Agilent Technologies 5975 Series User manual

Agilent Technologies
Agilent 5975
Series MSD
Operation Manual
for MassHunter

2 5975 Series MSD Operation Manual
Notices
© Agilent Technologies, Inc. 2013
No part of this manual may be reproduced in
any form or by any means (including elec-
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
G3170-90056
Edition
First edition, February 2013
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 sub-
ject to being changed, without notice,
in future editions. Further, to the max-
imum 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
limited to the implied warranties of
merchantability and fitness for a par-
ticular purpose. Agilent shall not be
liable for errors or for incidental or
consequential damages in connec-
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arate agreement shall control.
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.

5975 Series MSD Operation Manual for MassHunter 3
About This Manual
This manual contains information for operating and
maintaining the Agilent 5975 Series Gas Chromatograph/Mass
Selective Detector (GC/MSD) system.
1 “Introduction”
Chapter 1 describes general information about the 5975 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 Impact (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.
A “Chemical Ionization Theory”
Appendix A is an overview of chemical ionization theory.

4 5975 Series MSD Operation Manual for MassHunter
Online User Information
Now your Agilent instrument documentation is in one place, at
your fingertips.
The Instrument Utilities DVD that ships with your instrument
provides an extensive collection of online help, videos, and
books for the Agilent 7890A GC, 7820A GC, 6890N GC,6850 GC, 5975
Series MSD, 7693A ALS, and the 7683B ALS. Included are localized
versions of the information you need most, such as:
• Getting Familiar documentation
• Safety and Regulatory guides
• Site Preparation checklists
• Installation information
• Operating guides
• Maintenance information
• Troubleshooting details

5975 Series MSD Operation Manual for MassHunter 5
Contents
1 Introduction
5975 MSD Version 12
Abbreviations Used 13
The 5975 Series MSD 15
CI MSD Hardware Description 17
Important Safety Warnings 19
Hydrogen Safety 21
GC precautions 21
Safety and Regulatory Certifications 26
Cleaning/Recycling the Product 29
Liquid Spillage 29
Moving or Storing the MSD 29
2 Installing GC Columns
Columns 32
To Reconfigure a 6850 GC Column on its Basket 34
To Prepare a Capillary Column for Installation 39
To Install a Capillary Column in a Split/Splitless Inlet 41
To Condition a Capillary Column 43
To Install a Capillary Column in the GC/MSD Interface 45
Agilent 7890A and 7820A, and 6890 GCs 45
6850 GC 47
3 Operating in Electron Impact (EI) Mode
Operating the MSD from the Data System 53

5975 Series MSD Operation Manual for MassHunter 6
Operating the MSD from the LCP 53
Modes of operation 53
LCP Status Messages 55
ChemStation Loading <timestamp> 55
Executing <type>tune 55
Instrument Available <timestamp> 55
Loading Method <method name> 55
Loading MSD Firmware 55
Loading OS 56
<method> Complete <timestamp> 56
Method Loaded <method name> 56
MS locked by <computer name> 56
Press Sideplate 56
Run: <method> Acquiring <datafile> 56
To view system status during startup 56
LCP Menus 57
The EI GC/MSD Interface 60
Before You Turn On the MSD 62
Pumping Down 63
Controlling Temperatures 63
Controlling Column Flow 64
Venting the MSD 65
To View MSD Temperature and Vacuum in Manual Tune 66
To Set Monitors for MSD Temperature and Vacuum Status 67
To Set Analyzer Temperatures from the Instrument Control
View 69
To Set the GC/MSD Interface Temperature from MassHunter 71
To Monitor High Vacuum Pressure 72

5975 Series MSD Operation Manual for MassHunter 7
To Calibrate Column Flow Linear Velocity 74
To Tune the MSD in EI Mode 77
To Verify System Performance 79
To Perform High-Mass Testing (5975 Series MSDs) 80
To Remove the MSD Covers 83
To Vent the MSD 85
To Open the Analyzer Chamber 88
To Close the Analyzer Chamber 91
To Pump Down the MSD in EI Mode 95
To Move or Store the MSD 97
To Set the Interface Temperature from the GC 99
4 Operating in Chemical Ionization (CI) Mode
General Guidelines 102
The CI GC/MSD Interface 103
To Operate the CI MSD 105
To Switch from the EI Source to the CI Source 106
To Pump Down the MSD in CI Mode 107
To Set Up the Software for CI Operation 108
To Operate the Reagent Gas Flow Control Module 110
To Set Up Methane Reagent Gas Flow 114
To Use Other Reagent Gases 117
To Switch from the CI Source to the EI Source 121
CI Autotune 122
To Perform a PCI Autotune (Methane Only) 124

5975 Series MSD Operation Manual for MassHunter 8
To Perform an NCI Autotune (Methane Reagent Gas) 126
To Verify PCI Performance 128
To Verify NCI Performance 129
To Monitor CI Mode High Vacuum Pressure 130
5 General Maintenance
Before Starting 134
Maintaining the Vacuum System 139
To Replace the Primary Fuses 140
To Remove the EI Ion Source 142
To Disassemble the EI Source 144
To Clean the EI Source 146
To Assemble an EI Source 149
To Replace a Filament in an EI Source 152
To Reinstall the EI Ion Source 154
To Replace the Electron Multiplier Horn 156
6 CI Maintenance
General Information 160
To Set Up Your MSD for CI Operation 161
To Install the CI Ion Source 162
To Install the CI Interface Tip Seal 164
To Remove the CI Source 165
To Disassemble the CI Source 167
To Clean the CI Source 169
To Assemble the CI Source 171

5975 Series MSD Operation Manual for MassHunter 9
To Replace a Filament in a CI Source 173
A Chemical Ionization Theory
Chemical Ionization Overview 176
Positive CI Theory 178
Negative CI Theory 185

10 5975 Series MSD Operation Manual for MassHunter