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
retrieval or translation into a foreign lan-
guage) without prior agreement and
written consent from Agilent Technolo-
gies, Inc. as governed by United States
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