Agilent Technologies MSD 5977B Series User manual

Agilent 5977B Series MSD
Operating Manual

Notices
© Agilent Technologies, Inc. 2019
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Manual Part Number
G7077-90034
Edition
First edition, January 2019
Printed in USA
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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.


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

5977B Series MSD Operating Manual 11
To Connect/Disconnect non-HES Model Wiring from the CI
Source 236
To Connect/Disconnect EI HES Model Wiring to the CI
Source 237
To Disassemble the CI Source 238
To Clean the CI Source 241
To Assemble the CI Source 244
To Remove the CI Source Filament 247
To Install a CI Source Filament 249
To Install the CI Source 250

12 5977B Series MSD Operating Manual

5977B Series MSD Operating Manual 13
1Introduction
5977B Series MSD Version 14
Abbreviations Used 15
The 5977B Series MSD 17
MSD Hardware Description 19
Important Safety Warnings 21
Hydrogen Safety 24
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
5977B Series MSD Version
14 5977B Series MSD Operating Manual
5977B Series MSD Version
The 5977B 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 5977B 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 5977B
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
5977B MSD Diff Pump G7080B Diffusion pump EI/SS
5977B MSD Turbo Pump G7081B Turbo pump EI/SS
5977B Inert+ MSD EI Turbo G7077B Turbo pump EI/XTR
5977B EI/CI MSD G7078B Turbo pump EI/XTR
CI (PCI/NCI )
5977B HES MSD G7079B Turbo pump EI HES
field upgradeable to CI

1Introduction
Abbreviations Used
5977B Series MSD Operating Manual 15
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
16 5977B Series 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 5977B Series MSD
5977B Series MSD Operating Manual 17
The 5977B Series MSD
The 5977B Series MSD is a single-quadrupole GC/MS system for use with 
Agilent 8890, 9000, or 7890 GCs. The MSD features (See Table 3 on page 18):
•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 5977B models, when used with an 8890 or 7890 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 5977B 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
18 5977B Series 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 5977B 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 9000/8890/
8860/7890 Series
9000/8890/
8860/7890 Series
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
5977B Series MSD Operating Manual 19
MSD Hardware Description
The Agilent 5977B 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 6, “Operating in CI Mode”” on page 143.)
Figure 1. 5977B Series GC/MSD system, shown with an Agilent 8890 GC
ALS
8890 GC
Touchscreen
5977B Series
MSD
MSD power switch
GC power switch
System status LED

1Introduction
MSD Hardware Description
20 5977B Series MSD Operating Manual
The 5977B Series CI system field upgrade adds the following to the 5977B 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.