Thermo Scientific DSQ Series User manual

Xcalibur

Ion Trap and DSQ

Series

Direct Probe System User’s Guide

119327-0001 Revision G April 29, 2008

TRACE GC Ultra, FOCUS GC, PolarisQ, and ITQ are trademarks and/or product names of Thermo Fisher

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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.

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

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Sale shall govern all conflicting information between the two documents.

Release history: Rev G April 2008, Rev F August 2006, Rev E May 2005. Rev D March 2004. Rev C July

1999. Rev B May 1998. Rev A May 1997.

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.

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.

WEEE Compliance

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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:

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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.

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.

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

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produits Thermo Fisher Scientific qui peuvent aider la détection des substances sujettes à la directive RoHS sont

disponibles sur www.thermo.com/WEEERoHS.

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.

Thermo Scientific Ion Trap and DSQ Series Direct Probe System User’s Guide ix

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 . . . . . . . . . . . . . . . xvii

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

Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvii

Chapter 1 Using a Direct Insertion Probe (DIP) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1

How the Direct Probe System Works . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

Analyzing Cholesterol with the Ion Trap Series . . . . . . . . . . . . . . . . . . . . . . . . . . 4

Step 1: Connect the Direct Probe System . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Step 2: Change the Ion Volume . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Step 3: Deselect AS and GC Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Step 4: Tune and Calibrate the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . 10

Step 5: Program the DPC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

To retrieve methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Step 6: Prepare the Sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Step 7: Create a Method File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Step 8: Create a Sequence File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Step 9: Insert the Probe Using Xcalibur. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Step 10: Remove the Probe Using Xcalibur . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Step 11: Analyze the Data File. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Analyzing Cholesterol with the DSQ Series. . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Step 1: Connect the Direct Probe System . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Step 2: Change the Ion Volume . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Step 3: Deselect AS and GC Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Step 4: Tune and Calibrate the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . 26

Step 5: Program the DPC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

Contents

xIon Trap and DSQ Series Direct Probe System User’s Guide Thermo Scientific

To retrieve methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Step 6: Prepare the Sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Step 7: Create a Method File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Step 8: Create a Sequence File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Step 9: Insert the Probe Using Xcalibur. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Step 10: Remove the Probe Using Xcalibur . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Step 11: Analyze the Data File. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

Loading DIP Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Loading Liquid Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Loading Solid Samples. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

Cleaning the DIP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

Top Terms To Know . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

DIP Modes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

Probe Shaft . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Probe Tip . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Sample Cups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Top Safeguards to Know . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

Hints. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

Chapter 2 Using a Direct Exposure Probe (DEP) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .43

How the Direct Probe System Works . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

Analyzing Cholesterol with the Ion Trap Series . . . . . . . . . . . . . . . . . . . . . . . . . 46

Step 1: Connect the Direct Probe System . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

Step 2: Change the Ion Volume . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

Step 3: Deselect AS and GC Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

Step 4: Tune and Calibrate the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . 51

Step 5: Program the DPC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51

To retrieve methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

Step 6: Prepare the Sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

Step 7: Create a Method File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

Step 8: Create a Sequence File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

Step 9: Insert the Probe Using Xcalibur. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

Step 10: Remove the Probe Using Xcalibur . . . . . . . . . . . . . . . . . . . . . . . . . . 59

Step 11: Analyze the Data File. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60

Analyzing Cholesterol with the DSQ Series. . . . . . . . . . . . . . . . . . . . . . . . . . . . 62

Step 1: Connect the Direct Probe System . . . . . . . . . . . . . . . . . . . . . . . . . . . 63

Step 2: Change the Ion Volume . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64

Step 3: Deselect AS and GC Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

Step 4: Tune and Calibrate the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . 67

Step 5: Program the DPC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

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