Agilent Technologies MSD 5977B Series User manual

Agilent 5977B Series MSD
Operating Manual

Notices
© Agilent Technologies, Inc. 2019
No part of 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
G7077-90034
Edition
First edition, January 2019
Printed in USA
Agilent Technologies, Inc.
5301 Stevens Creek Boulevard 
Santa Clara, CA 95051
Warranty
The material contained in this docu-
ment is provided “as is,” and is subject
to being changed, without notice, in
future editions. Further, to the maxi-
mum 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 lim-
ited to the implied warranties of mer-
chantability and fitness for a particular
purpose. Agilent shall not be liable for
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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 Operating Manual 3
About This Manual
This manual contains information for operating and maintaining the Agilent
5977B Series Mass Selective Detector (MSD).
1“Introduction”
Chapter 1 describes general information about the 5977B 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 “Installing 7890 GC Columns”
Chapter 4 describes how to install a capillary column into a 7890 GC oven,
connect to the MSD through the GC/MSD interface, condition the column, and
calibrate the column flow.
5 “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.
6 “Operating in CI Mode”
Chapter 6 describes additional tasks necessary to operate in CI mode.
7 “General Maintenance”
Chapter 7 describes maintenance procedures common to both EI and CI
instruments.
8 “CI Maintenance”
Chapter 8 describes maintenance procedures unique to CI MSDs.


4 5977B Series MSD Operating Manual
Hardware User Information
Accompanying your hardware and software is a comprehensive collection of
manuals, videos, user applications, and method development tools. These are
located on the:
•Agilent GC and GC/MS User Manuals and Tools DVD set
•Agilent GC/MS Software Information and Manuals memory stick
See the Agilent 5977B MSD with MassHunter Quick Start document for
information on finding and installing the documentation located on this USB and
DVDs.
To Install Your Hardware Library
Insert Disk 1 into your DVD drive 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.
©2013 Agilent Technologies,Inc.
Allrights reserved.
Madein USA
Agilent Technologies
GC/GCMS Hardware User Manuals and Videos
S1
Disk2/3
Toinstall:
1.Insert disk into DVD drive
2.Follow the instructions on the screen.
3.If autoplay is not enabled, double-click
"index_xx.html" on the DVD
wherexxis:
enfor English
chfor中文
jpfor 日本語
VersionB.01.05
January,2013
©2013 Agilent Technologies,Inc.
Allrights reserved.
Madein USA
Agilent Technologies
GC/GCMS Hardware User Manuals and Videos
S1
Disk2/3
Toinstall:
1.Insert disk into DVD drive
2.Follow the instructions on the screen.
3.If autoplay is not enabled, double-click
"index_xx.html" on the DVD
wherexxis:
enfor English
chfor中文
jpfor 日本語
VersionB.01.05
January,2013

5977B Series MSD Operating Manual 5
Contents
About This Manual 3
Hardware User Information 4
1Introduction
5977B Series MSD Version 14
Abbreviations Used 15
The 5977B Series MSD 17
Physical description 17
Vacuum gauge 18
MSD Hardware Description 19
Important Safety Warnings 21
Many internal parts of the MSD carry dangerous
voltages 21
Electrostatic discharge is a threat to MSD electronics 22
Many parts are dangerously hot 22
The oil pan under the foreline pump can be a fire
hazard 23
Hydrogen Safety 24
GC precautions 24
Dangers unique to GC/MSD operation 25
Hydrogen accumulation in an MSD 25
Precautions 26
Safety and Regulatory Certifications 28
Information 29
Symbols 29
Electromagnetic compatibility 30
Sound emission declaration 30
Intended Use 31

6 5977B Series 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

5977B Series MSD Operating Manual 7
To Install the GC/MSD Interface Tip Seal 74
The GC/MSD Interface for a 9000 Series GC 76
4 Installing 7890 GC Columns
Columns 78
Conditioning columns 79
Conditioning ferrules 79
Tips and hints 79
To Install a Capillary Column in a Split/Splitless Inlet 80
To Condition a Capillary Column 83
To Install a Capillary Column in the GC/MSD Interface Using the
Self-Tightening Column Nut 84
To Install a Capillary Column in the GC/MSD Interface Using a
Standard Column Nut 89
To Install the GC/MSD Interface Tip Seal 93
To Calibrate Column Flow Linear Velocity in a 7890 GC 95
The GC/MSD Interface for a 7890B Series GC 98
5OperatinginEIMode
Operating the MSD from the DS 103
Operating the MSD from the 7890 GC Control Panel 104
Configuring the MSD through the Web User Interface
(WUI) 108
To change the network settings of the MSD 108
eModule Mini Display Readout 111
Front Panel Instrument Status LED 112
Before You Turn On the MSD 113
Pumping Down 114

8 5977B Series MSD Operating Manual
Controlling Temperatures 114
Controlling Column Flow 115
Controlling JetClean Hydrogen Flow 115
Venting the MSD 116
To View MSD Temperature and Vacuum in Manual
Tune 117
To Set Monitors for MSD Temperature and Vacuum
Status 119
To Set Analyzer Temperatures from the Instrument Control
View 122
To Set the GC/MSD Interface Temperature from
MassHunter 124
To Monitor High Vacuum Pressure 125
To Tune the MSD in EI Mode 127
To Set the Operation Mode for the Optional JetClean
System 129
To Set the JetClean Parameters for the Clean Only
Mode 130
To Verify EI System Performance 131
To Perform High-Mass Testing 132
To Open the MSD Covers 135
To Vent the MSD 136
To Pumpdown the MSD 139
6 Operating in CI Mode
General Guidelines 144
CI Autotune 145
To Operate the CI MSD 147

5977B Series MSD Operating Manual 9
To Pumpdown the MSD in CI Mode 148
To Set Up the Software for CI Operation 149
To Operate the Reagent Gas Flow Control Module 151
To Set Up Methane Reagent Gas Flow 154
To Use Other Reagent Gases 156
To Perform a PCI Autotune (Methane Only) 159
To Perform an NCI Autotune (Methane Reagent Gas) 161
To Verify PCI Performance 163
To Verify NCI Performance 164
To Monitor CI Mode High Vacuum Pressure 165
7 General Maintenance
Before Starting 168
Maintaining the Vacuum System 173
Maintaining the Analyzer 174
To Open the Analyzer Chamber 176
To Remove the EI HES 178
To Connect/Disconnect Wiring to the EI HES 180
To Disassemble the EI HES 181
To Clean the EI HES 184
To Assemble the EI HES 187
To Remove the EI HES filaments 192
To Install the EI HES Filament 194
To Install the EI HES 195
To Remove the EI XTR, SS, or Inert Source 196

10 5977B Series MSD Operating Manual
To Connect/Disconnect Wiring from the EI XTR, SS, and Inert
Sources 197
To Disassemble the EI SS or EI Inert Source 198
To Disassemble the EI XTR Source 201
To Clean an EI XTR, SS, or Inert Source 204
To Assemble an EI SS or Inert Source 209
To Assemble the EI XTR Source 212
To Replace a Filament in an EI XTR, SS, or Inert Source 215
To Install the EI XTR, SS, or Inert Source 217
To Replace the Electron Multiplier Horn 218
To Close the Analyzer Chamber 220
8 CI Maintenance
General Information 222
To set up your MSD for CI operation 222
To Switch from the EI HES to the CI Source 223
To Remove the EI HES Radiator 224
To Connect/Disconnect Wiring to the EI HES Radiator 225
To Install the CI Source Radiator 227
To Switch from the CI Source to the EI HES 229
To Remove the CI Source Radiator 230
To Install the EI HES Radiator 232
To Switch from an EI XTR, SS, or Inert Source to the CI
Source 233
To Switch from the CI Source to an EI XTR, SS, or Inert
Source 234
To Remove the CI Source 235