Agilent Technologies G7035A User manual

Agilent Technologies
Agilent 5977 Series
MSD
Operation Manual

2 5977 Series MSD Operation Manual
Notices
© Agilent Technologies, Inc. 2013
No part of this manual may be reproduced in
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tronic storage and retrieval or translation
into a foreign language) without prior agree-
ment and written consent from Agilent
Technologies, Inc. as governed by United
States and international copyright laws.
Manual Part Number
G3870-90003
Edition
First edition, February 2013
Printed in USA
Agilent Technologies, Inc.
5301 Stevens Creek Boulevard
Santa Clara, CA 95051
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in future editions. Further, to the max-
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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.

Agilent 5977 Series 3
About This Manual
This manual contains information for operating and
maintaining the Agilent 5977 Series Mass Selective Detector
(MSD) systems.
1 “Introduction”
Chapter 1 describes general information about the 5977 Series
MSDs, including a hardware description, general safety
warnings, and hydrogen safety information.
2 “Installing 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 “Operating in Electron Ionization (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.
4 “Operating in Chemical Ionization (CI) Mode”
Chapter 4 describes additional tasks necessary to operate in CI
mode.
5 “General Maintenance”
Chapter 5 describes maintenance procedures common to both
EI and CI instruments.
6 “CI Maintenance”
Chapter 6 describes maintenance procedures unique to CI
MSDs.

4 5977 Series MSD Operation Manual
Online User Information
Now your Agilent instrument documentation is in one place, at
your fingertips.
The software DVD that ships with your instrument provides an
extensive collection of online help, videos, and books for the
Agilent 7890 Series GC, 7820 GC,5977 Series MSD, and the 7693A.
Included are localized versions of the information you need
most, such as:
• Getting Familiar documentation
• Safety and Regulatory guides
• Installation information
• Operating guides
• Maintenance information
• Troubleshooting details

5977 Series MSD Operation Manual 5
Contents
1 Introduction
5977 Series MSD Version 10
Abbreviations Used 11
The 5977 Series MSD 13
MSD Hardware Description 15
Important Safety Warnings 17
Hydrogen Safety 19
GC precautions 19
Precautions 22
Safety and Regulatory Certifications 24
Cleaning/Recycling the Product 27
Liquid Spillage 27
Moving or Storing the MSD 27
To Replace the Primary Fuses 28
2 Installing GC Columns
Columns 32
To Install a Capillary Column in a Split/Splitless Inlet 34
To Condition a Capillary Column 37
To Install a Capillary Column in the GC/MS Interface 38
To Prepare the Column Ends for a CFT Fitting 41
3 Operating in Electron Ionization (EI) Mode
Operating the MSD from the Data System 46
Operating the MSD from the LCP 46
Modes of operation 46

6 5977 Series MSD Operation Manual
LCP status messages 48
To view system status during startup 49
LCP menus 50
The EI GC/MSD Interface 53
Before You Turn On the MSD 55
Pumping Down 56
Controlling Temperatures 56
Controlling Column Flow 56
Venting the MSD 57
To View MSD Temperature and Vacuum in Manual Tune 58
To Set Monitors for MSD Temperature and Vacuum Status 59
To Set Analyzer Temperatures from the Instrument Control
View 61
To Set the GC/MSD Interface Temperature from MassHunter 63
To Monitor High Vacuum Pressure 64
To Calibrate Column Flow Linear Velocity 66
To Tune the MSD in EI Mode 69
To Verify System Performance 71
To Perform High-Mass Testing (5977 Series MSDs) 72
To Open the MSD Covers 75
To Vent the MSD 76
To Open the Analyzer Chamber 78
To Close the Analyzer Chamber 80
To Pump Down the MSD in EI Mode 84
To Move or Store the MSD 86

5977 Series MSD Operation Manual 7
4 Operating in Chemical Ionization (CI) Mode
General Guidelines 90
The CI GC/MSD Interface 91
CI Autotune 93
To Operate the CI MSD 95
To Switch from the Standard or Inert EI ion source to the CI Ion
Source 96
To Switch from the Extractor EI Ion Source to the CI Ion
Source 97
To Pump Down the MSD in CI Mode 98
To Set Up the Software for CI Operation 99
To Operate the Reagent Gas Flow Control Module 101
To Set Up Methane Reagent Gas Flow 104
To Use Other Reagent Gases 106
To Switch from the CI Ion Source to the Standard or Inert EI Ion
Source 109
To Switch from the CI Ion Source to the Extractor EI Ion
Source 110
To Perform a PCI Autotune (Methane Only) 111
To Perform an NCI Autotune (Methane Reagent Gas) 113
To Verify PCI Performance 115
To Verify NCI Performance 116
To Monitor CI Mode High Vacuum Pressure 117
5 General Maintenance
Before Starting 120
Maintaining the Vacuum System 125

8 5977 Series MSD Operation Manual
Maintaining the Analyzer 126
To Remove the EI Ion Source 128
To Disassemble the Standard or Inert EI Ion Source 131
To Disassemble the Extractor EI Ion Source 134
To Clean the EI Ion Source 137
To Assemble a Standard or Inert EI Ion Source 142
To Assemble the Extractor EI Ion Source 145
To Replace a Filament in an EI Ion Source 148
To Install the EI Ion Source 150
To Replace the Electron Multiplier Horn 151
6 CI Maintenance
General Information 154
To set up your MSD for CI operation 154
To Install the CI/Extractor Interface Tip Seal 155
To Remove the CI Ion Source 157
To Disassemble the CI Ion Source 159
To Clean the CI Ion Source 162
To Assemble the CI Ion Source 164
To Install the CI Ion Source 167
To Replace a Filament in a CI Ion Source 168

9
Agilent 5977 Series MSD
Operation Manual
Agilent Technologies
1
Introduction
5977 Series MSD Version 10
Abbreviations Used 11
The 5977 Series MSD 13
MSD Hardware Description 15
Important Safety Warnings 17
Hydrogen Safety 19
Safety and Regulatory Certifications 24
Cleaning/Recycling the Product 27
Liquid Spillage 27
Moving or Storing the MSD 27
To Replace the Primary Fuses 28
This chapter describes general information about the 5977 Series MSDs,
including a hardware description, general safety warnings, and hydrogen
safety information.

10 5977 Series MSD Operation Manual
1Introduction
5977 Series MSD Version
5977 Series MSDs are equipped with a high performance turbomolecular
(turbo) pump or a diffusion pump, and a choice of three foreline pumps. In
addition, there are two types of analyzers (stainless steel or inert) and four
types of ion sources. The serial number label displays a product number
(Table 1) that indicates what type of MSD you have.
Table 1 Available high vacuum pumps
Model name Product number Description Ionization mode/Type
5977E MSD Diff Pump for 7820 GC G7035A Diffusion pump Electron ionization
(EI)/Stainless Steel
5977E MSD Turbo Pump for 7820 GC G7036A Performance Turbo pump Electron ionization
(EI)/Stainless Steel
5977A VL inert MSD
EI Diffusion Pump for 7890 Series GC
G7037A Diffusion pump MSD Electron ionization (EI) /Inert
5977A inert MSD EI Turbo for
7890 Series GC
G7038A Performance turbo pump
MSD
Electron ionization (EI) /Inert
5977A extractor MSD EI Perf Turbo
for 7890 Series GC
G7039A Performance turbo pump
MSD
Electron ionization
(EI)/Extractor
5977A EI/CI MSD for 7890 Series GC G7040A Performance turbo pump
MSD
Electron ionization
(EI) /Extractor
Chemical ionization /PCI, NCI