Thermo Scientific TSQ 8000 Evo User manual

TSQ 8000 Evo
Mass Spectrometer
User Guide
1R120586-0002 Revision C December 2015

© 2015 Thermo Fisher Scientific Inc. All rights reserved.
TSQ, TRACE 1300, TRACE 1310, TriPlus, and TraceFinder are trademarks, and Xcalibur is a registered
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registered trademark of McAfee, Inc. in the United States and other countries. Vespel is a registered trademark
of E.I. du Pont de Nemours and Company in the United States and other countries.
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.
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, July 2014; Revision B, February 2015; Revision C, December 2015.
Software version: Thermo Foundation 3.1 SP1, Xcalibur 4.0 or later
For Research Use Only. Not for use in diagnostic procedures.

Thermo Scientific TSQ 8000 Evo User Guide iii
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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 a GC-MS/MS System. . . . . . . . . . . . . . . . . . . . . . . . .xiv
Hydrogen Connection Guidelines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv
Purchasing Hydrogen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xvi
Properly Storing Hydrogen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvii
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 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Confirming Your Instrument is Working . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Checking Power to the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Verifying the Carrier Gas Flow Rate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Checking Your Carrier Gas Tank Pressure. . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Verify Collision Gas Tank Pressure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Checking the Vacuum and Temperature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Cleaning the Exterior of Your Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Configuring Your Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Chapter 2 Changing the Column . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
Determining the Column Type. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Replacing the Factory Installed Column . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Connecting the Column to the Transfer Line . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Chapter 3 Tuning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .31
Accessing Auto Tune. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Contents

Contents
iv TSQ 8000 Evo User Guide Thermo Scientific
Tuning the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Updating Tunes for New RF Lens. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Chapter 4 Creating a Method. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .45
Accessing the Method Editor. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Creating an Autosampler Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Creating a MS Instrument Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Creating a GC Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Validating and Troubleshooting Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Chapter 5 Optimizing Your Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .89
Changing the Chromatographic Separation. . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Finding the Best Way to Make an Injection . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
Improving the Way You Prepare Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
Changing the Dwell Time or Scan Rate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
Narrowing the Mass Range . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
Adjusting the Transfer Line and Ion Source Temperature . . . . . . . . . . . . . . . . . 91
Optimizing an SRM Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Optimizing an NCI Tune . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Modifying an Automatic Tune . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
Chapter 6 Computer Settings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .111
System Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Computer Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Excluding the Xcalibur Directory from Virus Scan . . . . . . . . . . . . . . . . . . . . . 114
Chapter 7 Troubleshooting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .115
Diagnostics Checks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
How to Know When Your System Needs Maintenance . . . . . . . . . . . . . . . . . 117
Investigating Baseline Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
Investigating Peak Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Investigating Results Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .127

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,
•recalibration,and
•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 and Safety Standards
• ITQ, and Ion Trap Series standards: EMC: EN 61326-1:2006. Safety: IEC 61010-1:2001, IEC 61010-2-081:2001
• Direct Probe Controller (DPC) standards: EMC: EN 61326-1:2013. Safety: IEC 61010-1:2001,
IEC 61010-2-081:2001
• ISQ Series standards: EMC: EN 61326-1:2013. Safety: IEC 61010-1:2010 (ed. 3); IEC 61010-2-081:2015 (ed.
2); IEC 61010-2-010:2014 (ed. 3); IECEE CB SCHEME CERT NO. DE 3-30000
• TSQ 8000 Evo and TSQ Duo standards: EMC: EN 61326-1:2013. Safety: IEC 61010-1:2010 (ed. 3); IEC
61010-2-081:2015 (ed. 2); IEC 61010-2-010:2014 (ed. 3); IECEE CB SCHEME CERT NO. DE 3-30034

Low Voltage Safety Compliance
This device complies with Low Voltage Directive 2011/95/EC.
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.
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.

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.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 TSQ 8000 Evo User Guide ix
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Preface
This guide contains detailed information about how to use your Thermo Scientific
TSQ 8000™ Evo triple-quadrupole GC/MS system. The TSQ 8000 Evo system provides the
selectivity and sensitivity of a triple-quadrupole GC/MS while also functioning as a
high-performance single quadrupole instrument. The 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 greatly reduced. The extractable source incorporates a cartridge that contains the
repeller, source lenses, and RF lens, all of which can be removed from the instrument without
breaking vacuum. What once took hours, or even an entire day, is now accomplished in
minutes.
In addition, the TSQ 8000 Evo system includes innovative Thermo Scientific software that
will help users new to triple-quadrupole GC/MS/MS systems develop selected reaction
monitoring (SRM) methods.
About Your System
Thermo Scientific systems provide the highest caliber gas chromatography/mass spectrometry
(GC/MS) instrumentation available on today’s market.
Contents
•About Your System
•Related Documentation
•System Requirements
•Safety and Special Notices
•Hydrogen Safety Precautions
•Hazardous Substances Precautions
•Contacting Us

Preface
Related Documentation
xTSQ 8000 Evo User Guide Thermo Scientific
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 by an autosampler and
then separated for presentation to the MS. The MS will generate a mass spectrum of the GC
eluate and its components. The mass spectrum can then be used for qualitative identification
as well as accurate and precise quantification of the individual compounds present in the
sample.
A triple-quadrupole GC/MS/MS system provides the extra selectivity required for trace
analysis of compounds in complex matrices.
Related Documentation
The TSQ 8000 Evo system includes Help and these manuals as PDF files:
•TSQ 8000 Evo Preinstallation Guide, PN 1R120586-0001
•TSQ 8000 Evo User Guide, PN 1R120586-0002
•TSQ 8000 Evo Hardware Manual, PN 1R120586-0003
•TSQ 8000 Evo Spare Parts Guide, PN 1R120586-0004
•TSQ 8000 Evo Auto SRM User Guide, PN 1R120586-0005
•Q Exactive GC, ISQ Series and TSQ 8000 Evo Direct Probe System User Guide, PN
1R120505-0006
To view product manuals
Open the desktop folder Manuals.
To open Help
• From the TSQ Series window, choose Help > TSQ Series 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.
WARNING 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 might be impaired. If
you maintain a system outside the specifications listed in this guide, failures of many
types, including personal injury or death, might 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.