Thermo Scientifi? Ion Trap Series Hardware Manual

Xcalibur

Ion Trap Series

Hardware Manual

120425-00HW Revision B November 30, 2009

© 2009 Thermo Fisher Scientific Inc. All rights reserved. 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 Scientific. Microsoft® is a registered trademark of Microsoft. Adobe® is a registered trademark of Adobe Systems Incorporated in the United States and/or other countries. Septum BTO® is a registered trademark of Chromatography Research Supplies, Inc. Swagelok® is a registered trademark of Swagelok Company. ETP is an SGE product. All other trademarks are the property of Thermo Fisher Scientific and its subsidiaries.

Ion Trap series refers to ITQ and PolarisQ instruments. DSQ series refers to all DSQ and DSQ II instruments. Information about the TRACE GC and FOCUS GC instruments is included in this document.

NSTRUMENT 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 errorfree 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, April 29, 2008, Rev B, November 30, 2009.

For Research Use Only. Not regulated for medical or veterinary diagnostic use by U.S. Federal Drug Administration or other competent authorities.

Reader’s Survey

Ion Trap Series Hardware Manual, 120425-00HW, Revision B

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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.

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.

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/

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

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Reader’s Survey . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iii

Customer Registration Card . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iii

Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii

About Your System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii

Power Ratings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiv

Safety Alerts and Special Notices. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiv

Safety Symbols and Signal Words . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv

Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xvi

To contact Technical Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xvi

To contact Customer Service for ordering information . . . . . . . . . . . . . . . . .xvi

To suggest changes to documentation or to Instrument Help . . . . . . . . . . . .xvi

Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvi

Chapter 1 Routine Operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1

Installing a GC Column . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

Removing a GC Column . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Starting Up . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Shutting Down . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Chapter 2 Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19

Main Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Recommended Maintenance Schedule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Removing the Covers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Assembling the Ion Source and Ion Trap. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

Cleaning Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

Cleaning the Ion Source Components. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

Cleaning the Ion Trap. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61

Maintaining the Ion Detector System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

Maintaining a High-Vacuum Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70

Maintaining a Rotary-Vane Pump. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

Finding Components and Assemblies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75

Replacing the Analog PCB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

Replacing a Fuse on the Analog PCB. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81

Balun PCB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82

Replacing the Calibration Gas Flow Module. . . . . . . . . . . . . . . . . . . . . . . . . . . 83

Thermo Scientific Ion Trap Series Hardware Manual ix

Contents

Adding Calibration Compound. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85

Replacing the CI Reagent Gas Flow Module . . . . . . . . . . . . . . . . . . . . . . . . . . . 87

Replacing the Conversion Dynode/Electron Multiplier Power Supply . . . . . . . 88

Replacing the Convectron Gauge and Foreline Adapter . . . . . . . . . . . . . . . . . . 90

Replacing the Digital PCB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92

Replacing the Electrometer PCB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93

Replacing the Variable Damping Gas Regulator . . . . . . . . . . . . . . . . . . . . . . . . 95

Replacing the Damping Gas Flow Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97

Replacing the Ion Gauge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99

Replacing the Lens Interface PCB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101

Replacing the Low Pass Filter PCB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102

Replacing the Power Module. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106

Replacing the Rear Cooling Fans. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108

Replacing the RF Detector PCB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111

Replacing the RF Generator PCB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113

Replacing a Fuse on the RF Generator PCB . . . . . . . . . . . . . . . . . . . . . . . . . . 114

Replacing the Transfer Line. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115

Replacing the Turbomolecular Pump Power Supply . . . . . . . . . . . . . . . . . . . . 117

Replacing the Vacuum Control PCB. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119

Replacing the Vent Valve Solenoid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120

Chapter 3 Troubleshooting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .123

Diagnostics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123

Running Diagnostics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124

Communication Symptoms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125

Contamination Symptoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129

Filament and Lens Control Symptoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132

Heated Zone Symptoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133

High Vacuum Symptoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135

Linearity Symptoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137

Power Supply Symptoms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138

RF Control Symptoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140

Sensitivity Symptoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142

Stability Symptoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145

Tuning Symptoms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146

Chapter 4 Vacuum System and Gas Inlets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .153

Vacuum System Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153

Convectron Gauge and Foreline Adapter. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155

High Vacuum Pump. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156

Turbomolecular Pumps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156

Ion Gauge (Upgrade Option) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158

Rotary-Vane Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159

Expansion Volume (Upgrade Option) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .160

Vacuum Manifold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161

x Ion Trap Series Hardware Manual Thermo Scientific

Contents

Gas Inlets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162

Calibration Gas Flow Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163

CI Reagent Gas Flow Module (Upgrade Option) . . . . . . . . . . . . . . . . . . . . . . 164

Damping Gas Flow Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165

Vent Valve Solenoid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166

Chapter 5 Ion Source Components and Inlet Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .167

Ion Source Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168

Filament Assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169

Ion Source Block Assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170

Ion Volume Assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171

Ion Source Lenses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172

Magnets and Magnet Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173

Inlet Valve (Upgrade Option) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174

Ball Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177

Guide Bar Housing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178

I/R Tool and Guide Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179

Inlet Valve Plug. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180

Inlet Valve Seal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181

Chapter 6 Ion Trap System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .183

Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184

Chapter 7 Ion Detector Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .187

Electron Multiplier . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188

Appendix A Replaceable Parts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .191

Vacuum Manifold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192

Analyzer Assembly. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194

Ion Source. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196

Ion Source Lenses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198

Ion Trap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200

Gas Inlets and Gauges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 202

PCBs and Cables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 206

Turbomolecular Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 214

Inlet Valve (Upgrade Option) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216

Installation Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 218

Miscellaneous Items . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219

Appendix B Functional Block Diagrams. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .221

Vacuum System and Gas Inlets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222

Electronic Assemblies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223

Power Distribution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224

Cable Connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225

Thermo Scientific Ion Trap Series Hardware Manual xi

Contents

Abbreviations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .227

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .231

xii Ion Trap Series Hardware Manual Thermo Scientific

Preface

This guide contains instructions to operate and maintain the instrument. It is also designed to increase understanding and knowledge of the mass spectrometer assembly and theory of operations.

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.

Thermo Scientific Ion Trap Series Hardware Manual xiii

Preface

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, 16 A max

• 230 V ac ±10%, 50/60 Hz, 16 A max

Detailed instrument specifications are in the Product Specification or Product Brochure.

Safety Alerts and Special Notices

Make sure you follow the precautionary notices presented in this guide. Safety and other special notices appear in boxes and include the following:

WARNING A warning safety alert is used to prevent actions that could cause personal injury. It highlights hazards to humans or the environment. When you see a safety alert on your instrument or in the documentation, carefully follow the safety instructions before proceeding.

CAUTION A cautionary safety alert is used 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. When you see a safety alert on your instrument or in the documentation, 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 Emphaizes important information about a task.

Tip Helpful information that can make a task easier.

xiv Ion Trap Series Hardware Manual Thermo Scientific

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.

Preface

Safety Alerts and Special Notices

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.

Thermo Scientific Ion Trap Series Hardware Manual xv

Preface

Contacting Us

There are several ways to contact Thermo Fisher Scientific.

Y To contact Technical Support

Phone 800-532-4752

Fax 561-688-8736

E-mail US.Techsupport.Analyzer@thermofisher.com

Find software updates and utilities to download at http://mssupport.thermo.com.

Y To contact Customer Service for ordering information

Phone 800-532-4752

Fax 561-688-8731

Web site http://www.thermo.com/com/cda/resources/resources_

detail/1,,12512,00.html

Y To 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

techpubsaustin@thermofisher.com.

Installing a GC Column

To install a column, you will need:

• Capillary column, 5MS, 30 m, 0.25 mm i.d., 0.25 μm (PN A0012-08143), or similar

• Column measuring tool (PN 119640-0550), optional

• Gloves, clean, lint- and powder-free

• Injector ferrule, for 0.25 mm column (PN 290 134 88)

• Leak detector (Thermo Scientific GLD Pro PN 66002-001 or equivalent)

• Lint-free tissue

• Magnifying glass

• Methanol or other suitable solvent

• Scoring wafer (or sapphire scribe) to cut capillary column

• Transfer Line ferrule, 0.4 mm i.d. (PN A0101-18100)

• Wrench, open-ended, 5/16-in.

• Wrench, two, open-ended, 7/16-in.

• Wrench, open-ended, 6 mm

Refer to the documentation supplied with your GC for additional setup information.

WARNING - BURN HAZARD. The injector, oven, and transfer line may be hot. Allow them to cool to room temperature before touching them.

1. Connect the column to the injector, as shown in Figure 1.

Figure 1. GC Injector (Front)

Distance

1Injector 4Column

2Injector Ferrule 5Column Outlet

3 Injector Nut 6 Transfer Line

Note Wear clean, lint- and powder-free gloves when you handle the column and injector ferrule.

2 Ion Trap Series Hardware Manual Thermo Scientific

Routine Operations

Installing a GC Column

a. Unwind about half a turn of the column.

b. Wipe about 100 mm (4 in). of the column with a tissue soaked in methanol.

c. Insert the column through the injector nut and ferrule (open end up).

Note Sliding a septum on the column before the injector nut will help you measure the proper distance between the nut and the end of the column.

d. Wipe the column again with a tissue soaked in methanol.

e. Score and then break the column about 2.5 cm (1 in). from the end with a scoring

wafer. With the magnifying glass, check for an even, flat cut. Repeat if necessary.

f. Insert the column into the injector so that the end of the column is the proper

distance from the back of the injector nut. Proper distances are as follows: splitless = 64 mm, split = 40 mm, PTV = 30 mm.

g. Tighten the injector nut by hand and then turn it an additional quarter turn with the

wrench.

h. Turn on the gas chromatograph.

2. Set up the gas chromatograph.

a. Set the oven and injector temperatures to 40 °C.

b. Set the injector flow to 1.0 mL/min.

c. Turn off vacuum compensation (under the right or left carrier menu).

d. Dip the column outlet in a small vial of methanol. Bubbles indicate there is flow

through the column.

e. Allow the column

to purge for at least 10 minutes.

3. Perform column characterization.

a. Raise the oven and injector temperatures to 50 °C and allow them to stabilize. Then

confirm that the carrier gas is on.

CAUTION - INSTRUMENT DAMAGE. Do not allow the clear plastic component to exceed 80 °C. Otherwise, it will melt and damage the instrument.

Thermo Scientific Ion Trap Series Hardware Manual 3

Routine Operations

Installing a GC Column

b. Carefully push the capillary column end into the flowmeter section of the

column-flow meter connector, as shown in Figure 2.

Figure 2. Flow Measure

c. Connect the flowmeter to the dedicated fitting on the column flow meter connector.

Note The available options (Right column or Left column) will differ depending on the configuration of your GC.

d. Press Column Eval to open the following menu:

COLUMN INFORMATION

Right column Left column <

Note Make sure the Vacuum Compensation parameter is set to OFF in the Carrier menu, which is accessed by pressing the Left Carrier or Right Carrier button. Otherwise an accurate column evaluation cannot be performed.

e. Scroll to the Right or Left column to evaluate and press Enter. The following menu

appears if you select the left column and and use the settings below to set the physical characteristics of the column.

LEFT1 COLUMN INFO

Length (m) 15.00 ID (mm) 0.25 Film th. (um) 0.25

1. These settings could also apply to a right column.

4 Ion Trap Series Hardware Manual Thermo Scientific

Routine Operations

Installing a GC Column

f. Select Pre/post column? yes (Y) or no (N).

• If a pre-/post-column is not present, select N.

• If a pre-/post-column is present, select Y. You must set the length and nominal internal diameter of the pre-/post-column in the same valid ranges for the column. The following two lines are added to the menu.

Pre/post column? Y P/p col. L 10.00 P/p col. ID 0.530

g. According to the physical characteristics of the column, the system calculates and

displays the relevant Column K-factor.

LEFT

COLUMN INFO

Column K= (0.8087) Calc’d ID (0.0000) Run Column eval?

1. These settings could also apply to a right column.

h. To evaluate the column, scroll to Run column eval.? and press ENTER.

The system will set the Column K factor by pressurizing the column to obtain a nominal carrier flow of 5 mL/min. The display shows the pressure.

i. Using the flowmeter, measure the carrier gas flow at the outlet of the column. Scroll

to Measured Flow and set the value of the flow.

EVALUATING L COLUMN

Pressure (162) Measured Flow: 4.90 Use <STOP> to abort

Note To abort column evaluation, you can press STOP.

j. The following message will display if the operation was successful.

L. COL. EVALUATION

COMPLETED

Calc’d ID 0.242

K. 0.9020

Thermo Scientific Ion Trap Series Hardware Manual 5

Routine Operations

Installing a GC Column

k. Expect a K-factor of about 0.7 – 0.9 for a 15 m, 0.25 mm i.d. column (1.3 – 2.0 for

a 30 m, 0.25 mm i.d. column). If the column does not report a K-factor within this range or within 0.1 units of the previous stored value, check for a leak or broken column using the leak detector. The K-factor is a measured resistance for the column. A K-factor that is too low may indicate a leak in the system, while a K-factor that is too high may indicate a blockage.

4. Perform a column leak check.

a. Carefully push the capillary column end into the column section of the column-flow

meter connector, as shown in Figure 3.

CAUTION - INSTRUMENT DAMAGE. Do not allow the clear plastic component to exceed 80 °C. Otherwise, it will melt and damage the instrument.

Figure 3. Leak Check

A B C

b. Press Leak Check to access the Leak Check Columns menu.

Note The available options (Right column or Left column) will differ depending on the configuration of your GC.

LEAK CHECK COLUMN

Right column Left column <

1. This item appears if the relevant channel is present and configured.

c. Scroll to a channel to open the left or right column’s leak check menu.

L. COL. LEAK CHECK

Start Leak Check Leak Check Settings

6 Ion Trap Series Hardware Manual Thermo Scientific

Routine Operations

Installing a GC Column

d. Scroll to Leak Check Settings.

L. COL. SETT.

Check Leak press 200 Sensitivity 5.0

e. In the Check at press line, set the pressure at which the leak check will be performed.

The value must be between 10 and 999 kPa (1.45 and 145 psi).

f. In the Sensitivity line, set the maximum pressure drop that is allowed during the test.

The value must be between 1 and 10 kPa (0.145 and 1.45 psi).

g. Press CLEAR to exit the Leak Check Settings menu and return to the previous menu.

L. COL. LEAK CHECK

Start leak check Leak Check settings

h. Select Start leak check to begin operation. The split and purge valves of the selected

channel are automatically closed and the channel is pressurized with carrier gas to the leak check set point.

CHECKING L COLUMN

Pressure (200) Elapsed time 0.90 Use <STOP> to abort

Note To abort a leak check, you can press STOP.

i. The system monitors the pressure for one minute. If the pressure does not drop more

than the maximum allowed sensitivity value, then the leak check will pass.

R/L.LEAK CHECK

COMPLETED

SUCCESSFULLY

Leak check passed.

If the leak check did not pass, you should use the leak detector to find and fix the leaks.

Tip Leaks can be caused by not tightening the fitting on the clear plastic component. We recommend that you check that fitting before looking elsewhere.

j. Repeat the column evaluation and leak check until no leaks are indicated.

Thermo Scientific Ion Trap Series Hardware Manual 7

Routine Operations

Installing a GC Column

5. Disconnect the column from the clear plastic component.

6. Remove the clear plastic component, including its fittings, from the oven and set it aside.

7. Condition the column before inserting it into the mass spectrometer.

CAUTION INSTRUMENT DAMAGE. The material released from the column during the conditioning (column bleed) will contaminate the ion source if the column is inserted into the transfer line. The ion source must then be cleaned.

a. Raise the injector temperature to the desired temperature (normally 250 °C).

b. Run the slow temperature program that is recommended by the manufacturer. For

example, hold the column at 40 °C for 15 minutes, then ramp it to 10 °C per minute up to 10 °C above the maximum temperature at which you will operate the column (normally 300+10 °C = 310 °C). Hold the column at this temperature for two hours.

CAUTION INSTRUMENT DAMAGE. Never exceed the column manufacturer’s maximum operating temperature.

8. Connect the column to the transfer line.

a. Shut down and vent the mass spectrometer, as described in “Shutting Down” on

page 16.

b. Lower the oven temperature to 40 °C and allow it to cool before continuing.

WARNING - BURN HAZARD. The injector, oven, and transfer line may be hot. Allow them to cool to room temperature before touching them.

c. Unwind about one turn of the column (shown in Figure 4) from the column outlet

end.

Figure 4. Column Measuring Tool

1 Column Measuring Tool* 4 Column

2 Transfer Line Ferrule 5 Septum

3Transfer Line Nut

* The Column Measuring Tool is sold separately and can be purchased through Thermo Fisher Scientific using part number 119640-0550.

8 Ion Trap Series Hardware Manual Thermo Scientific

Routine Operations

Installing a GC Column

Note Wear clean, lint- and powder-free gloves when you handle the column and transfer line ferrule.

d. Wipe about 300 mm (12 in). of the column with a tissue soaked in methanol.

e. Insert the column through the septum, transfer line nut, and ferrule. Wipe the

column again with a tissue soaked in methanol.

Note Sliding a septum on the column before the transfer line nut will help you measure the proper distance between the nut and the end of the column. The column should extend approximately 1–2 mm past the end of the transfer line.

f. Score and break the end of the column with a scoring wafer. With the magnifying

glass, check for an even, flat cut. Repeat, if necessary.

g. Insert the column into the transfer line using one of the following methods: Method

One, Method Two, or Method Three.

Method One

If you have a column measuring tool, follow these steps to insert the column:

1. Screw the transfer line nut onto the column measuring tool

2. Push the column past the end of the column measuring tool and score and break the end of the column with a scoring wafer. With the magnifying glass, check for an even, flat cut. Repeat if necessary.

3. Pull the column back so that it is flush with the end of the column measuring tool and tighten the transfer line nut.

4. Slide the septum up to the back of the transfer line nut.

5. Remove the column, transfer line nut and ferrule from the column measuring tool, as shown in Figure 5.

Figure 5. Transfer Line (Front)

Purchase the Column Measuring Tool PN 119640-0550 from Thermo Fisher Scientific.

Thermo Scientific Ion Trap Series Hardware Manual 9

Routine Operations

Installing a GC Column

Figure 5. Transfer Line (Front)

1 Septum 5 Transfer Line Union

2 Transfer Line Nut 4 Transfer Line

a. Insert the column into the transfer line. Be careful not to move the septum.

b. Tighten the transfer line nut and the transfer line union.

6. Condition the transfer line ferrule. Graphite/vespel ferrules like the transfer line ferrule require conditioning to ensure a leak-tight seal.

a. Raise the oven temperature to the maximum temperature you will operate the

column (normally 300 °C).

b. Wait 10 minutes.

c. Lower the oven temperature to 40 °C and allow it to cool before continuing.

WARNING - BURN HAZARD. The injector, oven, and transfer line may be hot. Allow them to cool to room temperature before touching them.

Method Two

d. Re-tighten the transfer line nut and the transfer line union.

7. Set up the gas chromatograph.

a. Make sure the column does not have any sharp bends and that it does not touch any

metal objects or walls inside the oven.

b. Raise the oven temperature to the initial temperature you will use (normally 40 °C).

c. Turn on the vacuum compensation (under the right or left carrier menu).

If you have the optional inlet valve, follow these steps to insert the column:

Tip Slide a septum on the column before adding the transfer line nut to make it easier to measure the proper distance between the nut and the end of the column. You can also use a white marker to mark the position of the column and nut.

1. Remove the mass spectrometer front cover so you can get a better view of the column.

2. Using the I/R tool, remove the ion volume, as described in “Cleaning the Ion Source

Components” on page 37.

3. Insert the column into the transfer line and tighten the transfer line nut by hand.

4. Push the column in until you can see it through the inlet valve.

5. Pull the column back just far enough that you cannot see it.

6. Tighten the transfer line nut and transfer line union.

10 Ion Trap Series Hardware Manual Thermo Scientific

Routine Operations

Installing a GC Column

7. Using the I/R tool, replace the ion volume, as described in “Cleaning the Ion Source

Components” on page 37.

8. Condition the transfer line ferrule. Graphite/vespel ferrules like the transfer line ferrule require conditioning to ensure a leak-tight seal.

a. Raise the oven temperature to the maximum temperature you will operate the

column (normally 300 °C).

b. Wait 10 minutes.

c. Lower the oven temperature to 40 °C and allow it to cool before continuing.

WARNING - BURN HAZARD. The injector, oven, and transfer line may be hot. Allow them to cool to room temperature before touching them.

d. Re-tighten the transfer line nut and the transfer line union.

9. Set up the gas chromatograph.

a. Make sure the column does not have any sharp bends and that it does not touch any

metal objects or walls inside the oven.

Method Three

b. Raise the oven temperature to the initial temperature you will use (normally 40 °C).

Note Turn on vacuum compensation (under the Right or Left Carrier menu).

If you do not have an inlet valve, follow these steps to insert the column:

1. Remove the front and top covers so you can get a better view of the column.

2. Remove the vacuum manifold cover, as described in “Removing the Vacuum Manifold

Cover” on page 28.

3. Remove the ion source assembly, as described in“Cleaning the Ion Source Components” on page 37.

4. Adjust the column so that it extends 1–2 mm past the end of the transfer line.

5. Tighten the transfer line nut and transfer line union.

6. Condition the transfer line ferrule. Graphite/vespel ferrules like the transfer line ferrule require conditioning to ensure a leak-tight seal.

a. Raise the oven temperature to the maximum temperature you will operate the

column (normally 300 °C).

b. Wait 10 minutes.

c. Lower the oven temperature to 40 °C and allow it to cool before continuing.

Thermo Scientific Ion Trap Series Hardware Manual 11

Routine Operations

Installing a GC Column

WARNING - BURN HAZARD. The injector, oven, and transfer line may be hot. Allow them to cool to room temperature before touching them.

d. Re-tighten the transfer line nut and the transfer line union.

7. Replace the ion source assembly, as described in “Cleaning the Ion Source Components” on page 37.

8. Replace the vacuum manifold cover.

9. Replace the front and top covers.

10. Condition the transfer line ferrule. Graphite/vespel ferrules like the transfer line ferrule require conditioning to ensure a leak-tight seal.

a. Raise the oven temperature to the maximum temperature you will operate the

column (normally 300 °C).

b. Wait 10 minutes.

c. Lower the oven temperature to 30 °C and allow it to cool before continuing.

WARNING - BURN HAZARD. The oven may be hot. Allow it to cool to room temperature before opening it. The injector will still be hot, so do not touch it.

d. Re-tighten the transfer line nut and the transfer line union.

11. Set up the gas chromatograph.

a. Make sure the column does not have any sharp bends and that it does not touch any

metal objects or walls inside the oven.

b. Raise the oven temperature to the initial temperature you will use (normally 40 °C).

Note Turn on vacuum compensation (under the Right or Left Carrier menu).

12 Ion Trap Series Hardware Manual Thermo Scientific

Removing a GC Column

To remove a GC column, you will need:

• Gloves, clean, lint- and powder-free

• Wrench, open-ended, 5/16-in.

• Wrench, open-ended, 7/16-in.

• Wrench, open-ended, 6 mm

1. Shut down the mass spectrometer.

a. Shut down and vent the mass spectrometer, as described in “Shutting Down” on

page 16.

b. Lower the oven, injector, and transfer line temperatures to 30 °C and allow them to

cool before continuing.

WARNING - BURN HAZARD. The injector, oven, and transfer line may be hot. Allow them to cool to room temperature before touching them.

c. Once the oven, injector, and transfer line are cool, turn off the gas chromatograph.

Routine Operations

Removing a GC Column

2. Remove the column from the transfer line, as shown in Figure 6.

Figure 6. Transfer Line (Front)

1 Septum 3 Transfer Line Union

2 Transfer Line Nut 4 Transfer Line

a. Unscrew the transfer line nut.

b. Remove the column from the transfer line.

Thermo Scientific Ion Trap Series Hardware Manual 13

Routine Operations

Starting Up

3. Remove the column from the injector, as shown in Figure 7.

Figure 7. Injector (Front)

Distance

Starting Up

1Injector 4Column

2 Injector Ferrule 5 Column Outlet

3 Injector Nut 6 Transfer Line

a. Unscrew the injector nut.

b. Remove the column from the injector.

1. Set up the mass spectrometer.

a. Install the GC column, as described in “Installing a GC Column” on page 2.

b. Verify that the gas chromatograph is on and there is carrier gas flowing through the

column into the mass spectrometer.

WARNING - INSTRUMENT DAMAGE. Damage may occur if you turn on the mass spectrometer without column flow. This forces air to be drawn through the column. This large air leak into the mass spectrometer may cause the ion source to require cleaning as well as potentially damaging the column.

c. Plug in the mass spectrometer power cord.

14 Ion Trap Series Hardware Manual Thermo Scientific

+ 220 hidden pages

Thermo Scientifi? Ion Trap Series Hardware Manual

Specifications and Main Features

Frequently Asked Questions

User Manual

Contents

Installing a GC Column

Method One

Method Two

Method Three

Removing a GC Column

Starting Up