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
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
G3870-90003
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-
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ject to being changed, without notice,
in future editions. Further, to the max-
imum extent permitted by applicable
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either express or implied, with regard
to this manual and any information
contained herein, including but not
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Agilent and the user have a separate
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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.

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

Introduction 1
5977 Series MSD Operation Manual 11
Abbreviations Used
The abbreviations in Table 2are 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
DC Direct current
DFTPP Decafluorotriphenylphosphine (calibrant)
DIP Direct insertion probe
DP Diffusion pump
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)
id Inside diameter
LAN Local Area Network
LCP Local control panel (on the MSD)
m/z Mass to charge ratio
MFC Mass flow controller
MSD Mass selective detector

12 5977 Series MSD Operation Manual
1Introduction
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
Torr Unit of pressure, 1 mm Hg
Turbo Turbomolecular (pump)
Table 2 Abbreviations (continued)
Abbreviation Definition

Introduction 1
5977 Series MSD Operation Manual 13
The 5977 Series MSD
The 5977 Series MSD is a stand-alone capillary GC detector for use with an
Agilent Series Gas Chromatograph (Table 3on page 14). The MSD features:
•Local control panel (LCP) for locally monitoring and operating the MSD
•One of two different high vacuum pumps
•One of three different foreline pumps
•Three different types of independently MSD heated electron-ionization (EI)
sources available: standard (stainless), inert, and extraction
•Optional chemical ionization (PCI/NCI) modes available that add a
chemical-ionization (CI) source, reagent gas flow controller and plumbing,
and CI tuning calibration
•Independently MSD heated hyperbolic quadrupole mass filter
•High-energy dynode (HED) electron multiplier detector
•Independently GC heated GC/MSD interface
Physical description
The 5977 Series MSD housing is approximately 41 cm high, 30 cm wide, and
54 cm deep. The weight is 39 kg for the diffusion pump models, 44 kg for the
standard EI performance turbo pump mainframe, and 46 kg for the EI/CI
performance 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: the frame/cover assemblies, the
local control panel, the vacuum system, the GC interface, the electronics, and
the analyzer.
Local control panel
The local control panel allows local monitoring and operation of the MSD. You
can tune the MSD, run a method or a sequence, and monitor instrument
status.

14 5977 Series MSD Operation Manual
1Introduction
Vacuum gauge
The 5977 Series MSD may be equipped with an ion vacuum gauge. The
MassHunter Data 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 chemical ionization (CI) operation.
Table 3 5977 series MSD models and features
Model
Feature G7035A G7036A G7037A G7038A G7039A G7040A
High vacuum pump Diffusion Performance
turbo
Diffusion Performance
turbo
Performance
turbo
Performance
turbo
Optimal He column flow
mL/min
1 1 to 2 1 1 to 2 1 to 2 1 to 2
Maximum recommended
gas flow mL/min*
1.5 4 1.5 4 4 4
Maximum gas flow, mL/min†2 6.5 2 6.5 6.5 6.5
Max column id 0.25 mm
(30 m)
0.53 mm
(30 m)
0.25 mm
(30 m)
0.53 mm
(30 m)
0.53 mm
(30 m)
0.53 mm
(30 m)
CI capability No No No No No Yes
Inert material No No Yes Yes No No
GC compatibility 7820 7820 7890 Series 7890 Series 7890 Series 7890 Series
Separate interface tip seal No No No No Yes Yes
Foreline pumps available DS42
MVP55
DS42,
MVP55
DS42,
MVP55
DS42, DS42i,
MVP55
IDP3-C
DS42i,
MVP55,
IDP3-C
DS42i,
MVP55,
IDP3-C
DIP‡capability (3rd party) Yes Yes Yes Yes Yes Yes
* Total gas flow into the MSD: column flow plus reagent gas flow (if applicable).
† Expect degradation of spectral performance and sensitivity.
‡ Direct insertion probe.

Introduction 1
5977 Series MSD Operation Manual 15
MSD Hardware Description
Figure 1 5977 Series GC/MSD system, shown with Agilent 7890B GC
ALS
7890B GC
Local control
panel
5977 Series
MSD
MSD power
switch
GC power switch

16 5977 Series MSD Operation Manual
1Introduction
The CI hardware allows the 5977 Series MSD to produce high-quality, classical
CI spectra, which include molecular adduct ions. A variety of reagent gases
can be used.
In this manual, the term “CI MSD” refers to the G7040A MSD and upgraded
G7038A and G7039A MSDs. It also applies, unless otherwise specified, to the
flow modules for these instruments.
The 5977 Series CI system adds to the 5977 Series MSD:
•EI/CI GC/MSD interface
•CI ion source with an interface tip seal that can also be used with and
extractor EI ion source
•Reagent gas flow control module
•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 MSD and is recommended for EI also.
The MSD CI system has been optimized to achieve the relatively high CI ion
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 ion sources takes less than an
hour, although 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.

Introduction 1
5977 Series MSD Operation Manual 17
Important Safety Warnings
There are several important safety notices to always keep in mind when using
the MSD.
Many internal parts of the MSD carry dangerous voltages
If the MSD is connected to a power source, even if the power switch is off,
potentially dangerous voltages exist on:
•The wiring between the MSD power cord and the AC power supply, the AC
power supply itself, and the wiring from the AC power supply to the power
switch.
With the power switch on, potentially dangerous voltages also exist on:
•All electronics boards in the instrument
•The internal wires and cables connected to these boards
•The wires for any heater (oven, detector, inlet, or valve box)
If one of the primary fuses has failed, the MSD will already be off, but for
safety you should switch off the MSD and unplug the power cord. It is not
necessary to allow air into the analyzer chamber.
Electrostatic discharge is a threat to MSD electronics
The printed circuit boards in the MSD can be damaged by electrostatic
discharge. Do not touch any of the boards unless it is absolutely necessary. If
you must handle them, wear a grounded wrist strap and take other antistatic
precautions.
WARNING All these parts are shielded by covers. With the covers in place, it should be difficult
to accidentally make contact with dangerous voltages. Unless specifically
instructed to, never remove a cover unless the detector, inlet, or oven are turned off.
WARNING If the power cord insulation is frayed or worn, the cord must be replaced. Contact
your Agilent service representative.
WARNING Never replace the primary fuses while the MSD is connected to a power source.

18 5977 Series MSD Operation Manual
1Introduction
Many parts are dangerously hot
Many parts of the GC/MSD operate at temperatures high enough to cause
serious burns. These parts include but are not limited to:
•The GC inlets
•The GC oven and its contents including the column nuts attaching the
column to a GC inlet, GC/MS interface, or GC detector
•The GC detector
•The GC valve box
•The foreline pump
•The heated MSD ion source, interface, and quadrupole
Always cool these areas of the system to room temperature before working on
them. They will cool faster if you first set the temperature of the heated zone
to room temperature. Turn the zone off after it has reached the setpoint. If you
must perform maintenance on hot parts, use a wrench and wear gloves.
Whenever possible, cool the part of the instrument that you will be
maintaining before you begin working on it.
The oil pan under the standard foreline pump can be a fire hazard
Oily rags, paper towels, and similar absorbents in the oil pan could ignite and
damage the pump and other parts of the MSD.
WARNING Be careful when working behind the instrument. During cool-down cycles, the GC
emits hot exhaust which can cause burns.
WARNING The insulation around the GC inlets, detectors, valve box, and the insulation cups is
made of refractory ceramic fibers. To avoid inhaling fiber particles, we recommend
the following safety procedures: ventilate your work area, wear long sleeves,
gloves, safety glasses, and a disposable dust/mist respirator; dispose of insulation
in a sealed plastic bag; wash your hands with mild soap and cold water after
handling the insulation.
WARNING Combustible materials (or flammable/non-flammable wicking material) placed
under, over, or around the foreline (roughing) pump constitutes a fire hazard. Keep
the pan clean, but do not leave absorbent material such as paper towels in it.

Introduction 1
5977 Series MSD Operation Manual 19
Hydrogen Safety
Hydrogen is a commonly used GC carrier gas. Hydrogen is potentially
explosive and has other dangerous characteristics:
•Hydrogen is combustible over a wide range of concentrations. At
atmospheric pressure, hydrogen is combustible at concentrations from 4%
to 74.2% by volume.
•Hydrogen has the highest burning velocity of any gas.
•Hydrogen has a very low ignition energy.
•Hydrogen that is allowed to expand rapidly from high pressure can
self-ignite.
•Hydrogen burns with a non luminous flame which can be invisible under
bright light.
GC precautions
When using hydrogen as a carrier gas, remove the large round plastic cover for
the MSD transfer line located on the GC left side panel. In the unlikely event of
an explosion, this cover may dislodge.
WARNING Using hydrogen as a GC carrier gas is potentially dangerous.
WARNING When using hydrogen (H2) as the carrier gas or fuel gas, be aware that hydrogen
can flow into the GC oven and create an explosion hazard. Therefore, be sure that the
supply is turned off until all connections are made and ensure that the inlet and
detector column fittings are either connected to a column or capped at all times
when hydrogen is supplied to the instrument.
Hydrogen is flammable. Leaks, when confined in an enclosed space, may create a
fire or explosion hazard. In any application using hydrogen, leak test all
connections, lines, and valves before operating the instrument. Always turn off the
hydrogen supply at its source before working on the instrument.

20 5977 Series MSD Operation Manual
1Introduction
Dangers unique to GC/MSD operation
Hydrogen presents a number of dangers. Some are general, others are unique
to GC or GC/MSD operation. Dangers include, but are not limited to:
•Combustion of leaking hydrogen
•Combustion due to rapid expansion of hydrogen from a high-pressure
cylinder
•Accumulation of hydrogen in the GC oven and subsequent combustion (see
your GC documentation and the label on the top edge of the GC oven door)
•Accumulation of hydrogen in the MSD and subsequent combustion
Hydrogen accumulation in an MSD
All users should be aware of the mechanisms by which hydrogen can
accumulate (Table 4on page 21) and know what precautions to take if they
know or suspect that hydrogen has accumulated. Note that these mechanisms
apply to all mass spectrometers, including the MSD.
WARNING The MSD cannot detect leaks in inlet and/or detector gas streams. For this reason,
it is vital that column fittings should always be either connected to a column or have
a cap or plug installed.