Thermo Scientific ISQ User manual

ISQ
User Guide
1R120555-0003 Revision D January 2013

© 2013 Thermo Fisher Scientific Inc. All rights reserved.
ISQ, TSQ 8000, TSQ Quantum, TRACE 1300, TRACE 1310, TRACE GC, TRACE GC Ultra,
TraceFinder, and FOCUS GC are trademarks, and Xcalibur is a registered trademark of Thermo Fisher
Scientific in the United States.
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registered trademark of E.I. du Pont de Nemours and Company in the United States and other countries.
All other trademarks are the property of Thermo Fisher Scientific and its subsidiaries.
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: Revision A, May 2010; Revision B, March 2012; Revision C, December 2012
Software version: Thermo Foundation 2.0 SP1, Thermo Xcalibur 2.2 SP1
For Research Use Only. Not for use in diagnostic procedures.

Thermo Scientific ISQ User Guide iii
C
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
About Your System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .ix
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
System Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xi
Safety and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xi
Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xi
Safety Symbols and Signal Words . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xi
Hydrogen Safety Precautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii
Using Hydrogen with ISQ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv
Hydrogen Connection Guidelines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xvi
Purchasing Hydrogen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvii
Properly Storing Hydrogen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xviii
Hydrogen Safety Codes, Standards and References . . . . . . . . . . . . . . . . . . . .xix
Hazardous Substances Precautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xx
Biological Hazard Warning Note. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xx
Venting Toxic Gases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xxi
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xxi
Chapter 1 Confirming Your GC/MS System is Working . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Checking Power to the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Verifying the Carrier Gas Flow Rate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Checking Your Carrier Gas Tank Pressure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Checking the Vacuum and Temperature. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Chapter 2 Changing the Column . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5
Replacing the Factory Installed Column . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Connecting the Column to the Transfer Line . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Chapter 3 Tuning the ISQ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23
Accessing ISQ Autotune . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Tuning the ISQ Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Chapter 4 Creating a Method. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33
Creating a Method for the Autosampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Creating a Method for the ISQ Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . 37
Contents

Contents
iv ISQ User Guide Thermo Scientific
Creating a Method for the GC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Creating a method for the TRACE 1300 or TRACE 1310 . . . . . . . . . . . . . . 43
Creating a Method for the TRACE GC Ultra . . . . . . . . . . . . . . . . . . . . . . . . 50
Creating a Method for the FOCUS GC . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Chapter 5 Running a Sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .61
Preparing Your Sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Running a Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Chapter 6 Exploring Your Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .75
Chapter 7 Optimizing Your Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .85
Changing the Chromatographic Separation. . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Finding the Best Way to Make an Injection . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Improving the Way You Prepare Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Changing the Scan Rate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Narrowing the Mass Range . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Adjusting the Transfer Line Temperature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Modifying an Automatic Tune . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Chapter 8 Troubleshooting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .103
No Ions Present in Scans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
Checking the ISQ System Firmware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
How to Know When Your System Needs Maintenance . . . . . . . . . . . . . . . . . 107
Investigating Baseline Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
Investigating Peak Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
Investigating Results Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Reconfiguring Your Instrument. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115

Declaration
Manufacturer: Thermo Fisher Scientific
Thermo Fisher Scientific is the manufacturer of the instrument described in this manual and, as such, is responsible for
the instrument safety, reliability and performance only if:
•installation
• re-calibration
•changesandrepairs
have been carried out by authorized personnel and if:
• the local installation complies with local law regulations
• the instrument is used according to the instructions provided and if its operation is only entrusted to qualified
trained personnel
Thermo Fisher Scientific is not liable for any damages derived from the non-compliance with the aforementioned
recommendations.
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 in the next section or sections by product name.
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. EMC Directive 89/336/EEC
EMC compliance has been evaluated by Professional Testing.
• Polaris Q, ITQ, and Ion Trap Series standards: EMC EN 61326-1:2006. Safety IEC 61010-1:2001,
IEC 61010-2-081:2001
• DSQ II standards: EMC EN 61326-1:1997 + A1:1998 + A2:2001. Safety EN 61010-1:2001
• Direct Probe Controller (DPC) standards: EMC EN 61326-1:2006. Safety IEC 61010-1:2001,
IEC 61010-2-081:2001
• ISQ and TSQ 8000 standards: EMC EN 61326-1:2006. Safety IEC 61010-1:2001, IEC 61010-2-081:2001
Low Voltage Safety Compliance
This device complies with Low Voltage Directive 2006/95/EC and harmonized standard EN 61010-1:2001.

FCC Compliance Statement
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.
THIS DEVICE COMPLIES WITH PART 15 OF THE FCC RULES. OPERATION IS SUBJECT TO
THE FOLLOWING TWO CONDITIONS: (1) THIS DEVICE MAY NOT CAUSE HARMFUL
INTERFERENCE, AND (2) THIS DEVICE MUST ACCEPT ANY INTERFERENCE RECEIVED,
INCLUDING INTERFERENCE THAT MAY CAUSE UNDESIRED OPERATION.
CAUTION 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
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.thermoscientific.com/
rohsweee 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.thermoscientific.com/rohsweee.

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.thermoscientific.com/rohsweee.

Thermo Scientific ISQ User Guide ix
P
Preface
This guide contains detailed information about how to use the Thermo Scientific ISQ™ single
quadrupole GC-MS system. The ISQ system is designed to stay cleaner, longer, to maximize
your instrument’s uptime and improve your lab’s productivity. The need to break vacuum,
cool off your system, and spend hours cleaning, reassembling, and restoring the system is
gone. The heated ion volume, lens stack, and ion optics path in the ISQ system ensure that
the system stays cleaner longer, but when the system no longer meets your analytical needs,
restoring performance is quick and easy. The ExtractaBrite source incorporates a cartridge that
contains the repeller, source lenses, and RF lens, all of which can be removed from the
instrument while still under vacuum. What once took hours, or even an entire day, is now
accomplished in minutes.
About Your System
Gas chromatography/mass spectrometry (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.
Contents
•About Your System
•Related Documentation
•System Requirements
•Safety and Special Notices
•Hydrogen Safety Precautions
•Hazardous Substances Precautions
•Contacting Us

Preface
Related Documentation
xISQ User Guide Thermo Scientific
Related Documentation
ISQ includes Help and these manuals as PDF files:
•ISQ Preinstallation Requirements Guide PN 1R120555-0001
•ISQ Hardware Manual PN 1R120555-0002
•ISQ User Guide PN 1R120555-0003
•ISQ Spare Parts Guide PN 1R120555-0004
•ISQ and TSQ 8000 Direct Probe System User Guide PN 1R120505-0006
To view product manuals
Go to Start > All Programs > Foundation 2.0 > Manuals > ISQ.
To open Help
• From the ISQ window, choose Help > ISQ Help.
• If available for a specific window or dialog box, click Help or press the F1 key for
information about setting parameters.
For more information, visit www.thermoscientific.com.