Agilent Technologies 5975 Series User manual

Agilent 5975/5977 MSD for OpenLAB CDS
Operating Manual

Notices
© Agilent Technologies, Inc. 2019
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Manual Part Number
G7077-90031
Edition
First Edition, January 2019
Printed in USA
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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.

5975/5977 Series MSD Operating 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 7890/7820/6890/6850 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 “Intuvo 9000 GC Column Maintenance”
Chapter 3 shows you how to install an Agilent Intuvo column, connect a flow
path from the column through the MS transfer line and into the ion source, and
maintain the column guard chip.
4 “Operating in EI Mode”
Chapter 4 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.
5 “General Maintenance”
Chapter 5 describes maintenance procedures common to both EI and CI
instruments.

4 5975/5977 Series MSD Operating 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 Operating Manual 5
Contents
Hardware User Information 4
5977B MSD 4
5975/5977 Series MSD prior to the 5977B MSD 4
1Introduction
5977B Series MSD Version 10
Abbreviations Used 11
The 5977B Series MSD 13
MSD Hardware Description 15
Important Safety Warnings 16
Hydrogen Safety 19
GC precautions 19
Precautions 21
Safety and Regulatory Certifications 23
Intended Use 26
Cleaning/Recycling the Product 26
Accidental Liquid Spillage 26
Moving or Storing the MSD 26
To Replace the Primary Fuses 27
2 Installing 7890/7820/6890/6850 GC Columns
Columns 30
To Install a Capillary Column in a Split/Splitless Inlet 32
To Condition a Capillary Column 35
To Install a Capillary Column in the GC/MS Interface Using the
Self-Tightening Column Nut 36

6 5975/5977 Series MSD Operating Manual
To Install a Capillary Column in the GC/MS Interface Using a
Standard Column Nut 41
To Install the Interface Tip Seal 44
To Calibrate Column Flow Linear Velocity 46
The GC/MSD Interface for a 7890B Series GC 49
3 Intuvo 9000 GC Column Maintenance
Columns 52
Conditioning columns 53
Tips and hints 53
Handling the Intuvo 9000GC Column and Bus
Components 54
To Replace an Intuvo GC Column 55
To Replace an Intuvo 9000 GC Gasket 59
To Install a Column Guard or Jumper Chip 60
To Replace the 9000 GC/MS Tail 64
To Condition an Intuvo Capillary Column 68
To Install the Interface Tip Seal 70
The GC/MS Interface for a 9000 Series GC 72
4OperatinginEIMode
Operating the MSD from the DS 76
Operating the MSD from the GC Control Panel 77
Configuring the MSD Through the Web User Interface
(WUI) 81
To change the network settings of the MSD 81
Operating the 5975/5977 MSD From the Local Control Panel
(LCP) 84
Modes of operation 84

5975/5977 Series MSD Operating Manual 7
LCP Status Messages 86
To view system status during startup 87
eModule Mini Display Readout 91
Front Panel Instrument Status LED 91
The GC/MSD Interface 92
Before You Turn On the MSD 94
Pumping Down 95
Controlling Temperatures 95
Controlling Column Flow 95
Venting the MSD 96
Set MS Analyzer Temperatures 97
Enable the GC/MS Interface and Oven 99
View MSD Temperatures and Vacuum 100
To Run an Autotune 102
To Open the MSD Covers 103
Vent the MSD 104
To Pump Down the MS 106
To Move or Store the MSD 109
5 General Maintenance
Before Starting 112
Maintaining the Vacuum System 116
Maintaining the Analyzer 117
To Open the Analyzer Chamber 119
To Remove the EI HES 121
To Connect/Disconnect Wiring to the EI HES 123

8 5975/5977 Series MSD Operating Manual
To Disassemble the EI HES 124
To Clean the EI HES 127
To Assemble the EI HES 130
To Remove the EI HES filaments 135
To Install the EI HES Filament 137
To Install the EI HES 138
To Remove the EI XTR, SS, or Inert Source 139
To Connect/Disconnect Wiring from the EI XTR, SS, and Inert
Sources 140
To Disassemble the EI SS or EI Inert Source 141
To Disassemble the EI XTR Source 144
To Clean an EI XTR, SS, or Inert Source 147
To Assemble an EI SS or Inert Source 151
To Assemble the EI XTR Source 154
To Replace a Filament in an EI XTR, SS, or Inert Source 157
To Install the EI XTR, SS, or Inert Source 159
To Replace the Electron Multiplier Horn 160
To Close the Analyzer Chamber 162

5975/5977 Series MSD Operating Manual 9
1Introduction
5977B Series MSD Version 10
Abbreviations Used 11
The 5977B Series MSD 13
MSD Hardware Description 15
Important Safety Warnings 16
Hydrogen Safety 19
Safety and Regulatory Certifications 23
Intended Use 26
Cleaning/Recycling the Product 26
Accidental 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.

1Introduction
10 5975/5977 Series MSD Operating Manual
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 three types of electron ionization (EI) sources available
on the 5977B Series MSD, a standard EI stainless steel (SS) source, an EI
Extractor (XTR) source available on the Inert+ MSD model, and a high efficiency
source (HES). The serial number label displays a product number that indicates
what type of MSD you have. (See Table 1.)
Table 1 Available high vacuum pumps

Model name
Product
number*

Description

Ionization mode/Type
5977B MSD Diff Pump G7080B Diffusion pump EI/SS
5977B MSD Turbo Pump G7081B Turbo pump EI/SS
5977B Inert+ MSD EI Turbo G7077B Turbo pump MSD EI/XTR
5977B EI/CI MSD G7078B Turbo pump MSD EI /XTR
CI /PCI, NCI
5977B HES MSD G7079B Turbo pump MSD EI HES
field upgradeable to CI
* Operation in CI mode or with the JetClean option is not supported in OpenLAB CDS 2.1.

1Introduction
5975/5977 Series MSD Operating Manual 11
Abbreviations Used
The abbreviations in Table 2 are 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
DA Data analysis
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)
HES High Efficiency Source. New generation EI source constructed from inert material
Inert Standard EI source constructed from inert materials
Inert+ MSD model designation equipped with an EI XTR source
id Inside diameter
LAN Local Area Network
LCP Local control panel
LVDS Low-voltage differential signaling

1Introduction
12 5975/5977 Series MSD Operating Manual
m/z Mass to charge ratio
MFC Mass flow controller
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
SS Stainless steel
Torr Unit of pressure, 1 mm Hg
Turbo Turbomolecular (pump)
WUI Web user interface
XTR EI Extractor source
Table 2 Abbreviations (continued)
Abbreviation Definition

1Introduction
5975/5977 Series MSD Operating 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 GC. 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 or a diffusion
vacuum pump with a Pfeiffer DUO 2.5 foreline pump
•Four different types of independently heated EI sources available:
•Standard source in SS material
•Standard source in Inert material
•XTR source
•HES
•Independently MSD heated hyperbolic Quad
•HED EM
•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 mainframe, 44 kg for the
standard EI turbo pump mainframe, and 46 kg for the EI/CI 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:
•Frame/cover assemblies
•Vacuum system
•GC interface
•Electronics
•Analyzer

1Introduction
14 5975/5977 Series MSD Operating Manual
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.
26.5
Max column id 0.25 mm (30 m) 0.53 mm (30 m)
Inert ion sources available Yes Yes
GC compatibility 6890/7820/7890
Series
6890/7820/7890 Series
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

1Introduction
5975/5977 Series MSD Operating Manual 15
MSD Hardware Description
Figure 1. 5977B Series GC/MSD system, shown with an Agilent 7890B GC
ALS
7890B GC
7890B GC control panel
5977B Series
MSD
MSD power switch
GC power switch
System status LED

1Introduction
16 5975/5977 Series MSD Operating Manual
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
•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,
switch off the MSD and unplug the power cord. It is not necessary to allow air
into the analyzer chamber.
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.

1Introduction
5975/5977 Series MSD Operating Manual 17
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.
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.
WARNING
Be careful when working behind the instrument. During cool-down cycles, the
GC emits hot exhaust which can cause burns.

1Introduction
18 5975/5977 Series MSD Operating Manual
The oil pan under the 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
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/nonflammable 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.

1Introduction
5975/5977 Series MSD Operating 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 nonluminous 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
The use of hydrogen as a GC carrier gas, or detector fuel 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, ensure that the supply is turned off until all connections are made
and that the inlet and detector column fittings are either connected to a
column or capped 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.

1Introduction
20 5975/5977 Series MSD Operating Manual
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 and know what precautions to take if they know or suspect that
hydrogen has accumulated. (See Table 4 on page 20.) Note that these
mechanisms apply to all mass spectrometers, including the MSD.
WARNING
The MSD cannot detect leaks in inlet 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
MS 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.
MS
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.
MS 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.