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
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
merchantability and fitness for a par-
ticular purpose. Agilent shall not be
liable for errors or for incidental or
consequential damages in connection
with the furnishing, use, or perfor-
mance of this document or of any
information contained herein. Should
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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 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

11
Agilent 5975T LTM GC/MSD
Troubleshooting and Maintenance Guide
Agilent Technologies
1
Introduction
Overview 12
Hardware Description 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
This manual describes the troubleshooting and maintenance of
the Agilent Technologies 5975T LTM GC/MSD. It assumes
familiarity with the procedures and information detailed in the
5975T LTM GC/MSD Operation Manual and with the Agilent
MSD ChemStation software.

12 Troubleshooting and Maintenance Guide
1Introduction
Overview
The 5975T LTM GC/MSD is a stand-alone instrument combining
a GC and an MSD (Table 1). The instrument features:
•LTM GC column with rapid heating and cooling capabilities
•Two capillary guard columns to minimize contamination of
the LTM column
•Local Control Panel (LCP) for locally monitoring the
instrument
•Choice of foreline pump - rotary vane (wet), scroll (dry), or
diaphragm (dry)
•Heated electron-ionization ion source
•Heated hyperbolic quadrupole mass filter
•High-energy dynode (HED) electron multiplier detector
•Heated GC/MSD interface
•ChemStation control for operating the GC/MSD
Physical description
The 5975T LTM GC/MSD is a rectangular box, approximately
41 cm high, 60 cm wide, and 54 cm deep. The weight is 46.5 kg
for the mainframe. The attached foreline (roughing) pump
weighs an additional 15 kg (standard pump) for wet and 4.5 kg
for dry.
The basic components of the instrument are: the frame/cover
assemblies, the local control panel, the vacuum system, the
EPC, the GC/MSD interface, the split/splitless inlet, the LTM
column module, the electronics, and the analyzer.
Local control panel
The local control panel displays the status of the instrument,
displays error messages, and allows setting and display of some
instrument parameters for the Agilent 5975T LTM GC/MSD.
These parameters are normally controlled using the Agilent
ChemStation.
Vacuum gauge
The 5975T LTM GC/MSD may be equipped with an optional
external vacuum gauge. Installation of the gauge controller is
described in this manual. Operation of the vacuum gauge is
described in the 5975T LTM GC/MSD Operation Manual.

Introduction 1
Troubleshooting and Maintenance Guide 13
Tab le 1 5975T LTM GC/MSD model and features
Model G3880A
Feature
High vacuum pump Standard turbo
Optimal He column flow mL/min 1.2
Maximum recommended gas flow mL/min*
* Total gas flow into the MSD: column flow.
2.0
Maximum gas flow, mL/min†
† Expect degradation of spectral performance and sensitivity.
2.4
Max column id 0.32 mm
(30 m)

14 Troubleshooting and Maintenance Guide
1Introduction
Hardware Description
Figure 1 is an overview of a typical 5975T LTM GC/MSD system.
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.
Figure 1 5975T LTM GC/MSD system
Local control
panel
MSD door
Power switch
LTM door

Introduction 1
Troubleshooting and Maintenance Guide 15
Abbreviations Used
The abbreviations in Table 2 are used in discussing this
product. They are collected here for convenience.
Tab le 2 Abbreviations
Abbreviatio
n
Definition
AC Alternating current
ALS Automatic liquid sampler
BFB Bromofluorobenzene (calibrant)
CFT Capillary flow technology
DC Direct current
DFTPP Decafluorotriphenylphosphine (calibrant)
DIP Direct insertion probe
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)
LTM Low thermal mass
m/z Mass to charge ratio
MFC Mass flow controller
MSD Mass selective detector
OFN Octafluoronaphthalene (calibrant)
PFHT 2,4,6-tris(perfluoroheptyl)-1,3,5-triazine (calibrant)
PFTBA Perfluorotributylamine (calibrant)
Quad Quadrupole mass filter
RF Radio frequency

16 Troubleshooting and Maintenance Guide
1Introduction
RFPA Radio frequency power amplifier
Torr Unit of pressure, 1 mm Hg
Turbo Turbomolecular (pump)
Tab le 2 Abbreviations (continued)
Abbreviatio
n
Definition

Introduction 1
Troubleshooting and Maintenance Guide 17
Important Safety Warnings
There are several important safety notices to always keep in
mind when using the GC/MSD.
Many internal parts of the GC/MSD carry dangerous voltages
If the GC/MSD is connected to a power source, even if the power
switch is off, potentially dangerous voltages exist on:
•The wiring between the GC/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, or inlet).
Electrostatic discharge is a threat to GC/MSD electronics
The printed circuit boards in the GC/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
instrument side covers.
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 inlet
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.

18 Troubleshooting and Maintenance Guide
1Introduction
•The guard column heated zone and its contents
•The guard column nuts attaching the guard columns to the
inlet, LTM column, and MSD.
•The foreline pump
Always cool these areas of the system to room temperature
before working on them. 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
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.

Introduction 1
Troubleshooting and Maintenance Guide 19
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.
WARNING
The use of hydrogen as a 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 guard column heated zone and
create an explosion hazard. Therefore, be sure that the supply is
turned off until all connections are made and ensure that the inlet,
MSD, and 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.

20 Troubleshooting and Maintenance Guide
1Introduction
Dangers unique to GC/MSD operation
Hydrogen presents a number of dangers. Some are general,
others are unique to GC or GC/MSD operation. Dangers include,
but are not limited to:
•Combustion of leaking hydrogen.
•Combustion due to rapid expansion of hydrogen from a
high-pressure cylinder.
•Accumulation of hydrogen in the guard column heated zone
and subsequent combustion.
•Accumulation of hydrogen in the MSD and subsequent
combustion.
Hydrogen accumulation in a GC/MSD
All users should be aware of the mechanisms by which
hydrogen can accumulate (Table 3) and know what precautions
to take if they know or suspect that hydrogen has accumulated.
Note that these mechanisms apply to all mass spectrometers,
including the GC/MSD.
WARNING
The instrument 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.
Tab le 3 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.