Agilent Technologies 5977C Series User manual

Agilent 5977C Series GC/MSD
Operating Manual

Notices
© Agilent Technologies, Inc. 2023
No partof this manual may be repro-
duced in any form or by any means
(including electronic storage and
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guage) without prior agreement and
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and international copyright laws.
Manual Part Number
G7077-90039
Edition
Second edition, June 2023
Printed in USA
Agilent Technologies, Inc.
5301 Stevens Creek Boulevard
Santa Clara, CA 95051
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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.

5977C GC/MSD Operating Manual 3
About This Manual
This manual contains information for operating and maintaining the Agilent
5977C Series Mass Selective Detector (MSD).
1“Introduction”
Chapter 1 describes general information about the 5977C Series MSDs, including
a hardware description, general safety warnings, and hydrogen safety
information.
2 “Installing 8890 GC Columns”
Chapter 2 shows you how to prepare a capillary column for use with the MSD,
install it in the GC oven, and connect it to the MSD using the GC/MSD interface.
3 “Installing Intuvo 9000 GC Columns”
Chapter 3 shows you how to install an Agilent Intuvo column, connect the flow
path from the inlet through the guard chip, bus components, and column to the
MS Tail assembly, and maintain the column guard chip.
4 “Operating in EI Mode”
Chapter 5 describes basic tasks such as setting temperatures, monitoring
pressures, tuning, venting, and pumpdown. Much of the information in this
chapter also applies to CI operation.
5 “Operating in CI Mode”
Chapter 6 describes additional tasks necessary to operate in CI mode.
6 “General Maintenance”
Chapter 7 describes maintenance procedures common to both EI and CI
instruments.
7 “CI Maintenance”
Chapter 8 describes maintenance procedures unique to CI MSDs.

4 5977C GC/MSD Operating Manual
Where to Find More Information
Accompanying your hardware and software is a comprehensive collection of
manuals, videos, user applications, and method development tools.
To access your GC Hardware Library
1Open a browser on a computer or other device that shares the same gateway
as the GC.
2Enter this URL http://xxx.xxx.xxx.xxx/info, where
xxx.xxx.xxx.xxx is the IP address or host name of the GC. For example,
Enter http://10.1.1.101/info.
3When the GC Help & Information Home screen opens, select
Knowledgebase, then scroll down and select User Manual PDFs.
4Select a GC manual from the PDF User Manuals screen.
See the Agilent 5977C CG/MS with MassHunter Quick Start document for
information on finding and installing the documentation located on these USBs.
To Install Your MS Hardware Library
Insert the memory stick into a USB port and follow the prompts.
This can be installed by anyone who has authority to copy
information onto the receiving computer.
To Install Your Software Library
Insert the memory stick into a USB port and follow the prompts.
This can be installed by anyone who has authority to copy
information onto the receiving computer.

5977C GC/MSD Operating Manual 5
Contents
About This Manual 3
Where to Find More Information 4
1Introduction
5977C Series MSD Version 12
Abbreviations Used 13
The 5977C Series MSD 15
Physical description 15
Vacuum gauge 16
MSD Hardware Description 17
Important Safety Warnings 19
Many internal parts of the MSD carry dangerous
voltages 19
Electrostatic discharge is a threat to MSD electronics 20
Many parts are dangerously hot 20
The oil pan under the foreline pump can be a fire
hazard 21
Hydrogen Safety 22
GC precautions 22
Dangers unique to GC/MSD operation 23
Hydrogen accumulation in an MSD 23
Precautions 24
Safety and Regulatory Certifications 28
Information 29
Symbols 29
Electromagnetic compatibility 30
Sound emission declaration 30
Intended Use 31

6 5977C GC/MSD Operating Manual
Cleaning/Recycling the Product 31
Accidental Liquid Spillage 31
Moving or Storing the MSD 31
To Replace the Primary Fuses 32
2 Installing 8890 GC Columns
Columns 36
Conditioning columns 36
Conditioning ferrules 37
Tips and hints 37
To Install a Capillary Column in a Split/Splitless Inlet 38
To Condition a Capillary Column 41
To Install a Capillary Column in the GC/MSD Interface Using the
Self-Tightening Column Nut 42
To Install a Capillary Column in the GC/MSD Interface Using a
Standard Column Nut 47
To Install the GC/MSD Interface Tip Seal 50
The GC/MSD Interface for an 8890 Series GC 52
3 Installing Intuvo 9000 GC Columns
Columns 56
Conditioning columns 57
Tips and hints 57
To Replace an Intuvo GC Column 59
To Replace an Intuvo 9000 GC Gasket 63
To Install a Column Guard or Jumper Chip 64
To Replace the 9000 GC/MS Tail 68
To Condition an Intuvo Capillary Column 72

5977C GC/MSD Operating Manual 7
To Install the GC/MSD Interface Tip Seal 74
The GC/MSD Interface for a 9000 Series GC 76
4OperatinginEIMode
Operating the MSD from the DS 79
Configuring the MSD through the Web User Interface
(WUI) 80
To change the network settings of the MSD 80
eModule Mini Display Readout 83
Front Panel Instrument Status LED 84
Before You Turn On the MSD 85
Pumping Down 86
Controlling Temperatures 86
Controlling Column Flow 87
Controlling JetClean Hydrogen Flow 87
Venting the MSD 88
To View MSD Temperature and Vacuum in Manual Tune 89
To Set Monitors for MSD Temperature and Vacuum
Status 91
To Set Analyzer Temperatures from the Instrument Control
View 94
To Set the GC/MSD Interface Temperature from
MassHunter 96
To Monitor High Vacuum Pressure 98
To Tune the MSD in EI Mode 100
To Set the Operation Mode for the Optional JetClean
System 102

8 5977C GC/MSD Operating Manual
To Set the JetClean Parameters for the Clean Only
Mode 103
To Verify EI System Performance 104
To Perform High-Mass Testing 105
To Open the MSD Covers 108
To Vent the MSD 109
To Pumpdown the MSD 112
5 Operating in CI Mode
General Guidelines 116
CI Autotune 117
To Operate the CI MSD 119
To Pumpdown the MSD in CI Mode 120
To Set Up the Software for CI Operation 121
To Operate the Reagent Gas Flow Control Module 123
To Set Up Methane Reagent Gas Flow 126
To Use Other Reagent Gases 128
To Perform a PCI Autotune (Methane Only) 131
To Perform an NCI Autotune (Methane Reagent Gas) 133
To Verify PCI Performance 135
To Verify NCI Performance 136
To Monitor CI Mode High Vacuum Pressure 137
6 General Maintenance
Before Starting 141
Maintaining the Vacuum System 146
Maintaining the Analyzer 147

5977C GC/MSD Operating Manual 9
To Open the Analyzer Chamber 149
To Remove the EI HES 151
To Connect/Disconnect Wiring to the EI HES 153
To Disassemble the EI HES 154
To Clean the EI HES 157
To Assemble the EI HES 160
To Remove the EI HES Filaments 165
To Install the EI HES Filament 167
To Install the EI HES 168
To Remove the EI XTR, SS, Inert, or Hydronert Source 169
To Connect/Disconnect Wiring from the EI XTR, SS, and Inert
Sources 170
To Connect/Disconnect Wiring from the EI Hydronert
Source 171
To Disassemble the EI SS or EI Inert Source 172
To Disassemble the EI XTR Source 175
To Disassemble the EI Hydronert Source 178
To Clean an EI XTR, SS, or Inert Source 181
To Clean the EI Hydronert Source 185
To Assemble an EI SS or Inert Source 188
To Assemble the EI XTR Source 191
To Assemble the EI Hydronert Source 194
To Replace a Filament in an EI XTR, SS, Inert, or Hydronert
Source 197
To Install the EI XTR, SS, Inert, or Hydronert Source 199
To Replace the Electron Multiplier Horn 200

10 5977C GC/MSD Operating Manual
To Close the Analyzer Chamber 202
7 CI Maintenance
General Information 204
To set up your MSD for CI operation 204
To Switch from the EI HES to the CI Source 205
To Remove the EI HES Radiator 206
To Connect/Disconnect Wiring to the EI HES Radiator 207
To Install the CI Source Radiator 209
To Switch from the CI Source to the EI HES 211
To Remove the CI Source Radiator 212
To Install the EI HES Radiator 214
To Switch from an EI XTR, SS, or Inert Source to the CI
Source 215
To Switch from the CI Source to an EI XTR, SS, or Inert
Source 216
To Remove the CI Source 217
To Connect/Disconnect non-HES Model Wiring from the CI
Source 218
To Connect/Disconnect EI HES Model Wiring to the CI
Source 219
To Disassemble the CI Source 220
To Clean the CI Source 223
To Assemble the CI Source 226
To Remove the CI Source Filament 229
To Install a CI Source Filament 231
To Install the CI Source 232

5977C GC/MSD Operating Manual 11
1Introduction
5977C Series MSD Version 12
Abbreviations Used 13
The 5977C Series MSD 15
MSD Hardware Description 17
Important Safety Warnings 19
Hydrogen Safety 22
Safety and Regulatory Certifications 28
Intended Use 31
Cleaning/Recycling the Product 31
Accidental Liquid Spillage 31
Moving or Storing the MSD 31
To Replace the Primary Fuses 32
This chapter describes general information about the MSD, including a hardware
description, general safety warnings, and hydrogen safety information.
If you are using the Agilent Intuvo 9000 Gas Chromatograph with your MSD,
Chemical Ionization (CI) is not currently supported.

1Introduction
5977C Series MSD Version
12 5977C GC/MSD Operating Manual
5977C Series MSD Version
The 5977C Series MSDs are equipped with a turbomolecular (turbo) pump and a
choice of three foreline pumps (Pfeiffer Duo, Pfeiffer MVP-070-3x, Agilent IDP-3
24V) or a diffusion pump paired with a Pfeiffer Duo foreline pump. There are
three types of electron ionization (EI) sources available on the 5977C Series
MSD, a standard EI stainless steel (SS) source, an EI Extractor (XTR) source
available on the Inert+ MSD model, and a high efficiency source (HES). The
optional 5977C chemical ionization (CI) system includes a positive chemical
ionization/negative chemical ionization (PCI/NCI) ion source, reagent gas flow
control system, CI calibration system, and other required hardware features. The
serial number label displays a product number that indicates what type of MSD
you have. (See Table 1.)
Table 1 Available MSD models
Model name Product number Description Ionization mode/Type
5977C MSD Diff Pump G7080B Diffusion pump EI/SS
5977C MSD Turbo Pump G7081B Turbo pump EI/SS
5977C Inert+ MSD EI Turbo G7077B Turbo pump EI/XTR
5977C EI/CI MSD G7078B Turbo pump EI/XTR
CI (PCI/NCI )
5977C HES MSD G7079B Turbo pump EI HES
field upgradeable to CI

1Introduction
Abbreviations Used
5977C GC/MSD Operating Manual 13
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
DA Data analysis
DC Direct current
DFTPP Decafluorotriphenylphosphine (calibrant)
Diff Diffusion
DIP Direct insertion probe
DS Data System
EI Electron 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)
HES High Efficiency Source. New generation EI source constructed from inert material
Inert Standard EI source constructed from inert materials
Inert+ MSD model designation equipped with an EI XTR source
id Inside diameter
LAN Local Area Network
LVDS Low-voltage differential signaling

1Introduction
Abbreviations Used
14 5977C GC/MSD Operating Manual
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
SS Stainless steel
Torr Unit of pressure, 1 mm Hg
Turbo Turbomolecular (pump)
WUI Web user interface
XTR EI Extractor source
Table 2 Abbreviations (continued)
Abbreviation Definition

1Introduction
The 5977C Series MSD
5977C GC/MSD Operating Manual 15
The 5977C Series MSD
The 5977C Series MSD is a single-quadrupole GC/MS system for use with
Agilent 8890 and 9000 GCs. The MSD features (See Table 3 on page 16):
•An optional JetClean system for cleaning the ion source in place under
vacuum
•WEB User Interface (WUI) for locally monitoring and operating the MSD
•A turbo vacuum pump with one of three different foreline pumps (Pfeiffer
Duo, Pfeiffer MVP-070-3x, Agilent IDP-3 24V) or a diffusion vacuum pump
with a Pfeiffer Duo foreline pump
•Five different types of ion sources available:
•Standard source in SS material
•Standard source in Inert material
•XTR source
•HES
•CI (PCI/NCI) source
•Turbo pump-equipped 5977C models, when used with an 8890 GC, are field
upgradeable to CI (PCI/NCI) modes. The upgrade adds a CI source, CI source
radiator for HES systems, CI flow module with an MFC, plumbing, and CI
tuning calibration.
•Independently MSD-heated hyperbolic quadrupole mass filter
•Independently MSD-heated ion source
•HED EM
•Independently GC-heated GC/MSD interface
Physical description
The 5977C Series MSD housing is approximately 41 cm high, 30 cm wide, and
54 cm deep. The weight is 39 kg for the diffusion pump mainframe, 44 kg for the
standard EI turbo pump mainframe, and 46 kg for the EI/CI turbo pump
mainframe. The foreline (roughing) pump weighs an additional 11 kg (standard
pump), and is usually located on the floor behind the MSD.
The basic components of the instrument are:
•Frame/cover assemblies
•Vacuum system

1Introduction
Vacuum gauge
16 5977C GC/MSD Operating Manual
•GC/MSD interface
•Electronics
•Analyzer
Vacuum gauge
The MSD may be equipped (or ordered) with an ion vacuum gauge. The Agilent
MassHunter GC/MS Acquisition software can be used to read the pressure (high
vacuum) in the vacuum manifold. Operation of the gauge controller is described
in this manual. The gauge is required for CI operation.
Table 3 5977C Series MSD features
Feature
High vacuum pump Diffusion Turbo
Optimal He column flow mL/min 1 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.
1.5 4
Maximum gas flow, mL/min†
† Expect degradation of spectral performance and sensitivity.
26.5
Max column id 0.25 mm (30 m) 0.53 mm (30 m)
CI capability‡
‡ Turbo pump models are field upgradeable to CI.
No Yes
Inert ion sources available Yes Yes
GC compatibility 9000 and 8890 9000 and 8890
Foreline pumps available Pfeiffer Duo Pfeiffer Duo,
Pfeiffer MVP-070-3x,
Agilent IDP-3 24V
DIP** capability (3rd party)
** Direct insertion probe.
Yes Yes

1Introduction
MSD Hardware Description
5977C GC/MSD Operating Manual 17
MSD Hardware Description
The Agilent 5977C MSD can be paired with one of several Agilent GCs (See
Figure 1).
In this manual, the term “CI MSD” refers to the G7078B MSD or to the G7077B,
G7079B, and G7081B models that were field upgraded for CI operation. It also
applies, unless otherwise specified, to the flow modules for these instruments.
The CI hardware upgrade allows the MSD to produce high-quality, classical
CI spectra, which include molecular adduct ions. A variety of reagent gases can
be used. (See Chapter 5, “Operating in CI Mode”” on page 115.)
Figure 1. 5977C Series GC/MSD system, shown with an Agilent 8890 GC
ALS
8890 GC
Touchscreen
5977C Series
MSD
MSD power switch
GC power switch
System status LED

1Introduction
MSD Hardware Description
18 5977C GC/MSD Operating Manual
The 5977C Series CI system field upgrade adds the following to the 5977C Series
MSD:
•EI/CI GC/MSD interface
•JetClean option that shares the same MFC system EI/CI GC/MSD interface
•CI source with the new common interface tip seal that can also be used with
an EI XTR source or HES
•Reagent gas MFC
•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 (G3397B) is integrated in the system. Its use is
required for CI, and it is recommended for EI also.
The CI system has been optimized to achieve the relatively high CI 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 tip seal
fits onto the ion source end of the GC/MSD interface.
Switching back and forth between CI and EI sources takes less than an hour,
however, a 1- to 2-hour wait is required to purge the reagent gas lines and bake
out water and other contaminants.

1Introduction
Important Safety Warnings
5977C GC/MSD Operating Manual 19
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
•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)
If one of the primary fuses has failed, the MSD will already be off, but for safety,
switch off the MSD and unplug the power cord. It is not necessary to allow air
into the analyzer chamber.
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.
WARNING
Never replace the primary fuses while the MSD is connected to a power
source.

1Introduction
Electrostatic discharge is a threat to MSD electronics
20 5977C GC/MSD Operating Manual
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.
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:
•GC inlets
•GC oven and its contents including the column nuts attaching the column to
a GC inlet, GC/MSD interface, or GC detector
•GC detector
•GC valve box
•Foreline pump
•Diffusion pump
•Heated MSD ion source, GC/MSD 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.
WARNING
Be careful when working behind the instrument. During cool-down cycles, the
GC emits hot exhaust which can cause burns.