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
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
G7077-90028
Edition
First edition, September 2016
Printed in USA
Agilent Technologies, Inc.
5301 Stevens Creek Boulevard
Santa Clara, CA 95052
Warranty
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
law, Agilent disclaims all warranties,
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to this manual and any information
contained herein, including but not
limited to the implied warranties of
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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

Introduction 1
5977B Series MSD Troubleshooting and Maintenance Manual 11
Abbreviations Used
The abbreviations in Table 2 are 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
DS Data system
EI Electron impact ionization
EM Electron multiplier (detector)
EMV Electron multiplier voltage
EPC Electronic pneumatic control
eV Electron volt
FW Firmware
GC Gas chromatograph
HED High-energy dynode (refers to detector and its power supply)
HES High efficiency source
id Inside diameter
Inert+ Extractor source
LAN Local Area Network

12 5977B Series MSD Troubleshooting and Maintenance Manual
1Introduction
LCP Local control panel (on the GC)
LVDS Low voltage data signal
m/z Mass to charge ratio
MFC Mass flow controller
MSD Mass selective detector
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
5977B Series MSD Troubleshooting and Maintenance Manual 13
The 5977B Series MSD
The 5977B Series MSD is a stand-alone capillary GC detector.
The MSD features:
•GC Compatibility includes the new Agilent Intuvo 9000 GC, Agilent 7890
Series GC, the Agilent 7820 GC, or the Agilent 6850 MSD
•WEB User Interface (WUI) for locally monitoring and operating the MSD
•A turbo vacuum pump with one of four different foreline pumps
•A diffusion vacuum pump with a Pfeiffer DUO 2.5 foreline pump
•A high efficiency ion source (HES)
•Three different non-HES types of independently heated MSD
electron-ionization (EI) sources available: standard source in both stainless
steel and inert material, and an extractor source.
•Inert ion sources available
•Field upgradeable to chemical ionization (PCI/NCI) modes that add a
chemical-ionization (CI) source, reagent gas flow controller and plumbing,
and CI tuning calibration
•Independently MSD heated hyperbolic quadrupole mass filter
•High-energy dynode (HED) electron multiplier detector
•Independently GC heated GC/MSD interface
•Direct insertion probe (DIP) capability (3rd party).

14 5977B Series MSD Troubleshooting and Maintenance Manual
1Introduction
Vacuum capability
Table 3 5977B HES Series MSD features
Feature
High vacuum pump Turbo
Optimal He column flow mL/min 1 to 2
Maximum recommended 
gas flow mL/min†
† Total gas flow into the MSD: column flow plus reagent gas flow (if
applicable). Based on helium gas use. For other gases the maximum
flow will vary.
4
Maximum gas flow, mL/min*
* Expect degradation of spectral performance and sensitivity.
6.5
Max column id 0.53 mm (30 m)
CI capability‡
‡ Turbo pump models are field upgradeable to CI.
Yes
Foreline pumps available Pfeiffer Duo 2.5, MVP-070-3,
MVP-070-3C, IDP3 24V

Introduction 1
5977B Series MSD Troubleshooting and Maintenance Manual 15
Physical description
The 5977B HES Series MSD housing is approximately 41 cm high, 30 cm wide,
and 54 cm deep. The weight is 39 kg for the diffusion pump models, and 46 kg
for the EI/CI turbo pump mainframe. The weight is 41 kg for the EI turbo
pump mainframe. The standard foreline (roughing) pump weighs an
additional 11 kg (standard pump), and the dry foreline pump weighs 16 kg.
The foreline pump is usually located on the floor behind the MSD.
The basic components of the instrument are the:
•Frame/cover assemblies
•Vacuum system
•GC interface
•Electronics
•Analyzer
Front Panel LED
The front panel LED allows the operator to monitor the MSD. The LED
displays the instrument status with color codes and patterns described in “GC
Control Panel, Power Switch, and Front Panel LED” on page 212.
Vacuum gauge
The 5977B HES Series MSD may be equipped with an ion vacuum gauge. The
Data Acquisition software can be used to read the pressure (high vacuum) in
the vacuum manifold.
The gauge is required for chemical ionization (CI) operation.

16 5977B Series MSD Troubleshooting and Maintenance Manual
1Introduction
MSD Hardware Description
Figure 1 is an overview of a typical GC/MSD system.
Figure 1 Agilent 5977B Series GC/MS system
ALS
GC control panel
7890 GC
5977B Series
MSD
MSD power switch
GC power
switch
Front panel LED

Introduction 1
5977B Series MSD Troubleshooting and Maintenance Manual 17
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.
There are three types of electron ionization sources available: the standard EI
ion source, which is available in stainless steel or inert material, the extractor
EI ion source (XTR) and the high efficiency ion source (HES).
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 5977B 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 upgraded G7077B, the upgraded
G7078B, or the upgraded G7079B MSD. It also applies, unless otherwise
specified, to the flow modules for these instruments.
The 5977B Series GC/MS CI system adds the following to the 5977B Series
MSD:
•An EI/CI GC/MSD interface
•A reagent gas flow control module
•A bipolar HED power supply for PCI and NCI operation
A required methane/isobutane gas purifier is provided. It removes oxygen,
water, hydrocarbons, and sulfur compounds.
A high vacuum gauge controller (G3397B) required for CI MSD is also
recommended for EI.
The MSD CI system has been optimized to achieve the relatively high source
pressure required for CI, while still maintaining a 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.

18 5977B Series MSD Troubleshooting and Maintenance Manual
1Introduction
Changing modes
Switching back and forth between CI and EI ion 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.

Introduction 1
5977B Series MSD Troubleshooting and Maintenance Manual 19
Important Safety Warnings
There are several important safety notices to 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 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.

20 5977B Series MSD Troubleshooting and Maintenance Manual
1Introduction
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:
•GC inlets
•GC oven and its contents, including the column nuts attaching the column
to a GC inlet, GC/MS interface, or GC detector
•GC detector
•GC valve box
•Foreline pump
•Heated MSD ion source, interface, and quadrupole
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 cooldown 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.