multiplier supply 64
Difficulty with the fan 64
Difficulty with the HED supply 65
Difficulty with the high vacuum pump 65
High foreline pressure 65
Internal MS communication fault 65
Lens supply fault 66
Log amplifier ADC error 66
No peaks found 66
Temperature control disabled 66
Temperature control fault 66
The high vacuum pump is not ready 67
The system is in standby 67
The system is in vent state 67
There is no emission current 68
There is not enough signal to begin tune 68
Air Leaks 69
Contamination 70
4 Not Ready Symptoms
Instrument Never Becomes Ready 74
Flow Never Becomes Ready 75

6 Troubleshooting and Maintenance Guide
Temperature Never Becomes Ready 76
Cannot Set a Flow or Pressure 77
A Gas Does Not Reach Setpoint Pressure or Flow 78
A Gas Exceeds Pressure Setpoint or Flow 79
The Inlet Pressure or Flow Fluctuates 80
Cannot Maintain a Pressure as Low as the Setpoint on a Split Inlet 81
The Measured Column Flow Does Not Equal the Displayed Flow 82
5 ALS Symptoms
Plunger Errors 84
Syringe Needle Bends During Injection into Inlet 85
6 Shutdown Symptoms
Column Shutdowns 88
Hydrogen Shutdowns 89
Thermal Shutdowns 90
7 Instrument Power On and Communication Symptoms
Instrument does not turn on 92
Foreline pump is not operating 93
MSD turns on but then the foreline pump shuts off 94
Local control panel says “No server found” 95
Instrument Turns On, Then Stops During Startup (During Self-Test) 96
PC Cannot Communicate with Instrument 97
8 Checking for Leaks
Leak Check Tips 100
To Check for External Leaks 101
To Check for Instrument Leaks 103
Leaks in Capillary Flow Fittings 104
9 Troubleshooting Tasks
To Measure a Split Vent or Septum Purge Flow 106
10 General Maintenance
Before Starting 110

Troubleshooting and Maintenance Guide 7
To Attach a Capillary Column Using SilTite Metal Fittings 114
To Disconnect Fused Silica Tubing From a SilTite Fitting 117
Maintaining the Vacuum System 118
To Check and Add Foreline Pump Oil 119
To Drain the Foreline Pump 121
To Refill the Foreline Pump 122
To Maintain the Dry Vacuum Pump 123
To Refill the EI Calibration Vial 125
To Purge the Calibration Valves 127
To Remove the EI Calibration and Vent Valve Assembly 128
To Reinstall the EI Calibration and Vent Valve Assembly 129
To Install a Micro-Ion Vacuum Gauge 130
To Remove the Micro-Ion Vacuum Gauge 132
To Lubricate the Side Plate O-Ring 133
To Lubricate the Vent Valve O-Ring 135
Maintaining the Analyzer 137
To Remove the EI Ion Source 139
To Disassemble the EI Ion Source 141
To Clean the EI Ion Source 143
To Reassemble the EI Ion Source 146
To Reinstall the EI Ion Source 148
To Remove a Filament 149
To Reinstall a Filament 151
To Remove the Heater and Sensor from the Ion Source 152
To Reinstall the Heater and Sensor in the Ion Source 154
To Remove the Heater and Sensor from the Mass Filter 155
To Reinstall the Heater and Sensor in the Mass Filter 156
To Replace the Electron Multiplier Horn 158
Maintaining the Electronics 160
To Adjust the Quad Frequency 162
To Replace the Primary Fuses 164

8 Troubleshooting and Maintenance Guide
11 Maintaining the Split/Splitless Inlet
Consumables and Parts for the Split/Splitless Inlet 168
Exploded Parts View of the Split/Splitless Inlet 171
To Clean the Septum Seat in the Insert Assembly of the Split/Splitless
Inlet 172
To Replace the Gold Seal on the Split/Splitless Inlet 174
To Replace the Filter in the Split Vent Line for the Split/Splitless
Inlet 176
To Clean the Split/Splitless Inlet 179
12 Vacuum System
Overview 182
Vacuum System Components 183
Common Vacuum System Problems 184
Foreline Pump 185
High Vacuum Pump 189
Turbo pump system 189
Analyzer Chamber 190
Turbo pump version 190
Side Plate 191
Vacuum Seals 193
Turbo Pump and Fan 195
Calibration Valve and Vent Valve 196
Micro-Ion Vacuum Gauge 198
13 Analyzer
Overview 200
EI Ion Source 202
Filaments 203
Other Source Elements 205
Quadrupole Mass Filter 207
Detector 210
Analyzer Heaters and Radiators 212
14 Electronics
Local Control Panel and Power Switch 217

Troubleshooting and Maintenance Guide 9
MSD Side Board 218
Electronics Module 219
LAN/MS Control Card 222
MSD Power Supplies 223
Side Panel Connectors 224
Interfacing to External Devices 227
15 Parts
To Order Parts 230
Electronics 231
Covers 237
Local Control Panel 238
Vacuum System 240
Analyzer 248
EI GC/MSD Interface 255
LTM System 256
Automatic Liquid Sampler 258
Reusable Shipping Containers 259
Consumables and Maintenance Supplies 260

10 Troubleshooting and Maintenance Guide