Agilent Technologies 5975T LTM GC User manual

Agilent Technologies
Agilent 5975T
LTM GC/MSD
Operation Manual

2 5975T LTM GC/MSD Operation Manual
Notices
© Agilent Technologies, Inc. 2010
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
G4360-90007
Edition
First edition, December 2010
Printed in USA
Agilent Technologies, Inc.
5301 Stevens Creek Boulevard
Santa Clara, CA 95052
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
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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
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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.

5975T LTM GC/MSD Operation Manual 3
About This Manual
This manual contains information for operating the Agilent 5975T LTM
GC/MSD system.
1 “Introduction”
Chapter 1 describes general information about the 5975T LTM GC/MSD,
including a hardware description, general safety warnings, and hydrogen
safety information.
2 “Installing LTM Columns”
Chapter 2 shows you how to prepare a LTM column module for use with the
MSD, install it in the instrument, and connect it to the inlet and 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.
4 “General Maintenance”
Chapter 4 describes routine maintenance tasks performed during normal
operation of the 5975T, such as baking out the column and changing the
source.

4 5975T LTM GC/MSD Operation Manual
Where to Find Information
In addition to this document, Agilent provides several learning products that
document how to install, operate, maintain, and troubleshoot the Agilent
5975T LTM GC/MSD system.
Before operating your instrument, be sure to read the safety and regulatory
information included on the Agilent GC and GC/MS Hardware User
Information & Utilities DVD. The most common safety hazards when working
on the instrument are:
• Burns caused by touching heated areas on or in the instrument
• Release of pressurized gas containing hazardous chemical compounds
caused by opening inlets
• Glass cuts or puncture wounds caused by sharp capillary column ends
• Use of hydrogen as a GC carrier gas
Online User Documentation
Now your Agilent instrument documentation is in one place, at your
fingertips.
The Agilent GC and GC/MS Hardware User Information & Utilities DVD that
ships with your instrument provides an extensive collection of online help,
videos, and books for current Agilent gas chromatographs, mass selective
detectors, and GC samplers. Included are localized versions of the information
you need most, such as:

5 5975T LTM GC/MSD Operation Manual
• Getting Familiar documentation
• Safety and Regulatory guide
• Site Preparation information
• Installation information
•Operatingguides
• Maintenance information
• Troubleshooting details
Agilent Customer Portal
Agilent also provides customized information for the products you own
through a customer portal. This web service provides many customizable
services as well as information related directly to your Agilent products and
orders. Log onto the portal at http://www.agilent.com/chem.

6 5975T LTM GC/MSD Operation Manual

5975T LTM-GC/MSD Operation Manual 7
Contents
1 Introduction
Abbreviations Used 12
The GC/MSD 14
GC/MSD Hardware Description 16
Important Safety Warnings 18
Hydrogen Safety 20
Safety and Regulatory Certifications 24
Cleaning/Recycling the Product 27
Liquid Spillage 27
Moving or Storing the GC/MSD 27
2 Installing LTM Columns
Overview 30
Columns 31
To Install an Inlet Guard Column in the Split/Splitless Inlet 33
To Install an MSD Guard Column in the GC/MSD Interface 38
To Install the LTM Module Assembly in the Instrument 42
To Remove the LTM Module Assembly from the Instrument 47
To Attach the Guard Columns to the LTM CFT Unions 52
To Condition the LTM Column Module 56
3 Operating in Electron Impact (EI) Mode
Operating the GC/MSD from the Data System 61
Operating the GC/MSD from the LCP 61
LCP Status Messages 63

5975T LTM-GC/MSD Operation Manual 8
LCP Menus 65
The GC/MSD Interface 69
Before You Turn On the GC/MSD 71
Pumping Down 73
Controlling Temperatures 73
Controlling Column Flow 73
Venting the MSD 75
To View MSD Analyzer Temperature and Vacuum Status 76
To Set Monitors for MSD Temperature and Vacuum Status 78
To Set the MSD Analyzer Temperatures 79
To Set the GC/MSD Interface Temperature from the
ChemStation 81
To Monitor High Vacuum Pressure 83
To Configure the LTM Column 85
To Measure Column Flow Linear Velocity 87
To Confirm Column Flow 88
To Tune the MSD 89
To Verify System Performance 90
High-Mass Testing (5975T LTM GC/MSDs) 91
To Open the LTM/Guard Column Enclosure Door 94
To Open the LCP/Analyzer Window 95
To Remove the Analyzer Top Cover 95
To Vent the MSD 97
To Open the Analyzer Chamber 99
To Close the Analyzer Chamber 102

5975T LTM-GC/MSD Operation Manual 9
To Pump Down the MSD 106
To Move or Store the Instrument 108
4 General Maintenance
Before Starting 112
Maintaining the Vacuum System 117
Maintaining the Analyzer 118
Maintenance Methods 120
To Change the Septum on the Split/Splitless Inlet 121
To Change the Liner and O-Ring on the Split/Splitless Inlet 123
To Bakeout the Column Flow Path 128
To Bakeout Contaminants from the Split/Splitless Inlet 131
To Remove the EI ion source 132
To Reinstall the EI Ion Source 135

10 5975T LTM-GC/MSD Operation Manual

11
Agilent 5975T LTM GC/MSD
Operation Manual
Agilent Technologies
1
Introduction
Abbreviations Used 12
The GC/MSD 14
GC/MSD Hardware Description 16
Important Safety Warnings 18
Hydrogen Safety 20
Safety and Regulatory Certifications 24
Cleaning/Recycling the Product 27
Liquid Spillage 27
Moving or Storing the GC/MSD 27
This chapter provides an overview of the instrument hardware, hydrogen
safety and other general safety precautions for the Agilent Technologies 5975T
LTM GC/MSD.

12 5975T LTM GC/MSD Operation Manual
1Introduction
Abbreviations Used
The abbreviations in Table 1 are used in discussing this product. They are
collected here for convenience.
Table 1 Abbreviations
Abbreviation Definition
AC Alternating current
ALS Automatic liquid sampler
BFB Bromofluorobenzene (calibrant)
DC Direct current
DFTPP Decafluorotriphenylphosphine (calibrant)
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
LTM Low thermal mass
m/z Mass to charge ratio
MSD Mass Selective Detector
OFN Octafluoronaphthalene (calibrant)
PFHT 2,4,6-tris(perfluoroheptyl)-1,3,5-triazine (calibrant)
PFTBA Perfluorotributylamine (calibrant)

Introduction 1
5975T LTM GC/MSD Operation Manual 13
Quad Quadrupole mass filter
RF Radio frequency
RFPA Radio frequency power amplifier
Torr Unit of pressure, 1 mm Hg
Turbo Turbomolecular (pump)
Table 1 Abbreviations (continued)
Abbreviation Definition

14 5975T LTM GC/MSD Operation Manual
1Introduction
The GC/MSD
The GC/MSD features:
•LTM GC column with rapid heating and cooling capabilities
•Capillary guard column to minimize contamination to the LTM
•Local Control Panel (LCP) for local monitoring
•Choice of foreline pump - rotary vane (wet), scroll (dry), or diaphragm (dry)
•Heated electron-ionization ion source
•Heated hyperbolic quadrupole mass filter
•High-energy dynode (HED) electron multiplier detector
•Heated GC/MSD interface
•ChemStation control for operating the GC/MSD
Physical description
The 5975T LTM GC/MSD is a rectangular box, approximately 41 cm high,
60 cm wide, and 54 cm deep. The weight is 46.5 kg for the mainframe. The
attached foreline (roughing) pump weighs an additional 15 kg (standard
pump) for wet, and 4.5 kg for dry.
The basic components of the instrument are: the frame/cover assemblies, the
local control panel, the vacuum system, the EPC, the GC/MSD interface, the
inlet, the LTM column module, the electronics, and the analyzer.
Local control panel
The local control panel displays the status of the instrument, displays error
messages, and allows setting and display of some instrument parameters for
the Agilent 5975T LTM GC/MSD. These parameters are normally controlled
using the Agilent ChemStation.
Vacuum gauge
The MSD may be equipped with an optional external vacuum gauge. Operation
of the gauge controller is described in this manual.

Introduction 1
5975T LTM GC/MSD Operation Manual 15
Table 2 5975T LTM GC/MSD models and features
Feature
High vacuum pump Standard turbo
Optimal He column flow mL/min 1.2
Maximum recommended column gas
flow mL/min
2
Maximum gas flow, mL/min*
* Expect degradation of spectral performance and sensitivity.
2.4

16 5975T LTM GC/MSD Operation Manual
1Introduction
GC/MSD Hardware Description
Figure 1 is an overview of a 5975T LTM GC/MSD system.
Figure 1 5975T LTM GC/MSD system
Local control
panel
MSD
Door
LTM
Door
Power switch

Introduction 1
5975T LTM GC/MSD Operation Manual 17
Figure 2 Top View of 5975T with ALS parking post
ALS parking
post

18 5975T LTM GC/MSD Operation Manual
1Introduction
Important Safety Warnings
There are several important safety notices to always keep in mind when using
the GC/MSD.
Many internal parts of the GC/MSD carry dangerous voltages
If the GC/MSD is connected to a power source, even if the power switch is off,
potentially dangerous voltages exist on:
•The wiring between the GC/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 GC/MSD electronics
The printed circuit boards in the GC/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.

Introduction 1
5975T LTM GC/MSD Operation Manual 19
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 inlet
•The guard column enclosure and its contents
•The guard column nuts attaching the guard columns to the inlet, LTM
column, and MSD.
•The analyzer
•The foreline pump
Always cool these areas of the system to room temperature before working on
them. 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 GC/MSD.
WARNING
The insulation around the inlet 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.

20 5975T LTM GC/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 nonluminous flame which can be invisible under
bright light.
WARNING
The use of hydrogen (H2) as a carrier gas is potentially dangerous.
WARNING
When using H2as the carrier gas or fuel gas, be aware that hydrogen gas can flow
into the guard column enclosure and create an explosion hazard. Therefore, be sure
that the supply is turned off until all connections are made and ensure that the inlet,
MSD, and column fittings are either connected to a column or capped at all times
when hydrogen gas 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.