Agilent Technologies 5977B Series User manual

Agilent Technologies
Agilent 5977B Series 
MSD
Operating Manual

Notices
© Agilent Technologies, Inc. 2016
No part of this manual may be reproduced in
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Manual Part Number
G7077-90026
Edition
First edition, September 2016
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.

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 7890 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 “Intuvo 9000 GC Column Maintenance”
Chapter 3 shows you how to install an Agilent Intuvo column,
connect a flow path from the column through the MS transfer
line and into the ion source, and maintain the column guard
chip.
4 “Operating in EI Mode”
Chapter 3 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 4 describes additional tasks necessary to operate in CI
mode.
6 “General Maintenance”
Chapter 5 describes maintenance procedures common to both
EI and CI instruments.

4 5977B Series MSD Operating Manual
7 “CI Maintenance”
Chapter 6 describes maintenance procedures unique to CI
MSDs.

5977B Series MSD Operating Manual 5

6 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.

5977B Series MSD Operating Manual 7
Contents
1 Introduction
5977B Series MSD Version 14
Abbreviations Used 15
The 5977B Series MSD 17
MSD Hardware Description 19
Important Safety Warnings 21
Hydrogen Safety 23
GC precautions 24
Precautions 26
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
2 Installing 7890 GC Columns
Columns 36
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/MS Interface Using the
Self-Tightening Column Nut 42
To Install a Capillary Column in the GC/MS Interface Using a
Standard Column Nut 47
To Install the Interface Tip Seal 50

8 5977B Series MSD Operating Manual
To Calibrate Column Flow Linear Velocity 52
The GC/MSD Interface for a 7890B Series GC 55
3 Intuvo 9000 GC Column Maintenance
Columns 58
Conditioning columns 59
Tips and hints 59
To Replace an Intuvo GC Column 61
To Replace an Intuvo 9000 GC Gasket 65
To Install a Column Guard or Jumper Chip 66
To Replace the 9000 GC/MS Tail 70
To Condition an Intuvo Capillary Column 74
To Install the Interface Tip Seal 76
The GC/MS Interface for a 9000 Series GC 77
4 Operating in EI Mode
Operating the MSD from the DS 80
Operating the MSD from the GC control panel 81
Configuring the MSD through the Web User Interface (WUI) 85
To change the network settings of the MSD 85
eModule Mini Display Readout 88
Front Panel Instrument Status LED 88
Before You Turn On the MSD 89
Pumping Down 90
Controlling Temperatures 90
Controlling Column Flow 90
Controlling JetClean Hydrogen Flow 91

5977B Series MSD Operating Manual 9
Venting the MSD 91
To View MSD Temperature and Vacuum in Manual Tune 93
To Set Monitors for MSD Temperature and Vacuum Status 95
To Set Analyzer Temperatures from the Instrument Control
View 98
To Set the MassHunter 7890 GC/MSD Interface Temperature
100
To Monitor High Vacuum Pressure 101
To Tune the MSD in EI Mode 104
To Set the Operation Mode for the Optional JetClean System 106
To Set the JetClean Parameters for the Clean Only Mode 107
To Verify EI System Performance 108
To Perform High-Mass Testing 109
To Open the MSD Covers 112
To Vent the MSD 113
To Pumpdown the MSD 116
5 Operating in CI Mode
General Guidelines 120
CI Autotune 121
To Operate the CI MSD 123
To Pumpdown the MSD in CI Mode 124
To Set Up the Software for CI Operation 125
To Operate the Reagent Gas Flow Control Module 127
To Set Up Methane Reagent Gas Flow 130
To Use Other Reagent Gases 132

10 5977B Series MSD Operating Manual
To Perform a PCI Autotune (Methane Only) 135
To Perform an NCI Autotune (Methane Reagent Gas) 137
To Verify PCI Performance 139
To Verify NCI Performance 140
To Monitor CI Mode High Vacuum Pressure 141
6 General Maintenance
Before Starting 144
Maintaining the Vacuum System 149
Maintaining the Analyzer 150
To Open the Analyzer Chamber 152
To Remove the EI HES 154
To Connect/Disconnect Wiring to the EI HES 156
To Disassemble the EI HES 157
To Clean the EI HES 160
To Assemble the EI HES 163
To Remove the EI HES filaments 168
To Install the EI HES Filament 170
To Install the EI HES 171
To Remove the EI XTR, SS, or Inert Source 172
To Connect/Disconnect Wiring from the EI XTR, SS, and Inert
Sources 173
To Disassemble the EI SS or EI Inert Source 174
To Disassemble the EI XTR Source 177
To Clean an EI XTR, SS, or Inert Source 180
To Assemble an EI SS or Inert Source 185

5977B Series MSD Operating Manual 11
To Assemble the EI XTR Source 188
To Replace a Filament in an EI XTR, SS, or Inert Source 191
To Install the EI XTR, SS, or Inert Source 193
To Replace the Electron Multiplier Horn 194
To Close the Analyzer Chamber 196
7 CI Maintenance
General Information 198
To set up your MSD for CI operation 198
To Switch from the EI HES to the CI Source 199
To Remove the EI HES Radiator 200
To Connect/Disconnect Wiring to the EI HES Radiator 201
To Install the CI Source Radiator 202
To Switch from the CI Source to the EI HES 204
To Remove the CI Source Radiator 206
To Install the EI HES Radiator 208
To Switch from an EI XTR, SS, or Inert Source to the CI
Source 209
To Switch from the CI Source to an EI XTR, SS, or Inert
Source 210
To Remove the CI Source 211
To Connect/Disconnect non-HES Model Wiring from the CI
Source 212
To Connect/Disconnect EI HES Model Wiring to the CI
Source 213
To Disassemble the CI Source 214
To Clean the CI Source 217

12 5977B Series MSD Operating Manual
To Assemble the CI Source 220
To Remove the CI Source Filament 223
To Install a CI Source Filament 224
To Install the CI Source 225

13
Agilent 5977B Series MSD
Operating Manual
Agilent Technologies
1
Introduction
5977B Series MSD Version 14
Abbreviations Used 15
The 5977B Series MSD 17
MSD Hardware Description 19
Important Safety Warnings 21
Hydrogen Safety 23
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 MS,
Chemical Ionization (CI) and the JetClean system are not currently supported.

1 Introduction 
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 four foreline pumps or a diffusion pump paired with a Pfeiffer DUO
2.5 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). A chemical ionization (CI) source includes a reagent
flow control system, a 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 high vacuum pumps
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 MSD EI/XTR
5977B EI/CI MSD G7078B Turbo pump MSD EI /XTR
CI /PCI, NCI
5977B HES MSD G7079B Turbo pump MSD EI HES
field upgradeable to CI

Introduction 1
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)
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

1 Introduction 
16 5977B Series MSD Operating Manual
LVDS Low-voltage differential signaling
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

Introduction 1
5977B Series MSD Operating Manual 17
The 5977B Series MSD
The 5977B Series MSD is a stand-alone capillary GC detector for use with
either an Agilent 7890B Series or an Agilent 7820 GC. The MSD features:
•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 four different foreline pumps or a
diffusion vacuum pump with a Pfeiffer DUO 2.5 foreline pump
•Four different types of independently heated EI sources available:
•Standard source in SS material
•Standard source in Inert material
•XTR source
•HES
•Turbo pump models with 7890B GCs are field upgradeable to CI (PCI/NCI)
modes. The upgrade adds an independently heated CI source, reagent gas
MFC and plumbing, and CI tuning calibration
•Independently MSD heated hyperbolic Quad
•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
•GC interface
•Electronics
•Analyzer

1 Introduction 
18 5977B Series MSD Operating Manual
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 6890/7820/7890
Series
7890 Series
Foreline pumps available Pfeiffer Duo 2.5 Pfeiffer Duo 2.5, MVP-070-3,
MVP-070-3C, IDP3 24V
DIP** capability (3rd party)
** Direct insertion probe.
Yes Ye s

Introduction 1
5977B Series MSD Operating Manual 19
MSD Hardware Description
Figure 1 5977B Series GC/MSD system, shown with an Agilent 7890B GC
ALS
7890B GC
7890B GC control panel
5977B Series
MSD
MSD power switch
GC power switch
System status LED

1 Introduction 
20 5977B Series MSD Operating Manual
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 119.)
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
insulating seal fits onto the 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. Switching from PCI to NCI requires
approximately 2 hours for the ion source to cool.