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-
tion with the furnishing, use, or per-
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information contained herein. Should
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.

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

11
Agilent 5975 Series MSD
5975 Series MSD Operation Manual for MassHunter
Agilent Technologies
1
Introduction
5975 MSD Version 12
Abbreviations Used 13
The 5975 Series MSD 15
CI MSD Hardware Description 17
Important Safety Warnings 19
Many internal parts of the MSD carry dangerous voltages 19
Electrostatic discharge is a threat to MSD electronics 19
Many parts are dangerously hot 20
The oil pan under the standard foreline pump can be a fire hazard 20
Hydrogen Safety 21
Dangers unique to GC/MSD operation 22
Hydrogen accumulation in an MSD 22
Precautions 24
Safety and Regulatory Certifications 26
Information 26
Symbols 27
Electromagnetic compatibility 28
Sound emission declaration 28
Cleaning/Recycling the Product 29
Liquid Spillage 29
Moving or Storing the MSD 29
This manual describes the operation, and routine maintenance of the Agilent
Technologies 5975 Series MSD.

12 5975 Series MSD Operation Manual for MassHunter
1Introduction
5975 MSD Version
5975 Series MSDs are equipped with a diffusion pump or one of two
turbomolecular (turbo) pumps. The serial number label displays a product
number (Table 1) that indicates what kind of MSD you have.
Table 1 Available high vacuum pumps
Model name Product number Description Ionization modes
5975C TAD VL MSD G3170A Diffusion Pump MSD Electron impact (EI)
5975C TAD inert
MSD
5975C TAD inert XL
MSD
G3171A
G3172A
Standard Turbo MSD
Performance Turbo MSD
Electron impact (EI)
Electron impact (EI)
5975C TAD inert XL
MSD
G3174A CI High Mass Performance
Turbo Pump
Electron impact (EI)
Negative chemical ionization (NCI)
Positive chemical ionization (PCI)
7820 MSD VL G3175A Diffusion Pump MSD Electron impact (EI)
7820 MSD G3176A Standard Turbo MSD Electron impact (EI)

Introduction 1
5975 Series MSD Operation Manual for MassHunter 13
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 impact 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)
LTM Low thermal mass
m/z Mass to charge ratio
MFC Mass flow controller

14 5975 Series MSD Operation Manual for MassHunter
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 Series MSD Operation Manual for MassHunter 15
The 5975 Series MSD
The 5975 Series MSD is a stand-alone capillary GC detector for use with an
Agilent Series Gas Chromatograph (Table 3). The MSD features:
•Local Control Panel (LCP) for locally monitoring and operating the MSD
•One of three different high vacuum pumps
•Rotary vane foreline pump
•Independently MSD heated electron-ionization ion source
•Independently MSD heated hyperbolic quadrupole mass filter
•High-energy dynode (HED) electron multiplier detector
•Independently GC heated GC/MSD interface
•Chemical ionization (EI/PCI/NCI) modes available
Physical description
The 5975 Series MSD is a rectangular box, approximately 42 cm high, 26 cm
wide, and 65 cm deep. The weight is 25 kg for the diffusion pump mainframe,
26 kg for the standard turbo pump mainframe, and 29 kg for the performance
turbo pump mainframe. The attached foreline (roughing) pump weighs an
additional 11 kg (standard pump).
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.
Vacuum gauge
The 5975 Series MSD may be equipped with a Micro-Ion Vacuum Gauge. The
MSD MassHunter software can be used to read the pressure (high vacuum) in
the vacuum manifold. Operation of the gauge controller is described in this
manual.

16 5975 Series MSD Operation Manual for MassHunter
1Introduction
The gauge is required for chemical ionization (CI) operation.
Table 3 5975 series MSD models and features
Model
Feature G3170A
G3175A
G3171A
G3176A
G3172A G3174A
High vacuum pump Diffusion Standard
turbo
Performance
turbo
Performance
turbo
Optimal He column flow mL/min 1 1 1 to 2 1 to 2
Maximum recommended gas flow
mL/min*
* Total gas flow into the MSD: column flow plus reagent gas flow (if applicable).
1.5 2.0 4.0 4
Maximum gas flow, mL/min†
† Expect degradation of spectral performance and sensitivity.
2 2.4 6.5 6.5
Max column id 0.25 mm
(30 m)
0.32 mm
(30 m)
0.53 mm
(30 m)
0.53 mm
(30 m)
CI capability No No No Yes
DIP‡capability (3rd party)
‡ Direct insertion probe.
Yes Yes Yes Yes

Introduction 1
5975 Series MSD Operation Manual for MassHunter 17
CI MSD Hardware Description
Figure 1is an overview of a typical 5975 GC/MSD system.
The CI hardware allows the 5975 Series MSD to produce high-quality, classical
CI spectra, which include molecular adduct ions. A variety of reagent gases
can be used.
Figure 1 5975 Series GC/MSD system
ALS
7890A GC
CI gas flow module
Local control panel
5975 Series MSD
MSD power switch
GC power switch

18 5975 Series MSD Operation Manual for MassHunter
1Introduction
In this manual, the term “CI MSD” refers to the G3174A MSD and upgraded
G3172A MSDs. It also applies, unless otherwise specified, to the flow modules
for these instruments.
The 5975 Series CI system adds to the 5975 Series MSD:
•EI/CI GC/MSD interface
•CI ion source and interface tip seal
•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 (G3397A) is required for CI MSD and is
recommended for EI also.
The MSD CI system has been optimized to achieve the relatively high 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 tip of the interface.
Switching back and forth between CI and EI 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 about
2 hours for the ion source to cool.

Introduction 1
5975 Series MSD Operation Manual for MassHunter 19
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).
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. Wear a grounded wrist strap any time you must remove the MSD
right side cover.
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.

20 5975 Series MSD Operation Manual for MassHunter
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 inlets
•The oven and its contents
•The detector
•The column nuts attaching the column to an inlet or detector
•The valve box
•The foreline pump
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 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.