Thermo Scientific DSQ II User manual

DSQ II
Hardware Manual
120299-0002 Revision C December 1, 2009

© December 2009 Thermo Fisher Scientific Inc. Xcalibur™, DSQ, DSQ II, TRACE DSQ, TRACE GC,
TRACE GC Ultra, FOCUS GC, PolarisQ, and ITQ are trademarks and/or product names of Thermo Fisher
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SGE product. All other trademarks are the property of Thermo Fisher Scientific and its subsidiaries.
Ion Trap series refers to ITQ and PolarisQinstruments. DSQ series refers to all DSQ and DSQ II instruments.
Information about the TRACE GC and FOCUS GC instruments is included in this document.
INSTRUMENT USAGE: Thermo Scientific systems operate safely and reliably under carefully controlled
environmental conditions. If the equipment is used in a manner not specified by the manufacturer, the
protections provided by the equipment may be impaired. If you maintain a system outside the specifications
listed in this guide, failures of many types may occur. The repair of such failures is specifically excluded from
the standard Warranty and service contract coverage.
Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the
product operation. This document is copyright protected and any reproduction of the whole or any part of this
document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.
The contents of this document are subject to change without notice. All technical information in this
document is for reference purposes only. System configurations and specifications in this document supersede
all previous information received by the purchaser.
Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or error-
free and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might
result from any use of this document, even if the information in the document is followed properly.
This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This
document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of
Sale shall govern all conflicting information between the two documents.
Release history: Rev A, August 2006. Rev B, December 2008, Rev C, December 2009.
For Research Use Only. Not regulated for medical or veterinary diagnostic use by U.S. Federal Drug
Administration or other competent authorities.

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Regulatory Compliance
Thermo Fisher Scientific performs complete testing and evaluation of its products to ensure full compliance with
applicable domestic and international regulations. When the system is delivered to you, it meets all pertinent
electromagnetic compatibility (EMC) and safety standards as described below.
EMC Directive 89/336/EEC
EMC compliance has been evaluated by Professional Testing.
•PolarisQ, ITQ, and Ion Trap Series standards: EMC EN 55011:1998 + EN 50082-1:1998,
Safety EN 61010-1:1990 + A1:1992 + A2:1995
• DSQ standards: EMC EN 61326-1:1998 + A1:1998. Safety EN 61010-1:1990 + A1:1992 + A2:1995
• DSQ II standards: EMC EN 61326-1:1997 + A1:1998 + A2:2001. Safety EN 61010-1:2001
• Direct Probe Controller (DPC) standards: EMC EN 55011:1991 + EN 50082-1:1992. Safety EN 61010-1:1994
Low Voltage Safety Compliance
This device complies with Low Voltage Directive 73/23/EEC and harmonized standard EN 61010-1:2001. Changes
that you make to your system may void compliance with one or more of these EMC and safety standards. Changes to
your system include replacing a part or adding components, options, or peripherals not specifically authorized and
qualified by Thermo Fisher Scientific. To ensure continued compliance with EMC and safety standards, replacement
parts and additional components, options, and peripherals must be ordered from Thermo Fisher Scientific or one of its
authorized representatives.
FCC Compliance Statement
Certifications, FCC part 15, Class A
This equipment has been tested and found to comply with the limits for a Class A digital device, pursuant
to part 15 of the FCC rules. These limits are designed to provide reasonable protection against harmful
interference when the equipment is operated in a commercial environment. This equipment generates, uses,
and can radiate radio frequency energy. If it is not installed and used in accordance with the instruction
manual, it may cause harmful interference to radio communication. Operation of this equipment in a
residential area is likely to cause harmful interference. In this case, users will be required to correct the
interference at their own expense. Detailed installation requirements are in the respective instrument’s
preinstallation guide.

Notice on Lifting and Handling of Thermo Scientific Instruments
For your safety, and in compliance with international regulations, the physical handling of this Thermo Fisher Scientific
instrument requires a team effort to lift and/or move the instrument. This instrument is too heavy and/or bulky for one
person alone to handle safely.
Notice on the Proper Use of Thermo Scientific Instruments
In compliance with international regulations: Use of this instrument in a manner not specified by Thermo Fisher
Scientific could impair any protection provided by the instrument.
Notice on the Susceptibility to Electromagnetic Transmissions
Your instrument is designed to work in a controlled electromagnetic environment. Do not use radio frequency
transmitters, such as mobile phones, in close proximity to the instrument.
For manufacturing location, see the label on the instrument.
WEEE Compliance
This product is required to comply with the European Union’s Waste Electrical & Electronic Equipment (WEEE)
Directive 2002/96/EC. It is marked with the following symbol:
Thermo Fisher Scientific has contracted with one or more recycling or disposal companies in each European Union
(EU) Member State, and these companies should dispose of or recycle this product. See www.thermo.com/
WARNING Read and understand the various precautionary notes, signs, and symbols
contained inside this manual pertaining to the safe use and operation of this product
before using the device.

WEEERoHS for further information on Thermo Fisher Scientific’s compliance with these Directives and the recyclers
in your country.
WEEE Konformität
Dieses Produkt muss die EU Waste Electrical & Electronic Equipment (WEEE) Richtlinie 2002/96/EC erfüllen. Das
Produkt ist durch folgendes Symbol gekennzeichnet:
Thermo Fisher Scientific hat Vereinbarungen mit Verwertungs-/Entsorgungsfirmen in allen EU-Mitgliedsstaaten
getroffen, damit dieses Produkt durch diese Firmen wiederverwertet oder entsorgt werden kann. Mehr Information
über die Einhaltung dieser Anweisungen durch Thermo Fisher Scientific, über die Verwerter, und weitere Hinweise, die
nützlich sind, um die Produkte zu identifizieren, die unter diese RoHS Anweisung fallen, finden sie unter
www.thermo.com/WEEERoHS.
Conformité DEEE
Ce produit doit être conforme à la directive européenne (2002/96/EC) des Déchets d'Equipements Electriques et
Electroniques (DEEE). Il est marqué par le symbole suivant:
Thermo Fisher Scientific s'est associé avec une ou plusieurs compagnies de recyclage dans chaque état membre de
l’union européenne et ce produit devrait être collecté ou recyclé par celles-ci. Davantage d'informations sur la
conformité de Thermo Fisher Scientific à ces directives, les recycleurs dans votre pays et les informations sur les produits
Thermo Fisher Scientific qui peuvent aider la détection des substances sujettes à la directive RoHS sont disponibles sur
www.thermo.com/WEEERoHS.

Thermo Scientific DSQ II Hardware Manual ix
C
Contents
Chapter 1 Basic Operations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Getting the Right Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Installing a Column into the GC/MS System . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Removing a Column from the GC/MS System . . . . . . . . . . . . . . . . . . . . . . . . . 15
Starting Up the GC/MS System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Shutting Down the GC/MS System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Chapter 2 Maintaining the DSQ II. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21
Components That Require Maintenance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
List of Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Recommended Maintenance Schedule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Running Benchmark Tests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Preparing the DSQ II for Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Removing the Front and Top Covers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Removing the Right Cover . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Removing the Left Cover. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Removing the Vacuum Manifold Cover . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Cleaning Stainless Steel Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Cleaning Non-Stainless Steel or Hybrid Components . . . . . . . . . . . . . . . . . . 36
Cleaning the Ion Source Components. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Cleaning the Ion Volume with an Inlet Valve . . . . . . . . . . . . . . . . . . . . . . . . 38
Cleaning the Ion Volume Without an Inlet Valve . . . . . . . . . . . . . . . . . . . . . 43
Cleaning the Ion Source, Lenses and Prefilter . . . . . . . . . . . . . . . . . . . . . . . . 45
Cleaning the Ion Source and Lenses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Cleaning the Prefilter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Replacing the Ion Source Filament . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Replacing the Electron Multiplier . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Maintaining the Turbomolecular Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62

Contents
xDSQ II Hardware Manual Thermo Scientific
Maintaining the Rotary-Vane Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Checking the Oil Level of a Rotary-Vane Pump . . . . . . . . . . . . . . . . . . . . . . 63
Adding Oil to a Rotary Vane Pump. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Purging Gas from the Oil in a Rotary-Vane Pump . . . . . . . . . . . . . . . . . . . . 65
Changing the Oil in a Rotary-Vane Pump. . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Maintaining Components Outside the Vacuum Manifold . . . . . . . . . . . . . . . . 70
Replacing the Analog Board . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Replacing the Analog Board Fuse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Replacing the Calibration Gas Flow Module . . . . . . . . . . . . . . . . . . . . . . . . . 75
Refilling the Calibration Gas Flow Module . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Replacing the CI Reagent Gas Flow Module . . . . . . . . . . . . . . . . . . . . . . . . . 79
Replacing the Conversion Dynode/Electron Multiplier Power Supply. . . . . . 81
Replacing the DC Driver. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Replacing the DC Driver Fuse. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Replacing the Digital Board. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Replacing the Electrometer Board . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Replacing the Foreline Pressure Gauge and Foreline Adapter. . . . . . . . . . . . . 91
Replacing the Inlet Valve Seal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Replacing the Ion Gauge (Optional Upgrade) . . . . . . . . . . . . . . . . . . . . . . . . 94
Replacing the Lens Interface Board . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
Replacing the Low Pass Filter Board . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
Replacing the Power Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Replacing the Power Module Fuses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
Replacing the Rear Cooling Fans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
Replacing the RF Detector Board . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
Replacing the RF Generator Board . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
Replacing the RF Generator Board Fuses. . . . . . . . . . . . . . . . . . . . . . . . . . . 110
Replacing the Transfer Line. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
Replacing the Turbomolecular Pump Power Supply . . . . . . . . . . . . . . . . . . 114
Replacing the Vacuum Control Board. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Replacing the Vent Valve Solenoid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
Chapter 3 Troubleshooting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .121
Using Diagnostics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Running Tune Diagnostics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
Communication Symptoms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
Contamination Symptoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
Filament and Lens Control Symptoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
Heated Zone Symptoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
High Vacuum Symptoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
Linearity Symptoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
Power Supply Symptoms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139

Contents
Thermo Scientific DSQ II Hardware Manual xi
RF and DC Control Symptoms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
Sensitivity Symptoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
Stability Symptoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
Tuning Symptoms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
Chapter 4 Vacuum System and Gas Inlets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .153
Vacuum System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
Fore Pressure Gauge and Foreline Adapter . . . . . . . . . . . . . . . . . . . . . . . . . 155
High Vacuum Pump (Single Turbomolecular Pump) . . . . . . . . . . . . . . . . . 156
High Vacuum Pump (Split-Flow Turbomolecular Pump). . . . . . . . . . . . . . 157
Ion Gauge (Upgrade). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158
Rotary-Vane Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
Vacuum Manifold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160
Gas Inlet Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
Calibration Gas Flow Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
CI Reagent Gas Flow Module (Upgrade) . . . . . . . . . . . . . . . . . . . . . . . . . . 164
Vent Valve Solenoid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
Chapter 5 Ion Source and Inlet Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .167
Ion Source. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
Filament . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
Ion Source. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170
Ion Volume . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
Lenses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
Magnets and Magnet Yoke . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
Inlet Valve (Upgrade) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
Ball Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177
Inlet Valve Lever . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
Guide Bar Housing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
I/R Tool and Guide Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
Inlet Valve Plug. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
Inlet Valve Seal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
Chapter 6 Prefilter and Quadrupole . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .183
Chapter 7 Ion Detector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .187
Conversion Dynode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
Electron Multiplier . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189

Contents
xii DSQ II Hardware Manual Thermo Scientific
Chapter A Reordering DSQ II Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .191
Vacuum Manifold Parts List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192
Ion Source Parts List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194
Ion Source Parts List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
Lens Assembly Parts List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
Quadrupole Parts List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
Gas Inlets and Gauges Parts List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
Boards and Cables Parts List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
Turbomolecular Pump Parts List. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 208
Split-Flow Turbomolecular Pump (Upgrade) Parts List. . . . . . . . . . . . . . . . . . 210
Inlet Valve (Upgrade) Parts List. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 212
Power Module Parts List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 214
Installation Kit Parts List. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 214
Documentation Parts List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
Miscellaneous Items Parts List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
Electronic Assemblies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 218
Power Distribution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219
Remote Start Cable Connections. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 220

Thermo Scientific DSQ II Hardware Manual xiii
P
Preface
This guide contains detailed instructions for operating, maintaining, and troubleshooting the
DSQ II mass spectrometer.
About Your System
Thermo Fisher Scientific systems provide the highest caliber gas chromatography/mass
spectrometry (GC/MS) instrumentation available on today’s market.
GC/MS represents a combination of two powerful analytical techniques: GC, which acts as a
separation technique and MS, which acts as a detection technique. Complex mixtures of
individual compounds can be injected into the GC, either manually or through the use of an
optional autosampler, and then separated for presentation to the MS. The MS will then
generate a mass spectrum of the GC eluent and its components, which can be used for
qualitative identification, as well as accurate and precise quantification of the individual
compounds present in the sample.
IMPORTANT Thermo Fisher Scientific systems are designed to optimize both the
separation and detection capabilities of GC/MS techniques and combine them in a
synergistic fashion to provide high performance analytical capabilities for both research
and routine applications. More information on the use of this system can be found in
related documentation sources and through the provided contact information.
WARNING Thermo Fisher Scientific systems operate safely and reliably under carefully
controlled environmental conditions. If the equipment is used in manner not specified by
the manufacturer, the protections provided by the equipment may be impaired. If you
maintain a system outside the specifications listed in this guide, failures of many types,
including personal injury or death, may occur. The repair of instrument failures caused by
operation in a manner not specified by the manufacturer is specifically excluded from the
Standard Warranty and service contract coverage.

Preface
Power Ratings
xiv DSQ II Hardware Manual Thermo Scientific
Power Ratings
Mass Spectrometer (MS)
• 120 V ac +6/-10%, 50/60 Hz, 15 A max
• 230 V ac ±10%, 50/60 Hz, 10 A max
Gas Chromatograph (GC)
• 120 V ac +6%/-10%, 50/60 Hz, 20 A max
• 230 V ac ±10%, 50/60 Hz, 10 A max
Detailed instrument specifications are in the Product Specification or Product Brochure.
Safety Alerts and Important Information
Make sure you follow the precautionary notices presented in this guide. Safety and other
special notices appear in boxes and include the following:
WARNING This is the general warning safety symbol and safety alert word to prevent
actions that could cause personal injury. It highlights hazards to humans or the
environment. Each WARNING safety alert is preceded with this safety symbol and
another appropriate safety symbol (see “Safety Symbols and Signal Words” on page xv.)
Then it is followed with an appropriate safety precautionary message. When you see a
safety alert on your instrument or in the publications, please carefully follow the safety
instructions before proceeding.
CAUTION This is the safety alert word to prevent actions that may cause personal injury
or instrument damage. We use it to highlight information necessary to prevent personal
injury or damage to software, loss of data, or invalid test results; or might contain
information that is critical for optimal system performance. A CAUTION safety alert is
always preceded with an appropriate safety symbol (see “Safety Symbols and Signal
Words” on page xv.) Then it is followed with an appropriate safety precautionary message.
When you see a safety alert on your instrument or in the publications, please carefully
follow the safety instructions before proceeding.
IMPORTANT Highlights information necessary to prevent damage to software, loss of
data, or invalid test results; or might contain information that is critical for optimal
performance of the system.
Note Emphasizes important information about a task.
Tip Helpful information that can make a task easier.

Preface
Safety Alerts and Important Information
Thermo Scientific DSQ II Hardware Manual xv
Safety Symbols and Signal Words
All safety symbols are followed by WARNING or CAUTION, which indicates the degree of risk
for personal injury and/or instrument damage. Cautions and warnings are following by a
descriptor, such as BURN HAZARD. A WARNING is intended to prevent improper actions that
could cause personal injury. Whereas, a CAUTION in intended to prevent improper actions
that may cause personal injury and/or instrument damage. The following safety symbols may
be found on your instrument and/or in this guide:
BURN HAZARD. This symbol indicates a hot surface that could or may cause
burn injuries.
ELECTRICAL SHOCK HAZARD. This symbol indicates that an electrical shock
could or may occur.
FIRE HAZARD. This symbol indicates a risk of fire or flammability, or that
fire/flammability damage could or may occur.
FLAMMABLE GAS HAZARD. This symbol alerts you to gases that are
compressed, liquefied or dissolved under pressure and can ignite on contact
with an ignition source. This symbol indicates this risk could or may cause
physical injury.
GLOVES REQUIRED. This symbol indicates that you must wear gloves when
performing a task or else physical injury could or may occur.
HAND AND CHEMICAL HAZARD. This symbol indicates that chemical
damage or physical injury could or may occur.
INSTRUMENT DAMAGE. This symbol indicates that damage to the
instrument or module may occur. This damage may not be covered under the
standard warranty.
LIFTING HAZARD. This symbol indicates two or more people are required to
lift the object to prevent a physical injury that could or may occur.
MATERIAL AND EYE HAZARD. This symbol indicates that eye damage could
or may occur.
RADIOACTIVE. This symbol indicates the presence of radioactive material
could or may occur.
READ MANUAL. This symbol alerts you to carefully read your instrument’s
operational instructions before usage to ensure your safety and the
instrument’s operational ability. Failing to carefully read the instructions could
or may put you at risk for a physical injury.
TOXIC SUBSTANCES HAZARD. This symbol indicates that exposure to a
toxic substance will, could,or may cause personal injury or death.
This is the general warning symbol that the ISO 3864-2 standard refers to as
the general warning signal to prevent personal injury. It is a triangle with an
exclamation mark that precedes the WARNING safety alert word. In the
vocabulary of ANSI Z535 signage, this symbol indicates a possible personal
injury hazard exists if the instrument is improperly used or if unsafe actions
occur. We use this symbol and another appropriate safety symbol to alert to
an imminent or potential hazard that could cause personal injury.

Preface
Contacting Us
xvi DSQ II Hardware Manual Thermo Scientific
Contacting Us
There are several ways to contact Thermo Fisher Scientific.
YTo contact Technical Support
Find software updates and utilities to download at http://mssupport.thermo.com.
YTo contact Customer Service for ordering information
YTo suggest changes to documentation or to Instrument Help
• Fill out a reader survey online at www.thermo.com/lcms-techpubs.
• Send an e-mail message to the Technical Publications Editor at
[e-mail].
Related Documentation
In addition to this guide, Thermo Scientific provides the following documents for the
DSQ II. These documents are also available on a “Print-By-Request” basis.
DSQ II Document Set, PN 120299
•DSQ II Preinstallation Guide, PN 120299-0001
•DSQ II Hardware Manual, PN 120299-0002
•DSQ II User’s Guide, PN 120299-0003
•Instrument Help is available from within the Tu n e software.
To suggest ways we can improve the documentation, use your browser to complete our
documentation survey.
Phone [phone]
Fax [phone]
E-mail [e-mail]
Phone [phone]
Fax [phone]
Web site http://www.thermo.com/com/cda/resources/resources_
detail/1,,12512,00.html

Thermo Scientific DSQ II Hardware Manual 1
1
Basic Operations
This chapter describes basic operations of the TRACE GC Ultra and DSQ II.
Contents
•“Installing a Column into the GC/MS System” on page 4
•“Removing a Column from the GC/MS System” on page 15
•“Starting Up the GC/MS System” on page 17
•“Shutting Down the GC/MS System” on page 18

1Basic Operations
Getting the Right Tools
2DSQ II Hardware Manual Thermo Scientific
Getting the Right Tools
The following table contains the tools and parts you will need to install the DSQ II system.
Some items are included with the system and some are not.
Table 1. DSQ II System Installation Tools
Tools Needed
Aluminum plug (PN 290 326 55)
Brass back ferrules, Swagelok (PN A0101-02500)
Brass front ferrules, Swagelok (PN A0101-08500)
Brass nuts, Swagelok (PN A0101-15500)
Cable, PC to DSQ II, 15 ft Ethernet crossover (PN 76396-0052)
Cable, Serial, PC to TRACE GC Ultra (PN 230 980 00)
Cable, GC to DSQ II remote start (PN 76396-0050)
Capillary column, TR5MS, 15 m, 0.25 mm i.d., 0.25 μm (PN 76317-3015)
CI Ion Volume (PN 119650-0230), if applicable
Column measuring tool (PN 119640-0550)
Copper tubing, clean (PN 76381-0041, 1/8-in. o.d., 0.030-in. wall)
Digital voltmeter (Fluke model 77 or equivalent)
Dusting spray containing tetrafluoroethane (Falcon® Dust-Off®, MicroCare® MicroBlast™,
or equivalent)
Flashlight, small hand-held
Flow meter, Thermo Scientific GFM Pro (PN 66002-010)
Forceps (PN 76360-0400)
Gas filter, helium (PN A0950-01600)
Gloves, clean, lint and powder-free (medium PN 23827-0008, large PN 23827-0009)
Hex nut driver, 5.5 mm
Injector ferrule for 0.25 mm column (PN 290 134 88)
Injector nut (PN 350 324 23)
Ion volume tool (PN 119270-0001)
I/R tool and guide bar, if applicable
Leak detector (Thermo Scientific GLD Pro PN 66002-001 or equivalent)
Magnifying glass
Methanol or other suitable solvent
Potentiometer adjustment tool

1Basic Operations
Getting the Right Tools
Thermo Scientific DSQ II Hardware Manual 3
Power cords with appropriate plugs
Preinstallation Guide (PN 120299-0001)
Scoring wafer (or sapphire scribe) to cut capillary column
Screwdriver, flat blade
Screwdriver, Phillips #1
Screwdriver, Phillips #2
Syringe, 10 μL, 70 mm needle (PN 3650-0103)
Tap e m eas ure
Teflon® thread tape
Tissue, lint-free
Tubing cutter
Test mix, octafluoronaphthalene and benzophenone (PN 120150-TEST)
Transfer line ferrule, 0.4 mm i.d. (PN A0101-18100)
Wrench, (adjustable) 12-in.
Wrench, (Allen) 1/16-in.
Wrench set, (Allen) 5, 2, 2.5, 3, 4, 5 mm (PN 3812-0100)
Wrench set, (open-ended) 5–17 mm
Wrench set, (open-ended) 1/4-in., 5/16-in., 7/16-in. (2), 9/16-in.,1/2-in.
Table 1. DSQ II System Installation Tools, continued
Tools Needed

1Basic Operations
Installing a Column into the GC/MS System
4DSQ II Hardware Manual Thermo Scientific
Installing a Column into the GC/MS System
To install a column, you will need:
• Capillary column, 5MS, 15 m, 0.25 mm i.d., 0.25 μm
• Column Measuring Tool
• Gloves, clean, lint- and powder-free
• Injector ferrule, for 0.25 mm column
• Magnifying glass
• Methanol or other suitable solvent
• Scoring wafer (or sapphire scribe) to cut capillary column
• Leak detector (Thermo Scientific GLD Pro PN 66002-001 or equivalent)
• Flowmeter (Thermo Scientific GFM Pro flowmeter PN 66002-010 or equivalent)
• Tissue, lint-free
• Transfer line ferrule, 0.4 mm i.d.
• Wrench, open-ended, 5/16-in.
• Wrench, open-ended, 6 mm
• Wrenches (two), open-ended, 7/16-in.
For information about setting up the TRACE GC Ultra or FOCUS GC, refer to the
documentation supplied with the instrument.
1. Connect the column to the injector that is inside the TRACE GC Ultra.
Figure 1. GC Injector (Front)
WARNING - BURN HAZARD: The injector, oven, and transfer line may be hot. Allow
them to cool to room temperature before touching them.
1Injector 4Column
2 Injector Ferrule 5 Column Outlet
3 Injector Nut 6 Transfer Line
1
4
3
4
2
65