Agilent Technologies 5975 MSD User manual

Agilent Technologies
Agilent 5975/5977 MSD
for OpenLAB CDS
Operation Manual

2 5975/5977 Series MSD Operation Manual
Notices
© Agilent Technologies, Inc. 2015
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
G7077-90014
Edition
First edition, August 2015
Printed in USA, August 2015
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-
tion with the furnishing, use, or per-
formance of this document or of any
information contained herein. Should
Agilent and the user have a separate
written agreement with warranty
terms covering the material in this
document that conflict with these
terms, the warranty terms in the sep-
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.

5975/5977 Series MSD Operation Manual 3
About This Manual
This manual contains information for operating and
maintaining the Agilent 5975 through 5977 series of MSD with
OpenLAB CDS software. Agilent OpenLAB CDS is a new
operating system for Agilent instruments.
The Agilent 5977B Series Mass Selective Detector (MSD) is the
base instrument described in this manual. Agilent instruments
manufactured prior to the 5977B share many features and
hardware with this new instrument. Where older Agilent
models differ from the 5977B, that difference is usually noted.
Please refer to the operating and maintenance documentation
that was delivered with your instrument if other hardware
differences are found.
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 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 “General Maintenance”
Chapter 4 describes maintenance procedures common to both
EI and CI instruments.

4 5975/5977 Series MSD Operation Manual
Hardware User Information
5977B MSD
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.
See the Agilent 5977B MSD System Quick Start document
(G7077-90103) for more details on how to install this
information on your computer.
5975/5977 Series MSD prior to the 5977B MSD
Users of Agilent MSD instruments manufactured prior to the
5977B should refer to the documentation delivered to them
when their MSD was purchased. The information in this manual
is intended to supplement that documentation. Information
included here will help you more effectively use the OpenLAB
CDS operating system with your instruments.
Additionally, there is extensive online Help and Learning
material provided with OpenLAB.

5975/5977 Series MSD Operation Manual 5
Contents
About This Manual 3
Hardware User Information 4
5977B MSD 4
5975/5977 Series MSD prior to the 5977B MSD 4
1 Introduction
5977B Series MSD Version 10
Abbreviations Used 11
The 5977B Series MSD 13
MSD Hardware Description 15
Important Safety Warnings 16
Hydrogen Safety 18
GC precautions 18
Precautions 20
Safety and Regulatory Certifications (5977B) 23
Cleaning/Recycling the Product 26
Liquid Spillage 26
Moving or Storing the MSD 26
To Replace the Primary Fuses 27
2 Installing GC Columns
Columns 30
To Install a Capillary Column in a Split/Splitless Inlet 33
To Condition a Capillary Column 36
To Install a Capillary Column in the GC/MS Interface Using the
Self-Tightening Column Nut 37
GCMS transfer line tip seals 41

6 5975/5977 Series MSD Operation Manual
To Install a Capillary Column in the GC/MS Interface Using a
Standard Column Nut 42
3 Operating in Electron Ionization (EI) Mode
Operating the MSD from the Data System 46
Operating the MSD from the GC control panel 47
Configuring the MSD through the Web User Interface (WUI) 51
To change the network settings of the MSD 51
Operating the 5975/5977 MSD from the local control panel
(LCP) 54
Modes of operation 54
To view system status during startup 57
eModule mini display readout 61
Front Panel Instrument Status LED 61
The GC/MSD Interface 62
Before You Turn On the MSD 64
Pumping Down 65
Controlling Temperatures 65
Controlling Column Flow 65
Venting the MSD 66
Set MS Analyzer Temperatures 67
Enable the GC/MS Interface and Oven 69
View MSD Temperatures and Vacuum 70
To Calibrate Column Flow Linear Velocity 72
To Run an Autotune 74
To Open the MSD Covers 76
Vent the MSD 77

5975/5977 Series MSD Operation Manual 7
To Pump Down the MS 79
To Move or Store the MSD 82
4 General Maintenance
Before Starting 86
Maintaining the Vacuum System 91
Maintaining the Analyzer 92
To Open the Analyzer Chamber 94
To Remove the EI Ion Source 96
To Disassemble the Standard or Inert EI Ion Source 99
To Disassemble the Extractor EI Ion Source 102
To Clean the EI Ion Source 105
To Assemble a Standard or Inert EI Ion Source 110
To Assemble the Extractor EI Ion Source 113
To Replace a Filament in an EI Ion Source 116
To Install the EI Ion Source 118
To Attach Wiring from the Ion Source to the feedthrough
board 119
To Replace the Electron Multiplier Horn 122
To Close the Analyzer Chamber 125

8 5975/5977 Series MSD Operation Manual

9
Agilent 5977B Series Agilent 5975/5977 MSD for OpenLAB CDS
Operation Manual
Agilent Technologies
1
Introduction
5977B Series MSD Version 10
Abbreviations Used 11
The 5977B Series MSD 13
MSD Hardware Description 15
Important Safety Warnings 16
Hydrogen Safety 18
Safety and Regulatory Certifications (5977B) 23
Cleaning/Recycling the Product 26
Liquid Spillage 26
Moving or Storing the MSD 26
To Replace the Primary Fuses 27
This chapter describes general information about the MSD, including a
hardware description, general safety warnings, and hydrogen safety
information.

10 5975/5977 Series MSD Operation Manual
1Introduction
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 two types of EI sources, a standard stainless steel
EI source and an extraction EI source available on the Inert Plus MSD model.
A CI ion source includes a reagent flow control system, a CI calibration
system, and other required hardware features. 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
5977B MSD Diff Pump G7080B Diffusion pump Electron ionization
(EI)/Stainless Steel
5977B MSD Turbo Pump G7081B Turbo pump Electron ionization
(EI)/Stainless Steel
5977B Inert+ MSD
EI Turbo
G7077B Turbo pump MSD Electron ionization
(EI)/Extractor
5977B EI/CI MSD*G7078B Turbo pump MSD Electron ionization
(EI)/Extractor
Chemical ionization /PCI, NCI
* Operation in CI mode is not supported on the initial version of OpenLAB CDS