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-
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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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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

Introduction 1
5975/5977 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
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)
Inert Standard EI source constructed from inert materials
Inert+ Extractor EI source constructed from inert materials
id Inside diameter
LAN Local Area Network
m/z Mass to charge ratio
MFC Mass flow controller

12 5975/5977 Series MSD Operation Manual
1Introduction
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
Torr Unit of pressure, 1 mm Hg
Turbo Turbomolecular (pump)
Table 2 Abbreviations (continued)
Abbreviation Definition

Introduction 1
5975/5977 Series MSD Operation Manual 13
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 Gas Chromatograph. The
MSD features:
•WEB User Interface (WUI) for locally monitoring and operating the MSD
•A turbo vacuum pump with one of four different foreline pumps
•A diffusion vacuum pump with a Pfeiffer DUO 2.5 foreline pump
•Three different types of independently heated MSD electron-ionization (EI)
sources available: standard source in both stainless steel and inert material,
and an extractor source.
•Independently MSD heated hyperbolic quadrupole mass filter
•High-energy dynode (HED) electron multiplier detector
•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 model, 44 kg for the
turbo pump model (EI), and 46 kg for the turbo pump model (EI/CI). The
foreline (roughing) pump weighs an additional 11 kg and is usually located on
the floor behind the MSD.
The basic components of the instrument are: the frame/cover assemblies, the
vacuum system, the GC interface, the electronics, and the analyzer.

14 5975/5977 Series MSD Operation Manual
1Introduction
Vacuum gauge
The MSD may be equipped (or ordered) with an ion vacuum gauge. The
OpenLAB CDS 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.
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.
2 6.5
Max column id 0.25 mm (30 m) 0.53 mm (30 m)
Inert ion sources available Yes Yes
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 Yes

Introduction 1
5975/5977 Series MSD Operation Manual 15
MSD Hardware Description
Figure 1 5977B Series GC/MSD system, shown with Agilent 7890B GC
ALS
7890B GC
Local control panel
5977B Series
MSD
MSD power switch
GC power switch
Front panel LED

16 5975/5977 Series MSD Operation Manual
1Introduction
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.

Introduction 1
5975/5977 Series MSD Operation Manual 17
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 diffusion 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, and do not leave absorbent material such as paper towels in it.

18 5975/5977 Series MSD Operation Manual
1Introduction
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.

Introduction 1
5975/5977 Series MSD Operation Manual 19
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 19) 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.
Table 4 Hydrogen accumulation mechanisms
Mechanism Results
Mass spectrometer turned off A mass spectrometer can be shut down deliberately. It can
also be shut down accidentally by an internal or external
failure. There is a safety feature that will shut down the flow
of carrier gas in the event of an MSD foreline pump shut
down. However, if this feature fails, hydrogen may slowly
accumulate in the mass spectrometer.
Mass spectrometer automated
shutoff valves closed
Some mass spectrometers are equipped with automated
diffusion pump shutoff valves. In these instruments,
deliberate operator action or various failures can cause the
shutoff valves to close. Shutoff valve closure does not shut
off the flow of carrier gas. As a result, hydrogen may slowly
accumulate in the mass spectrometer.

20 5975/5977 Series MSD Operation Manual
1Introduction
Precautions
Take the following precautions when operating a GC/MSD system with
hydrogen carrier gas.
Mass spectrometer manual shutoff
valves closed
Some mass spectrometers are equipped with manual
diffusion pump shutoff valves. In these instruments, the
operator can close the shutoff valves. Closing the shutoff
valves does not shut off the flow of carrier gas. As a result,
hydrogen may slowly accumulate in the mass spectrometer.
GC off A GC can be shut down deliberately. It can also be shut
down accidentally by an internal or external failure.
Different GCs react in different ways. If a 7890 Series GC
equipped with Electronic Pressure Control (EPC) is shut off,
the EPC stops the flow of carrier gas. If a GC’s carrier flow is
not under EPC control, the flow increases to its maximum.
This flow may be more than some mass spectrometers can
pump away, resulting in the accumulation of hydrogen in
the mass spectrometer. If the mass spectrometer is shut off
at the same time, the accumulation can be fairly rapid.
Power failure If the power fails, both the GC and mass spectrometer shut
down. The carrier gas, however, is not necessarily shut
down. As described previously, in some GCs, a power failure
may cause the carrier gas flow to be set to maximum. As a
result, hydrogen may accumulate in the mass spectrometer.
Table 4 Hydrogen accumulation mechanisms (continued)
Mechanism Results
WARNING Once hydrogen has accumulated in a mass spectrometer, extreme caution must be
used when removing it. Incorrect startup of a mass spectrometer filled with
hydrogen can cause an explosion.
WARNING After a power failure, the mass spectrometer may start up and begin the pumpdown
process by itself. This does not guarantee that all hydrogen has been removed from
the system or that the explosion hazard has been removed.