TSQ8000_UG 1R120587 0002 TSQ Duo User Guide
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TSQ Duo
Mass Spectrometer
User Guide
1R120587-0002 Revision D October 2016
© 2016 Thermo Fisher Scientific Inc. All rights reserved.
TSQ, TRACE, TriPlus, Chromeleon, and TraceFinder are trademarks, and Xcalibur is a registered trademark
of Thermo Fisher Scientific in the United States.
The following are registered trademarks in the United States and other countries: Microsoft, Windows, and
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Incorporated. SilTite is a registered trademark of SGE Analytical Science in the United States. McAfee is a
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.
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, September 2014; Revision B, March 2015; Revision C, December 2015;
Revision D, October 2016
Software version: Thermo Foundation 3.0 SP2 or later, Thermo Scientific™ Dionex™ Chromeleon™ 7 (release
7.2 SR3 MUa or later.
For Research Use Only. Not for use in diagnostic procedures.
Thermo Scientific TSQ Duo 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 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. . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Verify Collision Gas Tank Pressure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Checking the Vacuum and Temperature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Cleaning the Exterior of Your Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
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 Duo User Guide Thermo Scientific
Tune Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
EI Initial Tune . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
EI Standard Tune . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
EI Standard Quick Tune . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
EI SRM Tune . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
EI SRM Quick Tune. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
EI Tune Check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
EI Diagnostics Only . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
EI Target Tune . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Fast Scan Tune . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Negative CI Tune . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Positive CI Tune . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Tuning the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Updating Tunes for New RF Lens. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Chapter 4 Creating a Method. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .53
Accessing the Method Editor. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Creating a GC-MS method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Running a Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
Chapter 5 Optimizing Your Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .91
Changing the Chromatographic Separation. . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
Finding the Best Way to Make an Injection . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Improving the Way You Prepare Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Changing the Dwell Time or Scan Rate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Narrowing the Mass Range . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Adjusting the Transfer Line and Ion Source Temperature . . . . . . . . . . . . . . . . . 93
Optimizing an SRM Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
Modifying an Automatic Tune . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Chapter 6 Computer Settings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .109
System Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
Computer Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
Excluding the Xcalibur Directory from Virus Scan . . . . . . . . . . . . . . . . . . . . . 112
Chapter 7 Troubleshooting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .113
Setting Instrument Conditions for Troubleshooting . . . . . . . . . . . . . . . . . . . . 114
Checking Air/Water Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Diagnostics Checks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
How to Know When Your System Needs Maintenance . . . . . . . . . . . . . . . . . 121
Investigating Baseline Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
Investigating Peak Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
Investigating Results Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .133
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
•changes and repairs
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 61326-1:2006. Safety IEC 61010-1:2001,
IEC 61010-2-081:2001
• ISQ standards: EMC EN 61326-1:2013. Safety IEC 61010-1:2010, IEC 61010-2-010:2014,
IEC 61010-2-081:2015
• TSQ 8000 Evo and TSQ Duo standards: EMC EN 61326-1:22013. Safety IEC 61010-1:2010,
IEC 61010-2-010:2014, IEC 61010-2-081:2015
Low Voltage Safety Compliance
This device complies with Low Voltage Directive 2014/35/EU 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.
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 Duo User Guide ix
P
Preface
This guide contains detailed information about how to use your Thermo Scientific TSQ Duo
triple-quadrupole GC/MS system. The TSQ Duo 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. In addition, the TSQ Duo 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.
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.
Contents
•About Your System
•Related Documentation
•System Requirements
•Safety and Special Notices
•Hydrogen Safety Precautions
•Hazardous Substances Precautions
•Contacting Us
Preface
Related Documentation
xTSQ Duo User Guide Thermo Scientific
A triple-quadrupole GC/MS/MS system provides the extra selectivity required for trace
analysis of compounds in complex matrices.
Related Documentation
The TSQ Duo system includes Help and these manuals as PDF files:
•TSQ Duo Preinstallation Guide, PN 1R120587-0001
•TSQ Duo User Guide, PN 1R120587-0002
•TSQ Duo Hardware Manual, PN 1R120587-0003
•TSQ Duo Spare Parts Guide, PN 1R120587-0004
•TSQ Duo Auto SRM User Guide, PN 1R120587-0005
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.
Preface
System Requirements
Thermo Scientific TSQ Duo User Guide xi
System Requirements
Your data system must meet these minimum requirements.
Safety and Special Notices
Make sure you follow the precautionary statements presented in this guide. The safety and
other special notices appear in boxes.
Special Notices
Special notices include the following:
Safety Symbols and Signal Words
All safety symbols are followed by WARNING or CAUTION, which indicates the degree of risk
for personal injury, instrument damage, or both. Cautions and warnings are following by a
descriptor. A WARNING is intended to prevent improper actions that could cause personal
injury. A CAUTION is intended to prevent improper actions that might cause personal injury
or instrument damage. You can find the following safety symbols on your instrument or in
this guide.
System Requirements
Hardware • 4.6 GHz processor with 16GB RAM
•DVD/CD-ROM drive
• Video card and monitor capable of 1680 ×1050 resolution
• 1000 GB hard drive
• Quad core processor
Software • Microsoft™ Windows™ 7 SP1 Operating System (64-bit)
• Thermo Foundation 3.0 SP2 (Thermo Scientific software)1
• Thermo Scientific™ Dionex™ Chromeleon™ 7 (release 7.2 SR3 MUa
or later)2.
1Check release notes for compatibility with TSQ Series instrument control software.
2Check release notes for compatibility with Thermo Foundation and TSQ Series instrument control software.
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 Highlights information of general interest.
Tip Highlights helpful information that can make a task easier.
Preface
Safety and Special Notices
xii TSQ Duo User Guide Thermo Scientific
Symbol Descriptor
BIOHAZARD: Indicates that a biohazard will, could, or might occur.
BURN HAZARD: Alerts you to the presence of a hot surface that could or
might cause burn injuries.
ELECTRICAL SHOCK HAZARD: Indicates that an electrical shock could or
might occur.
FIRE HAZARD: Indicates a risk of fire or flammability could or might occur.
FLAMMABLE GAS HAZARD: 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 might cause physical
injury.
GLOVES REQUIRED: Indicates that you must wear gloves when performing
a task or physical injury could or might occur.
HAND AND CHEMICAL HAZARD: Indicates that chemical damage or
physical injury could or might occur.
INSTRUMENT DAMAGE: Indicates that damage to the instrument or
component might occur. This damage might not be covered under the
standard warranty.
LIFTING HAZARD: Indicates that a physical injury could or might occur if
two or more people do not lift an object.
MATERIAL AND EYE HAZARD: Indicates that eye damage could or might
occur.
RADIOACTIVE HAZARD: Indicates that exposure to radioactive material
could or might occur.
Preface
Hydrogen Safety Precautions
Thermo Scientific TSQ Duo User Guide xiii
Hydrogen Safety Precautions
Hydrogen is a colorless, odorless, highly flammable gas with the molecular formula H2 and an
atomic weight of 1.00794, making it the lightest element. Hydrogen gas presents a hazard as
it is combustible over a wide range of concentrations: at ambient temperature and pressure,
this ranges from about 4% to 74.2% by volume.
Hydrogen has a flash point of - 423 °F (- 253 °C) and an auto-ignition temperature of
1,040 °F (560 °C). It has a very low ignition energy and the highest burning velocity of any
gas. If hydrogen is allowed to expand rapidly from high pressure, it can self-ignite. Hydrogen
burns with a flame that can be invisible in bright light.
Before you begin using hydrogen, you should conduct a risk assessment based on the quantity
of hydrogen to be used and the conditions of your laboratory. You should ask yourself:
“What hydrogen hazards associated with this project are most likely to occur?”
“What hydrogen hazards associated with this project have the potential to result in the
worst consequences?”
• Try to reduce or eliminate the higher risks by using the proper ventilation to remove
hydrogen gas before an ignitable concentration can accumulate. You should also consider
purging the hydrogen to further reduce hazards and ensure anyone who will be working
with hydrogen has basic hydrogen safety training.
READ MANUAL: Alerts you to carefully read your instrument’s
documentation to ensure your safety and the instrument’s operational
ability. Failing to carefully read the documentation could or might put you at
risk for a physical injury.
TOXIC SUBSTANCES HAZARD: Indicates that exposure to a toxic substance
could occur and that exposure could or might cause personal injury or death.
For the prevention of personal injury, this general warning symbol precedes
the WARNING safety alert word and meets the ISO 3864-2 standard. In the
vocabulary of ANSI Z535 signs, this symbol indicates a possible personal
injury hazard exists if the instrument is improperly used or if unsafe actions
occur. This symbol and another appropriate safety symbol alerts you to an
imminent or potential hazard that could cause personal injury.
Symbol Descriptor
WARNING FIRE HAZARD: The use of hydrogen as a carrier gas is dangerous. Hydrogen is
potentially explosive and must be used with extreme care. Any use of hydrogen gas must
be reviewed by appropriate health and safety staff and all installations of hydrogen systems
must be performed to applicable codes and standards. Thermo Fisher Scientific assumes
no liability for the improper use of hydrogen as a carrier gas.
Preface
Hydrogen Safety Precautions
xiv TSQ Duo User Guide Thermo Scientific
• As with laboratory safety in general, be sure to wear safety glasses, laboratory coats,
gloves, etc. Typically there are no specific requirements for gaseous hydrogen, other than
eye protection when working with a compressed gas. If working with liquid (cryogenic)
hydrogen, insulated gloves and protective shoes should be worn in addition to eye
protection.
• You should post “No Smoking” and “No Open Flames” signs to identify hydrogen
sources and cylinders. Maintain, inspect and leak-test all hydrogen sources regularly.
• All hydrogen shutoff valves should be clearly marked and permanent hydrogen piping
should be labeled as such at the supply or discharge point and at regular intervals along its
length. Where hydrogen gas piping passes through a wall, the piping should be labeled on
both sides of the wall.
• There should also be contingency plans in place should an incident occur.
• The site emergency response team, as well as the local fire department, should know the
location of all hydrogen storage tanks.
Using Hydrogen with a GC-MS/MS System
To use hydrogen with the mass spectrometer, you must always shut off the GC carrier gas
before venting or turning off the mass spectrometer. There are three hydrogen safety screws on
the mass spectrometer that must be in place. These are attached to your instrument at the
factory.
Figure 1. Hydrogen Safety Screws on the Mass Spectrometer
Before powering on the GC-MS/MS system, ensure that:
Left Top
Cover Screw
Right Top
Cover Screw
Front Panel
Screw
Preface
Hydrogen Safety Precautions
Thermo Scientific TSQ Duo User Guide xv
• All the covers and panels of the GC-MS/MS system are firmly attached.
• The vent valve is tightly closed if you vented the system.
• All fittings, ferrules, and o-rings are sealed.
Hydrogen Connection Guidelines
Use the following guidelines to safely connect hydrogen to your system:
•Piping—Hydrogen must be delivered to equipment using appropriate piping and be
done in such a way as to pose essentially no hazard to end-users. Piping systems for the
delivery of hydrogen should be designed and installed by a person qualified by specific
training and experience with hydrogen piping systems.
Stainless steel is usually recommended because it is a safe, cost-effective material. Piping
of black iron or copper must not be used, as the pipe can become brittle with age.
Elastomeric/plastic tubing of various plastics and polymers should not be used, unless the
tubing is approved for use with hydrogen. If elastomeric/plastic tubing is used for
hydrogen gas delivery, the tubing should be tested for hydrogen permeability to minimize
leakage.
The hydrogen piping system must be flexible enough to endure routine thermal
expansion and contraction. The system should also include considerations for the most
severe condition of temperature and pressure expected during service. Piping and
supports must be able to withstand static loading introduced by such things as ice and
snow; and dynamic loading from high wind and earthquake.
Caution should be used if burying hydrogen piping. Proper controls should be used to
protect against damage and corrosion, and also to prevent Hydrogen from entering a
building if there is any leakage.
•Fittings—All fittings must be of the proper type approved or designed for use with
hydrogen gas. Use as few fittings as possible to minimize the potential for leaks. After
installation, ensure that leak testing is carried out prior to system use, and on a regular
basis.
There must be no PTFE tape or other things like plumber's putty used to enhance a seal, as
this actually is a detriment to a good seal. Ideally the best installation would use stainless
steel tubing with appropriate gas-tight fittings.
Welding is usually preferred for joints in hydrogen piping systems since welding provides
a better connection and reduces the potential for leaks compared to mechanical fittings.
Soft solder joints are not permitted for hydrogen systems (due to the low melting point of
soft solder and its potential for brittle failure at cryogenic temperatures). Brazed joints are
permitted, but such joints should be protected against the possibility of external fire.
Tubing connections should be clamped to barbed or press-fit type connections. Hose
clamps or jubilee clamps must not be used.
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Hydrogen Safety Precautions
xvi TSQ Duo User Guide Thermo Scientific
•Valves—All valves must be suitable for hydrogen service and for the specific operating
conditions. Valves, including regulators, must not be used for hydrogen, unless they are
designed and identified for such a use. Ball valves are often chosen because of their
superior leak tightness through the valve seat. Pneumatic operators are usually chosen for
remotely operated valves so that potential ignition sources (electricity) are remote from
the valve.
Manual shutoff valves should be provided near each point of use, within immediate reach.
If a hydrogen cylinder or hydrogen generation system is located within immediate reach,
a separate point-of-use shutoff valve is usually not necessary.
Line regulators that have their source away from the point of use should have a manual
shutoff valve near the point of use.
An emergency gas shutoff device in an accessible location outside the use area should be
provided in addition to the manual point-of-use valve in each educational and
instructional laboratory space that has a piped gas supply system.
If necessary, the piping system should have uninterruptible pressure relief. The pressure
relief system should be designed to provide a discharge rate sufficient to avoid further
pressure increase and should vent to a safe location outside or to a ventilation system
exhaust.
Purchasing Hydrogen
Use the following guidelines when purchasing hydrogen:
•Hydrogen Generator—Because it minimizes the amount of hydrogen present and
reduces the degree of hazard, a hydrogen generator (also called an electrolyzer) is the safest
way to purchase hydrogen in the quantity used in GC/MS.
However, to minimize the degree of hazard, the hydrogen generator must only be
operated in a non-explosive environment because hydrogen buildup can be ignitable.
This means that your ventilation system for the room or lab hood must maintain an air
exchange rate that is at least two orders of magnitude greater than the maximum
hydrogen production rate of the hydrogen generator. Be sure to follow the manufacturers'
directions about proper use and maintenance of the regulator.
To prevent the possibility of releasing hydrogen, the hydrogen generator should be set to
shut down if:
– There is a loss of flow to the ventilation system
– A hydrogen detector alarms at 25% of the lower flammable limit of hydrogen in air.
The oxygen exhausted by the electrolyzer should be vented to the outside as well.
Preface
Hydrogen Safety Precautions
Thermo Scientific TSQ Duo User Guide xvii
•Hydrogen Cylinder—Hydrogen can be delivered in standard laboratory gas bottles or
cylinders. These cylinders have a limited amount of hydrogen in them and are a safe way
to transport and store hydrogen. However, compressed hydrogen gas cylinders, like all
compressed gas cylinders, must be secured in an upright position, ideally with a
non-combustible chain or cable. If the cylinder falls over, the valve can be knocked off
and the pressurized cylinder can take off like a rocket, which leads to the release of
hydrogen and possibly an explosion, severe injury, or death. Never crack a hydrogen
cylinder valve to remove dust or dirt from fittings prior to attaching a regulator, as there is
a risk of self-ignition.
Properly Storing Hydrogen
Storing and handling compressed hydrogen gas and cryogenic liquid hydrogen present
potential health and safety hazards. Using proper storage and handling techniques is essential
to maintaining a safe work environment.
Use the following guidelines when storing hydrogen:
• Store spare hydrogen gas cylinders outside and away from doors, windows, building air
intake vents, structures, and vehicle routes. This precaution applies when the hydrogen is
or is not in use. Indoor storage of spare hydrogen cylinders has special requirements,
which is beyond the scope of this document. Documentation for each vessel should
include a description of the vessel, a list of available drawings or other documents, the
most recent inspection results, and the responsible person's name.
• Prevent spare cylinders from toppling by wrapping them with chains. The chains should
also be protected against corrosion and excessive heat.
• Separate spare hydrogen cylinders from oxidizing gases (such as oxygen) with a 5 ft
(1.5 m) tall fire barrier with a half-hour fire rating or place the cylinders at least 20 ft
(6 m) apart.
• When moving hydrogen cylinders:
– Remove the regulator and replace the cylinder valve cap before moving.
– Move cylinders on cylinder carts or with other appropriate transport devices.
– Never roll or drop a cylinder and never lift a cylinder by its protective cap.
• Bulk hydrogen systems include either gaseous or liquid hydrogen in fixed installations; in
some gas systems a semi-permanent trailer (tube trailer) can be used. Storage vessels for
compressed hydrogen gas or liquid hydrogen should be designed, constructed, tested, and
maintained in accordance with applicable codes and standards. Bulk hydrogen systems
represent a level of complexity again which is beyond the scope of this document;
however some general guidelines are provided.
Preface
Hydrogen Safety Precautions
xviii TSQ Duo User Guide Thermo Scientific
• The bulk hydrogen storage system should not be located beneath electric power lines,
close to other flammable gases/liquids, or close to public areas. It should be readily
accessible to authorized personnel and delivery equipment, but protected from physical
damage or tampering.
• As liquid hydrogen systems also have a cryogenic hazard, additional safety considerations
for the use of cryogenic liquids might be necessary.
Preface
Hydrogen Safety Precautions
Thermo Scientific TSQ Duo User Guide xix
Hydrogen Safety Codes, Standards and References
The following list of safety codes, standards and references is in no way an exhaustive list. In
fact, there might be federal, state or local codes that apply to your specific location. Check
with all appropriate agencies with jurisdiction before installing or using a hydrogen system.
• Air Products Safetygram #4 Gaseous Hydrogen
• ANSI/AIAA standard for hydrogen safety guidelines is AIAA G-095-2004, Guide to
Safety of Hydrogen and Hydrogen Systems
• ASME B31.1, Power Piping Code
• ASME B31.3, Process Piping Code
• ASME B31.8, Gas Transmission and Distribution Systems
• BCGA Code Of Practice CP4 Industrial Gas Cylinder Manifolds and Gas Distribution
Pipework
• BCGA Code Of Practice CP33 The Bulk Storage of Gaseous Hydrogen at Users'
Premises
• CGA G-5, Hydrogen
• CGA G-5.4, Standard for Hydrogen Piping Systems at Consumer Locations
• CGA G-5.5, Hydrogen Vent Systems
• CGA G-5.6, Hydrogen Pipeline Systems
• CGA G-5.8, High Pressure Hydrogen Piping Systems at Consumer Locations.
• FM Global Property Loss Prevention Data Sheets 7-50: Compressed Gases in Cylinders
• FM Global Property Loss Prevention Data Sheets 7-91: Hydrogen
• IGC Doc 121/04/E, Hydrogen Transportation Pipelines System Design Features
• NASA
• NSS 1740.16 Safety Standard For Hydrogen And Hydrogen Systems Guidelines for
Hydrogen System Design, Materials Selection, Operations, Storage, and Transportation
• NFPA 52, Vehicular Fuel Systems Code
• NFPA 55, Standard for the Storage, Use, and Handling of Compressed Gases and
Cryogenic Fluids in Portable and Stationary Containers, Cylinders, and Tanks, 2005
Edition
• NFPA 68, Standard on Explosion Protection by Deflagration Venting
• NFPA 70, National Electrical Code
Preface
Hazardous Substances Precautions
xx TSQ Duo User Guide Thermo Scientific
• NFPA 497, Recommended Practice for the Classification of Flammable Liquids, Gases,
or Vapors and of Hazardous (Classified) Locations for Electrical Installations in Chemical
Process Areas
• NFPA 13, Standard for the Installation of Sprinkler Systems
• NFPA 45, Standard on Fire Protection for Laboratories Using Chemicals
• NFPA 55, Standard for the Storage, Use, and Handling of Compressed Gases and
Cryogenic Fluids in Portable and Stationary Containers, Cylinders, and Tanks
• NFPA 68, 2007 Standard on Explosion Protection by Deflagration Venting
• NFPA 69, Standard on Explosion Prevention Systems
• NFPA 91, Standard for Exhaust Systems for Air Conveying of Vapors
• NFPA 255, Standard Method of Test of Surface Burning Characteristics of Building
Materials
• OSHA 29CFR1910.103 1910.103 Hydrogen
Hazardous Substances Precautions
Biological Hazard Warning Note
In laboratories where samples with potential biological hazards are handled, the user must
label any equipment or parts which might become contaminated with biohazardous material.
The appropriate warning labels are included with the shipment of the instrument. It is the
user’s responsibility to label the relevant parts of the equipment.
When working with biohazardous materials, you are responsible for fulfilling the following
mandatory requirements:
• Providing instructions on how to safely handle biohazardous material.
• Training operators to be aware of potential hazards.
WARNING Before using hazardous substances (toxic, harmful, and so on), please read the
hazard indications and information reported in the applicable Material Safety Data Sheet
(MSDS). Use personal protective equipment according to the safety requirements.
Preface
Contacting Us
Thermo Scientific TSQ Duo User Guide xxi
• Providing personal protective equipment.
• Providing instructions for what to do if operators are exposed to aerosols or vapors during
normal operation (within the intended use of the equipment) or in case of single fault
situations such as a broken vial. The protective measures must consider potential contact
with the skin, mouth, nose (respiratory organs), and eyes.
• Providing instructions for decontamination and safe disposal of relevant parts.
Venting Toxic Gases
When analyzing toxic compounds, be aware that during the normal operation of the GC
some of the sample might be vented outside the instrument through the split and purge flow
vents; therefore, be sure to vent the exhaust gases to a fume hood. Consult local
environmental and safety regulations for instructions in exhausting fumes from your system.
Contacting Us
There are several ways to contact Thermo Fisher Scientific for the information you need.
To find out more about our products
Go to www.thermoscientific.com/en/products/mass-spectrometry.html for information
about our products.
To get local contact information for sales or service
Go to www.thermoscientific.com/en/support-landing/support.html.
To suggest changes to documentation or to Help
• Fill out a reader survey online at www.surveymonkey.com/s/PQM6P62.
• Send an e-mail message to the Technical Publications Editor at
techpubs-austin@thermofisher.com.
WARNING The user or operator is responsible for the safe handling of hazardous
chemicals or biological compounds including (but not limited to) bacterial or viral
samples and the associated waste, according to international and local regulations.
Thermo Scientific TSQ Duo User Guide 1
1
Introduction
Use the information in this chapter to determine whether your TSQ Duo system is working
properly and to check its basic systems.
Confirming Your Instrument is Working
After installing a new column, confirm that your GC/MS-MS system has power, the carrier
gas flow and collision gas delivery pressure are correct, the gas tanks have enough pressure, and
the system is leak-free and has reached vacuum and temperature.
Checking Power to the System
To confirm that the TSQ Duo system is powered on, check that the power light on the front
panel is lit and solid green. See Figure 1. If it is not, the instrument is not powered on.
IMPORTANT You will likely want to change the GC column before setting up a method.
See Chapter 2, “Changing the Column,” for instructions on changing the column.
Contents
•Confirming Your Instrument is Working
•Checking Power to the System
•Verifying the Carrier Gas Flow Rate
•Checking Your Carrier Gas Tank Pressure
•Verify Collision Gas Tank Pressure
•Checking the Vacuum and Temperature
•Cleaning the Exterior of Your Instrument
•Configuring Your Instrument
1 Introduction
Confirming Your Instrument is Working
2TSQ Duo User Guide Thermo Scientific
To power on the TSQ Duo instrument
Lift up the power switch located on the upper left side panel of the instrument near the
back.
Figure 1. Front Panel of the TSQ Duo Instrument
To power on the TRACE 1300/1310 GC
Reach over the top right of the instrument and pull up on the large plastic ribbed power
switch on the back.
To confirm that a TRACE 1300 is powered on
Confirm that the power light on the status panel is solid green.
To confirm that a TRACE 1310 is powered on
Confirm that the touchscreen main menu has appeared.
Verifying the Carrier Gas Flow Rate
Once you confirm that the system is powered on, verify that the carrier gas rate is correct.
To check the carrier gas flow rate on the TRACE 1310 GC
1. Choose Instrument Control and then Front/Back inlet.
2. Display the column flow.
1 Introduction
Confirming Your Instrument is Working
Thermo Scientific TSQ Duo User Guide 3
If the actual and set point amounts in Col. Flow are the same, then you have good carrier
gas flow. If the amounts are different, refer the Troubleshooting section of the
TRACE 1300/1310 GC Series User Guide.
To check the carrier gas flow rate on a TRACE 1300
1. Go to Start > Thermo Chromeleon > Chromeleon and open the Chromeleon Console.
2. Click Instruments in the left-hand menu.
3. Select Command from the top menu.
4. A status page for all the configured instruments.
Figure 2. Checking Instrument Status in Chromeleon Software
5. Verify the column flow rate beside in the status pane.
Checking Your Carrier Gas Tank Pressure
Make sure you have enough pressure in the carrier gas tank to accommodate the number of
samples you plan to run. If the pressure is too low, you might run out of gas in the middle of
a run, which could compromise the results of your data.
Command
Settings
Instruments
1 Introduction
Confirming Your Instrument is Working
4TSQ Duo User Guide Thermo Scientific
To check your carrier gas tank pressure
1. Locate your carrier gas tank. It might be in a different room, depending on how your lab
is set up.
2. Look at the pressure gauge on the tank.
3. Ensure the pressure is more than 100 psi at the primary (or first) regulator stage. If it is
not, you may want to replace the tank if you have to run a lot of samples.
Verify Collision Gas Tank Pressure
Check that the input pressure of your collision gas is at 59–61 psig for Argon or 56–58 psig
for Nitrogen and that the tank is connected to the mass spectrometer.
Checking the Vacuum and Temperature
Use the lights on the front of your TSQ Duo system to check the vacuum and temperature of
the instrument.
To check the vacuum, look at the Vacuum light. See Figure 3. When the light is a solid green,
the mass spectrometer is under sufficient vacuum. If the Vacuum light is slowly blinking
orange, you have not yet achieved vacuum. If the Vacuum light is blinking orange quickly,
you have a large leak that has prevented the instrument from achieving vacuum. In this case,
you must turn the power off and find and fix the leak. Most likely, the column nut must be
tightened, the column was not installed correctly, or the vent valve was not completely closed.
See Troubleshooting for more information.
Figure 3. Using the Lights on the TSQ Duo Instrument
CAUTION Collision gas input pressure must remain constant for proper instrument
performance. The regulator used to supply the collision gas must be able to deliver
60 ± 1 psig. Ensure that the regulator is marked clearly at 60 psig and is stable enough to
supply constant pressure at 60 ± 1 psig.
Heaters
Busy
Vacuum
Power
1 Introduction
Cleaning the Exterior of Your Instrument
Thermo Scientific TSQ Duo User Guide 5
To check the temperature, look at the Heaters light. When the Heaters light is a solid green,
the GC-MS/MS system is at temperature. If the Heaters light is blinking orange, the ion
source, ion optics and/or transfer line are not at temperature. If the Heaters light is not lit, the
heaters are not turned on.
You may also use the TSQ Series Dashboard to check the vacuum of your system. If your
system has achieved sufficient vacuum, a green check mark appears next to Vacuum on the
dashboard.
Figure 4. Checking System Vacuum on the Dashboard
Cleaning the Exterior of Your Instrument
When the exterior of your instrument gets dirty, wipe it with a clean, dry, lint-free cloth.
Note Until the Vacuum light is a solid green (high vacuum is achieved), the heaters will
not power on and the Heaters light will not be lit.
Vacuum
1 Introduction
Configuring Your Instrument
6TSQ Duo User Guide Thermo Scientific
Configuring Your Instrument
Initially, the field service engineer will configure your TSQ Duo instrument. However, if you
have reinstalled the instrument’s software or you have a new computer or device, follow these
instructions to reconfigure it.
To configure your TSQ Duo instrument
1. From the Start menu on your computer desktop, choose Start | All Programs | Thermo
Chromeleon 7 | Services Manager.
2. The Chromeleon Services Manager window opens. See Figure 5.
Figure 5. Chromeleon Services Manager
3. Click Configure Instruments. The Chromeleon Instrument Configuration Manager
opens. See Figure 6.
Figure 6. Finding Available Devices
4. Right-click the PC icon and select Add Instrument. See Figure 7.
1 Introduction
Configuring Your Instrument
Thermo Scientific TSQ Duo User Guide 7
Figure 7. Adding an Instrument
5. The Add Module to Instrument dialog box opens. Under Manufacturers, select
Thermo Scientific > GC: Modules to add your system’s gas chromatograph and
autosampler. See Figure 8
Figure 8. Adding a GC and Autosampler
6. Click OK.
7. To add the mass spectrometer, right-click the PC icon again and select Add Instrument.
The Add Module to Instrument dialog box opens. Under Manufacturers, select
Thermo Scientific > Mass Spectrometry. Select Mass Spectrometer from the Modules
list. See Figure 9.
1 Introduction
Configuring Your Instrument
8TSQ Duo User Guide Thermo Scientific
Figure 9. Adding the Mass Spectrometer
8. Click OK.
9. Click Mass Spectrometer on the left menu. The Mass Spectrometer Configuration
page opens. On the General page, set the pressure units.
Figure 10. Setting the Pressure Units
10. Set the remote start, which tells the TSQ Duo system when the GC has started a run.
When you configure the GC, you can tell it what to send out to the instrument. Make
Note You only need to set up the pressure units if you have an ion gauge or
convectron gauge installed on your system. The readbacks from these components
will display in the units set in this dialog box.
1 Introduction
Configuring Your Instrument
Thermo Scientific TSQ Duo User Guide 9
sure the value in this dialog box matches what you set on the GC. The default is Active
Low. See Figure 11.
Figure 11. Setting the Remote Start
11. Check Always Show Method Portability Between Instrument Methods if you need to
create methods for older model TSQ 8000 or TSQ 8000 Evo systems.
Figure 12. Enabling Method Portability
1 Introduction
Configuring Your Instrument
10 TSQ Duo User Guide Thermo Scientific
12. Click Communications to reset the network IP address and assign a TCP port. See
Figure 13. This tells the instrument method how to find the TSQ Duo system if you
changed the IP address using Instrument Configuration. For security purposes, you may
also want to modify the TCP port. Consult your local IT Department for help.
Figure 13. Setting up the Network
13. Click the Maintenance Intervals tab to set the number of days until you plan to perform
maintenance on certain components of your GC/MS system. See Figure 14.
Figure 14. Setting the Maintenance Intervals
14. Select the Foreline Pump Oil check box to enable the maintenance intervals. Then set
the number of days after which you want to be reminded to check the oil. The
manufacturer recommends changing the oil every 125 days. Select the Turbo Pu m p
Oil/Bearing check box to enable the maintenance reminder. Then set the number of days
after which you want to be reminded to check the oil. Refer to the Turbo Pump manual
for the manufacturer's recommended maintenance intervals.
15. Select the Filament 1 check box to enable the maintenance reminder. In a leak-free
system, expect the filament to last between 30-360 days, depending on usage.
1 Introduction
Configuring Your Instrument
Thermo Scientific TSQ Duo User Guide 11
16. Select the Filament 2 check box to enable the maintenance reminder. Then set the
number of days after which you want to be reminded to check filament 2. In a leak-free
system, expect the filament to last between 30-360 days, depending on usage.
17. Select the Ion source check box to enable the maintenance reminder. Then set the
number of days after which you want to be reminded to check the ion source. The time
between cleaning depends very strongly on your analysis. You will have to determine the
correct length of time between source cleanings.
18. Select the Multiplier check box to enable the maintenance reminder. Then set the
number of days after which you want to be reminded to check the electron multiplier.
19. Click OK to return to the main Instrument Configuration home page.
20. Select TRACE 1300 Series GC II from the left side menu to configure the GC
handshaking parameters.
21. Under the Signals tab, set the handshaking parameters as shown in Tab le 1.
Table 1. GC Handshaking Parameters
Remote Start In High to Low
Inhibit Ready In When High
End of Run Out High to Low
Start of Run Out High to Low
GC Ready Out When Low
Prep Run Out When Low
1 Introduction
Configuring Your Instrument
12 TSQ Duo User Guide Thermo Scientific
Figure 15. GC Handshaking Parameter Configuration
22. Click OK once you have entered the correct GC handshaking parameters.
23. Close the Instrument Configuration window.
24. Check the status of the configured instruments in the Status Pane of the TSQ Series
Dashboard.
Note For the remainder of the GC configuration settings, refer to the TRACE 1300
and TRACE 1310 Series GC User Guide. Refer to your autosampler user
documentation for the correct autosampler configuration settings.
1 Introduction
Configuring Your Instrument
Thermo Scientific TSQ Duo User Guide 13
Figure 16. TSQ Series Dashboard
Status Pane
Thermo Scientific TSQ Duo User Guide 15
2
Changing the Column
The TSQ Duo GC-MS/MS system ships with a factory-tested 15 m × 0.25 mm ID TG-SQC
column, which the field service engineer uses to qualify the instrument. This column is for
system qualification purposes only and not for regular testing and should be replaced. For best
results, choose a column that will give you the best possible resolution, analysis speed, and
quantitation.
Determining the Column Type
When determining the type of column for your particular needs, here are a few things to
consider:
•Column Material—Columns made out of fused silica are economical and widely used.
Columns made out of this material have a wide range of stationary phases and are
available in many sizes that can be used with a mass spectrometer.
Large diameter columns made of steel are widely used in process gas analysis, but they are
not typically used on mass spectrometers. There are also metal-clad, fused silica columns,
which have the advantages of fused silica, but the metal makes them resistant to breakage.
These columns are less common and more expensive.
•Stationary Phase—The stationary phase is the most important consideration when
selecting a column. The interaction between the stationary phase and the analyte
determines how well the analytes separate from each other (resolution) and also affects
how quickly the separation occurs (analysis time). Choose a stationary phase that is
compatible with the nature of your analytes and the maximum GC oven temperature that
you will use.
Contents
•Determining the Column Type
•Replacing the Factory Installed Column
•Connecting the Column to the Transfer Line
2 Changing the Column
Replacing the Factory Installed Column
16 TSQ Duo User Guide Thermo Scientific
•Internal Diameter—The smaller the diameter of the column, the better the separation.
However, smaller diameter columns do not have as much capacity for matrix or analytes.
As a result, smaller diameter columns are subject to overloading, which leads to retention
time shifts and peak shape changes. Larger diameter columns can accept larger
concentrations of material, but will require longer columns or slower GC oven
temperature ramps (which increase the analysis time) to match the separation power of
smaller-diameter columns. Typical column sizes for GC/MS have inside diameters (ID)
of 0.25 mm. Smaller ID columns, such as the 0.18 and 0.10 mm, are becoming
increasingly popular. Additionally, 0.32 and 0.53 mm ID columns are commonly used.
•Film Thickness—With larger film thicknesses, there is more capacity for the analyte.
This capacity can aid in the separation of high concentration samples and in the
separation of very volatile samples because thicker stationary phases allow more
opportunities for the analytes to interact with the stationary phase. The optimal film
thickness depends on the internal diameter of the column, and the maximum total
capacity needed for sample analysis.
Thick films with small internal diameters give very strong interactions with the analytes,
which can result in longer analysis time and peak tailing. Large ID columns with thin
films have very little interaction with the analytes, which will result in very fast analysis
times with little separation. Typical film thicknesses are 0.25 μm for a column with an ID
of 0.25 mm. Other common film thicknesses are 0.1, 0.5, and 1.0 μm.
Be careful when selecting columns for mass spectrometers. Some columns with large
inner diameters that work fine with other GC detectors may need lower head pressure
when operated with vacuum at the outlet. This lower head pressure can allow air diffusion
into the column through the carrier gas flow module's split and purge valves.
•Length—The length of the column affects how much time the analyte has to interact
with the stationary phase. Longer columns typically have better resolutions and higher
capacities, but longer analysis times. Longer columns are also more expensive. Typical
column lengths are 15 or 30 m for GC/MS, but 100 m columns may be needed for very
complex mixtures like gasoline. Very short columns (2.5, 5, and 10 m) are also available.
Replacing the Factory Installed Column
To replace the factory-installed column in the TSQ Duo system
1. Cool down the GC oven and injector. See the GC documentation for information.
Tip The Thermo Scientific™ TG-5MS column is suitable for many applications.
Note Contact your local sales representative to order a Thermo Scientific column. You
can also refer to our catalog or visit our Web site at www.thermoscientific.com/columns.
Note If you are running samples, stop the acquisition before powering off the system.
2 Changing the Column
Replacing the Factory Installed Column
Thermo Scientific TSQ Duo User Guide 17
2. Open the TSQ Series Dashboard and click Shut Down.
During the shutdown procedure the vacuum and heaters lights will remain off. Once the
procedure is complete and the instrument is ready to be powered off, the power light will
turn amber and start blinking rapidly. At this point it is safe to power off the TSQ Duo
system.
3. On the left side of the instrument, push down on the power switch to power-off the
TSQ Duo system.
Figure 17. Powering Off the TSQ Duo Instrument
4. Open the front door of the instrument.
5. Turn the vent knob counterclockwise to vent the system.
6. Wait 5 minutes for the instrument to vent.
7. Remove the current column:
a. Make sure the heated zones of the GC are cooled down. Refer to the GC
documentation for instructions.
b. Turn off the carrier gas and if used, the detector gas. See the GC documentation for
information about using detector gases.
c. Open the front door of the GC.
Power Switch
WARNING BURN HAZARD: The injector, oven, and transfer line may be hot.
Allow them to cool to room temperature before touching them.
2 Changing the Column
Replacing the Factory Installed Column
18 TSQ Duo User Guide Thermo Scientific
d. Unscrew the transfer line nut and remove the column from the transfer line.
e. Unscrew the injector nut and remove the column.
f. Remove the column from the column rack and from the GC.
8. Connect the new column to the injector inside the GC.
a. Unwind the column enough to easily connect its ends to the injector and detector.
b. Wipe about 100 mm (4 in.) of the column with a tissue soaked in methanol.
c. Insert the column through the injector retaining nut and ferrule (larger end up). If
the M4 retaining nut is used, slide it on the column through the side cut. Wipe the
column again with a tissue soaked in methanol.
d. Use a scoring wafer to score and break the column about 1 cm (0.4 in.) from the end.
Use a magnifying glass to check for an even, flat cut. Repeat if necessary.
e. Insert a notched septum on the column to hold the retaining nut at this position.
Thread the retaining nut into the injector but do not tighten.
f. Ensure that the end of the column is the proper distance (splitless = 5 mm,
split = 10 mm, PTV and PTVBKF = 30 mm) from the back of the injector nut.
g. Adjust the column position so that the septum contacts the bottom of the retaining
nut. Use your fingers to tighten the retaining nut until it starts to grip the column.
h. Tighten the column nut finger-tight until it starts to grip the column plus a quarter
turn.
i. Remove the notched septum from the column.
9. Set up the GC parameters:
a. Set the oven and injector temperature to 50 °C (122 °F).
b. Set the carrier gas flow to 1.0 mL/min.
c. Turn off vacuum compensation, which is located on the Carrier menu of the GC.
d. Use the column flowmeter connector to verify that there is flow through the column.
If you do not have a flowmeter, dip the column outlet in a small vial of methanol.
Bubbles indicate there is flow through the column. If there is no flow, check that the
carrier gas is on, the GC inlet is pressurized, and the column is not plugged. If there is
still no flow, consult the GC documentation or contact Technical Support.
e. Allow the column to purge for at least 10 minutes. If you used methanol to detect
column flow, remove column from methanol during purge time.
Note Wear clean, lint- and powder-free gloves when you handle the column and
injector ferrule.
Tip Slide a notched septum on the column before the injector retaining nut to
make it easier to measure the proper distance between the nut and end of the
column.
2 Changing the Column
Replacing the Factory Installed Column
Thermo Scientific TSQ Duo User Guide 19
f. Insert the column into the fitting of the column flowmeter connector that blocks the
column flow.
10. Perform a column leak check:
a. On the TRACE 1310, select the Leak Check icon in the Maintenance menu.
Otherwise, perform the leak check through the Chromatography Data System. Refer
to the TRACE 1300 and TRACE 1310 Series GC User Guide for instructions.
b. Start the leak check.
The split and purge valves of the selected channel are automatically closed, and the
channel is pressurized with carrier gas to the leak check setpoint.
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. If the leak
check does not pass, use the leak detector to find and fix any leaks.
c. Repeat the leak check until no leaks are indicated.
11. Calibrate the carrier gas flow (column evaluation):
a. Carefully push the capillary column end into the flowmeter section of the column
flowmeter connector.
Figure 18. Column Flowmeter Connector
b. Connect the flowmeter to the dedicated fitting on the column flowmeter connector.
c. If you have a TRACE 1310, select the Back or Front Column icon in the
Configuration menu. Otherwise, perform the column evaluation through the
Tip Leaks can be caused by not tightening the fitting on the column flowmeter
connector. Check the fitting before looking for the leak elsewhere.
CAUTION INSTRUMENT DAMAGE: Do not allow the column flowmeter
connector to exceed 80 °C (176 °F). Otherwise, it will melt and damage the
instrument.
A B C
To flowmeter
2 Changing the Column
Replacing the Factory Installed Column
20 TSQ Duo User Guide Thermo Scientific
Chromatography Data System. See the TRACE 1300 and TRACE 1310 User Guide
for instructions.
d. Select Column and input the column’s physical characteristics.
e. If a pre-/post column is present, 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.
f. Start the column evaluation. According to the physical characteristics of the column,
the system calculates and displays the relevant column K-factor. At the end of the
routine, a message will indicate that the evaluation was successful.
g. Expect a K-factor of approximately 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.
Fix any issues found and rerun column evaluation until an appropriate K-factor is
achieved.e a leak in the system, while a K-factor that is too high might indicate a
blockage.
12. Disconnect the column flowmeter:
a. Disconnect the column from the column flowmeter connector.
b. Remove the clear plastic component, including its fittings, from the oven and set
them aside.
c. Close the GC door.
13. Condition the column before inserting it into the TSQ Duo system. Column
conditioning consists of passing a carrier gas flow through the column heated to a
programmed temperature as described in the column manufacturer’s instructions.
a. If there are no conditioning instructions, perform the column conditioning by setting
a final temperature 10 °C–20 °C below the column’s recommended maximum
temperature.
Note For the most reproducible results, you should conduct a more detailed
column evaluation. However, the following steps, while recommended, are not
required.
CAUTION INSTRUMENT DAMAGE: The material released from the column
(column bleed) during conditioning may contaminate the ion source if the
column is inserted into the transfer line during the high-temperature stage of
conditioning.
2 Changing the Column
Connecting the Column to the Transfer Line
Thermo Scientific TSQ Duo User Guide 21
b. Run the slow temperature program that is recommended by the manufacturer. A
typical program would hold the column at 40 °C (104 °F) for 15 minutes, and then
ramp at 10 °C/min (50 °F/min) up to 10–20 °C below the maximum allowed
column temperature. Hold the column at this temperature for two hours.
Connecting the Column to the Transfer Line
When connecting the column to the transfer line, you may use either the spring loaded
transfer line nut with the graphite Vespel™ ferrule or the regular transfer line nut
.
To connect the column using the spring loaded transfer line nut
1. Lower the oven temperature and allow it to cool.
2. If the TSQ Duo system is running, shut down and vent it. See the instrument’s hardware
manual for instructions.
3. Unwind about one turn of the column from the column outlet end.
4. Wipe approximately 300 mm (12 in.) of the column with a tissue soaked in methanol.
5. Choose an appropriate ferrule for the outer diameter of your column.
6. Insert the column through the spring loaded transfer line nut and ferrule, entering
through the tapered end of the ferrule.
WARNING FIRE HAZARD: Do not use hydrogen as the carrier gas for
conditioning your column. It could vent into the oven and present an explosion
hazard.
CAUTION INSTRUMENT DAMAGE: Never exceed the column manufacturer’s
maximum operating temperature.
Note For best results, we recommend you use the spring loaded transfer line nut.
Note If you use a graphite Vespel ferrule with your column, Thermo Fisher Scientific
recommends using the spring loaded transfer line nut with it. See the spare parts guide for
ordering information.
CAUTION BURN HAZARD: The injector, detectors, oven, and transfer line may be hot.
Allow them to cool before touching them.
Note Wear clean, lint- and powder-free gloves when you handle the column and
transfer line ferrule.
2 Changing the Column
Connecting the Column to the Transfer Line
22 TSQ Duo User Guide Thermo Scientific
7. Wipe the column again with a tissue soaked in methanol.
Figure 19. Transfer Line Nut and Graphite Vespel Ferrule Orientation
8. Insert the column into the measuring tool (see Figure 20), which is in the MS Toolkit, so
that it is even with the lines at the end of the column. Figure 21 indicates proper
positioning of the column in the tool for accurate measuring.
9. Use a scoring wafer to score and break the column. Use a magnifying glass to check for an
even, flat cut. Repeat if necessary.
10. Use a 5/16 in. wrench to hold the column measuring tool steady.
Figure 20. Column Measuring Tool
11. While holding the column measuring tool steady, tighten the spring loaded transfer line
nut with a 1/4” wrench until the column just stops moving in the ferrule.
12. Turn the spring loaded transfer line nut 1 flat backward so the column is able to move in
the ferrule with slight resistance.
13. Line up the outlet of the column with the arrows on the end of the column measuring
tool.
Spring Loaded Transfer
Line Nut
Ferrule
Flat on the
Transferline Nut
2 Changing the Column
Connecting the Column to the Transfer Line
Thermo Scientific TSQ Duo User Guide 23
Figure 21. Lining Up the Column in the Column Measuring Tool
14. Place a septum with a notch cut into it behind the transfer line nut. The septum marks
the place on the column where it should exit the nut.
15.
Figure 22. Positioning the Septum
16. Pull the column back from the spring loaded transfer line nut. Do not move the septum
from its position on the column.
Column Outlet
Spring Loaded
Transfer Line Nut
Septum
Column
Measuring Tool
Column
2 Changing the Column
Connecting the Column to the Transfer Line
24 TSQ Duo User Guide Thermo Scientific
Figure 23. Pulling the Column Back from the Spring Loaded Transfer Line Nut
17. Loosen the transfer line nut from the column measuring tool.
18. Remove the column, transfer line nut and ferrule from the column measuring tool,
making sure not to move the septum from its location on the column.
19. Insert the column into the transfer line.
Figure 24. Inserting the Column into the Transfer Line
20. Tighten the spring loaded transfer line nut until it is just secure enough so that you
cannot move it.
21. Loosen the nut by turning it exactly 1 flat backward.
Note The ferrule should still be able to move on the column. Use the septum to mark the
correct location where the column should exit the nut.
Column
Spring Loaded
Transfer Line Nut
Septum
Transfer Line
Column
Spring Loaded
Transfer Line Nut
Septum
2 Changing the Column
Connecting the Column to the Transfer Line
Thermo Scientific TSQ Duo User Guide 25
22. Position the column in the transfer line using the cut septum to measure the correct
length you should insert the column.
Figure 25. Positioning the Column in the Transfer Line
23. Tighten the spring loaded transfer line nut 1 flat forward—back to where it is secure
enough in the transfer line that you cannot move it.
24. Tighten the spring loaded transfer line nut 1 additional quarter turn.
25. Remove the cut septum.
26. Condition the graphite Vespel ferrule:
a. Raise the oven temperature to the maximum temperature you will operate the GC.
b. Wait 10 minutes.
c. Lower the oven temperature to 40 °C (104 °F) and allow it to cool before continuing.
27. Close the front door of the GC.
28. Restore working conditions.
a. Raise the oven temperature to the initial temperature that you will use.
b. Turn on vacuum compensation on the GC.
29. Power on the TSQ Duo instrument. See Chapter 1, “Introduction,” for instructions.
30. Once the instrument is pumped down and able to scan, view air water spectra and look
for evidence of leaks with a large m/z 28 signal. If you observe a leak, stop scanning and
gently tighten the nut in small increments until no leaks appear when scanning.
Column
Transfer Line
Spring Loaded Transfer
Line Nut
Septum
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.
2 Changing the Column
Connecting the Column to the Transfer Line
26 TSQ Duo User Guide Thermo Scientific
To connect the column using the regular transfer line nut
1. Lower the oven temperature and allow it to cool.
2. If the TSQ Duo system is running, shut down and vent it. See the instrument’s hardware
manual for instructions.
3. Unwind about one turn of the column from the column outlet end.
4. Wipe approximately 300 mm (12 in.) of the column with a tissue soaked in methanol.
5. Choose an appropriate ferrule for the outer diameter of your column.
6. Insert the column through the transfer line nut and ferrule, entering through the tapered
end of the ferrule. Wipe the column again with a tissue soaked in methanol.
Figure 26. Transfer Line Nut and SilTite Ferrule Orientation
Note For best results, we recommend you use the spring loaded transfer line nut. See “To
connect the column using the spring loaded transfer line nut” on page 21.
CAUTION BURN HAZARD: The injector, detectors, oven, and transfer line may be hot.
Allow them to cool before touching them.
Note Wear clean, lint- and powder-free gloves when you handle the column and
transfer line ferrule.
Note If the maximum oven temperature in your method is ≥ 290 °C (554 °F),
Thermo Fisher Scientific recommends using a spring loaded transfer line nut with a
graphic Vespel ferrule or a SilTite™ nut and ferrule. By cycling the oven at and above
this temperature, expansion and contraction of the graphite Vespel material can cause
leaks in the transfer line.
Transfer Line Nut
SilTite Ferrule
Flat on the
Transferline Nut
2 Changing the Column
Connecting the Column to the Transfer Line
Thermo Scientific TSQ Duo User Guide 27
7. Insert the column into the measuring tool, which is in the MS Toolkit (See Figure 27), so
that it is even with the lines at the end of the column. Figure 28 indicates proper
positioning of the column in the tool for accurate measuring.
8. Use a scoring wafer to score and break the column. Use a magnifying glass to check for an
even, flat cut. Repeat if necessary.
9. Use a 5/16 in. wrench to hold the column measuring tool steady.
Figure 27. Column Measuring Tool
10. While holding the column measuring tool steady, tighten the transfer line nut with a 1/4”
wrench until the column just stops moving in the ferrule.
11. Turn the transfer line nut 1 flat backward so the column is able to move in the ferrule
with slight resistance.
12. Line up the outlet of the column with the arrows on the end of the column measuring
tool.
Figure 28. Lining Up the Column in the Column Measuring Tool
13. Place a septum with a notch cut into it behind the transfer line nut. The septum marks
the place on the column where it should exit the nut.
Column Outlet
2 Changing the Column
Connecting the Column to the Transfer Line
28 TSQ Duo User Guide Thermo Scientific
Figure 29. Positioning the Septum
14. Pull the column back from the transfer line nut. Do not move the septum from its
position on the column.
Figure 30. Pulling the Column Back from the Transfer Line Nut
15. Loosen the transfer line nut from the column measuring tool.
16. Remove the column, transfer line nut and ferrule from the column measuring tool,
making sure not to move the septum from its location on the column.
17. Insert the column into the transfer line.
18.
Transfer Line
Nut
Septum
Column
Measuring Tool
Transfer Line
Nut
Septum
Column
2 Changing the Column
Connecting the Column to the Transfer Line
Thermo Scientific TSQ Duo User Guide 29
Figure 31. Inserting the Column into the Transfer Line
19. Tighten the transfer line nut until it is just secure enough so that you cannot move it.
20. Loosen the nut by turning it exactly 1 flat backward.
21. Position the column in the transfer line. Use the septum as a guide to measure the correct
length you should insert the column. Be careful not to change the location of the septum
on the column.
Figure 32. Positioning the Column in the Transfer Line
22. Tighten the nut 1 flat forward—back to where it is secure enough in the transfer line that
you cannot move it.
23. Tighten the nut 1 additional quarter turn.
24. Remove the cut septum.
Transfer Line
Column
Transfer Line
Nut
Ferrule
Septum
Transfer Line Column
Septum
2 Changing the Column
Connecting the Column to the Transfer Line
30 TSQ Duo User Guide Thermo Scientific
25. Condition the graphite Vespel ferrule:
a. Raise the oven temperature to the maximum temperature you will operate the GC.
b. Wait 10 minutes.
c. Lower the oven temperature to 40 °C (104 °F) and allow it to cool before continuing.
d. Retighten the transfer line nut.
26. Close the front door of the GC.
27. Restore working conditions.
a. Raise the oven temperature to the initial temperature that you will use.
b. Turn on vacuum compensation on the GC.
c. Power on the instrument. See Chapter 1, “Introduction,” for instructions.
d. Once the instrument is pumped own and able to scan, view air water spectra and
look for evidence of leaks with a large m/z 28 signal. If you observe a leak, stop
scanning and gently tighten the nut in small increments until no leaks appear when
scanning.
Note If you are using a SilTite ferrule, follow the instructions that come with SilTite
ferrules. If you are using a graphite Vespel ferrule, they require conditioning to ensure
a leak-tight seal. See the spare parts guide for information about ordering these
ferrules.
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.
Thermo Scientific TSQ Duo User Guide 31
3
Tuning
Tuning will improve the performance of your TSQ Duo system. For optimum stability, you
must wait until the power, vacuum, and heaters lights on the front of the instrument are a
solid green. These lights indicate that the instrument has reached vacuum and that it is at the
last set temperature. If the system has been powered off for a period of time (that is, a cold
system), the system components take up to 4 hours to thermally stabilize after reaching the
temperature setpoint. If you did not vent the instrument (that is, the system is hot), the
components take approximately 10 minutes to thermally stabilize after reaching the
temperature setpoint.
You can tune the TSQ Duo system by using the TSQ Series Dashboard.
Accessing Auto Tune
To access TSQ Series Auto Tune
• Double-click the TSQ Series Dashboard shortcut on your desktop to open the
TSQ Series Dashboard and then click Auto Tune. See Figure 33.
Contents
•Accessing Auto Tune
•Tu n e Ty p es
•Tuning the Mass Spectrometer
•Updating Tunes for New RF Lens
IMPORTANT Be sure to give the MS system enough time to stabilize. Otherwise, you may
see mass drift, mass spectral changes, or changes in the fragmentation of your data.
Note If you are running samples with heavy matrix, running the samples before the
source has had time to stabilize at high temperature will prematurely dirty the ion volume
and optics.
3 Tuning
Tune Types
Thermo Scientific TSQ Duo User Guide 33
EI Initial Tune
EI Initial Tune—Creates a default tune file. It requires a clean instrument, and it sets the
repeller to 0 V and the quadrupole voltages to low values. This tune is used to reset parameters
for all the other tunes after cleaning the ion source. As a result, use this tune only when the
ion source is clean. The EI initial tune should also be used when changing from an SRM tune
to a standard tune. The EI initial tune has higher resolution and lower sensitivity than the EI
standard tune. This tune starts with the tune file stored in the instrument at the factory. It
then performs a mass calibration and leak check, sets the repeller to 0 V, and tunes the lenses.
The quadrupole offset voltage is set to a low value to improve resolution, which is also tuned.
The detector gain is calibrated to generate 300,000 electrons for every ion that strikes the
detector. Additionally, this tune generates spectra that are the closest in appearance to the
factory tune.
EI Standard Tune
EI Standard Tune—Provides EI tuning and is used to completely retune the system. It takes
the longest amount of time to run, but it has the advantage of reoptimizing nearly all the
parameters affecting the signal. This type of tune performs a mass calibration, tunes the lenses
and resolution, and performs a leak check. It adjusts the detector sensitivity to generate a
m/z 219 ion with an intensity of 20,000,000 counts. Unless your SOP requires it, this is not
the best tune to use on a daily basis because of the length of time required to run it.
Figure 34 shows a typical tune report for an EI Standard Tune on a system using helium as a
carrier gas.
EI Diagnostics Only
EI Target Tune
Fast Scan Tune
Negative CI Tune
Positive CI Tune
3 Tuning
Tune Types
34 TSQ Duo User Guide Thermo Scientific
Figure 34. Typical EI Standard Tune Report
Typical results for an EI Standard Tune are listed below.
• Peak Intensities:
– Base Peak is m/z 69 or 219
– Base Peak ~ 20,000,000
• Water Background: m/z 18:69 < 240%
• Repeller Voltage:
– Helium carrier gas = 3–8 V
– Hydrogen carrier gas = 7–15 V
• Foreline Pressure: < 100 mTorr
3 Tuning
Tune Types
Thermo Scientific TSQ Duo User Guide 35
• Ion Gauge Pressure: <5e-5 Torr
• Leak Check: < 10%
Run the EI Standard Tune if you suspect a system problem. The following conditions could
indicate an issue:
• Increased detector gain—Detector gain is related to multiplier voltage, so if the detector
gain is increased, multiplier voltage will also increase.
• Leak check change—Leak check results change over time base on instrument conditions.
Recently vented systems exposed to air should be lower than 10% after one day of
pumping down. Assuming the system is leak free, the instrument leak check should
constantly decrease over time until stabilizing.
EI Standard Quick Tune
EI Standard Quick Tune—A shortened version of the EI Standard Tune recommended for
use when subsequent maintenance tuning is needed after an EI Standard Tune. This tunes the
repeller in conjunction with Q3 to overcome the effects of matrix buildup in the source. It
starts with the last saved tune and sets the detector sensitivity to generate a m/z 219 ion with
an intensity of 20,000,000 counts.
EI SRM Tune
EI SRM Tune—Provides EI tuning and completely retunes the system. This tune reoptimizes
nearly all the parameters affecting the signal. This type of tune performs a mass calibration,
tunes the lenses and resolution, and performs a leak check. Unless your SOP requires it, this is
not the best tune to use on a daily basis because of the length of time required to run it. This
tune is more sensitive for high mass than the EI Standard Tune, making it more sensitive to
many SRM transitions. It sets the detector sensitivity to generate a m/z 219 ion with an
intensity of 20,000,000 counts and verifies the correct mass calibration.
SRM tunes adjust the resolution of each mass at 50% peak height by design. This tune may
provide slightly larger peak intensities than a Standard tune because it allows a slightly wider
peak through Q1 and Q3. These tune types are intended for EI SRM analysis only and not EI
Full Scan data acquisition.
Figure 35 shows a typical tune report for an EI SRM Tune on a system using helium as a
carrier gas.
Note Foreline and ion gauge pressures are dependent on column flow rate.
3 Tuning
Tune Types
36 TSQ Duo User Guide Thermo Scientific
Figure 35. Typical EI SRM Tune Report
Typical results for an EI SRM Tune are listed below.
• Peak Intensities:
– Base Peak is m/z 69 or 219
– Base Peak ~ 20,000,000
• Water Background: m/z 18:69 < 240%
• Repeller Voltage:
– Helium carrier gas = 3–8 V
– Hydrogen carrier gas = 7–15 V
Note Isotope Abundance and Isotope Ratios are only valid when using a tune type that
tunes the resolution at 10% peak height.
3 Tuning
Tune Types
Thermo Scientific TSQ Duo User Guide 37
• Foreline Pressure: < 100 mTorr
• Ion Gauge Pressure: <5e-5 Torr
• Leak Check: < 10%
EI SRM Quick Tune
EI SRM Quick Tune—A shortened version of the EI SRM Tune that is recommended for use
when subsequent maintenance tuning is needed after an EI SRM Tune. This tunes the
repeller in conjunction with Q3 to overcome the effects of buildup in the source. It starts with
the last saved tune and sets the detector sensitivity to generate a m/z 219 ion with an intensity
of 20,000,000 counts.
SRM tunes adjust the resolution of each mass at 50% peak height by design. This tune may
provide slightly larger peak intensities than a Standard tune because it allows a slightly wider
peak through Q1 and Q3. These tune types are intended for EI SRM analysis only and not EI
Full Scan data acquisition.
EI Tune Check
EI Tune Check—Used to check how well your last tune is performing. As it is the fastest tune
type, it allows you to quickly update the detector sensitivity as the system gets dirty. This
allows the sample intensity to remain constant for longer periods without running a full
retune of the instrument.The daily tune check performs a leak check, makes sure the mass
calibration is correct, and sets the detector sensitivity to generate a m/z 219 ion with an
intensity of 20,000,000 counts. If your SOP allows it, you can use this tune to rapidly verify
that the previous lens tune is still generating good spectra.
EI Diagnostics Only
EI Diagnostics Only—Runs a complete set of diagnostics, including a leak check, and
generate a report. No tuning is performed. Uses the parameters from the last saved tune.
EI Target Tune
EI Target Tune—Starts with the last saved tune and adjusts the ion ratios of the calibration
gas to those expected of classic single quadrupole MS analysis. This tune is intended to be run
after full calibration using an EI Standard Tune. If your SOP was developed in response to
regulatory requirements for classic single-quadrupole MS analysis, or you require classic single
quadrupole spectra for spectral library matching, use this tune. It also sets the detector
sensitivity to generate a m/z 219 ion with an intensity of approximately 20,000,000 counts
and verifies correct mass calibration.
Note Foreline and ion gauges are optional devices. Their pressures depend on
column flow.
3 Tuning
Tune Types
38 TSQ Duo User Guide Thermo Scientific
Fast Scan Tune
Fast Scan Tune—This tune retunes the system with fixed Q1 voltages necessary for fast
scanning. By increasing the ion energies and shortening ion flight times through the mass
analyzer, this tune provides increased ion signal required to tune resolution and perform mass
calibration at a high scan rate. This tune may cause high mass ions to exhibit more fronting
than the other built-in tune types. This tune performs a leak check and sets the detector gain
to 300,000. It does not tune the detector gain. Run a fast scan tune when scanning above
10,000 amu/s to improve the mass calibration for high mass ions.
Negative CI Tune
CI- Tune—Used to analyze samples with negative CI. The standard NCI tune performs a
mass calibration, then tunes the lenses and sets the resolution. This type of tune assumes you
are using methane as the CI reagent gas and tunes the system with a 1.0 mL/min flow. This
tune does not set the detector gain. The built-in CI- tune will start with the most recent
AutoTune_NCI tune file, so have an appropriate tune file saved on the instrument's PC.
Figure 36 shows a typical CI- Tune report where methane is the CI reagent gas.
Note If you are starting with a clean source, first run the EI Initial Tune as a reset tune.
After this tune is complete, follow it with your preferred tune.
Note Chemical ionization tunes are very different from the electron ionization tunes. Do
not use a CI tune unless your instrument has a CI ion volume and CI reagent gas installed.
Note If the instrument was last used in EI mode and tuned with a high repeller voltage
before switching to a clean CI ion Source, a tune file with a low repeller voltage should be
loaded in manual tune and saved to the instrument before tuning in CI mode.
3 Tuning
Tune Types
Thermo Scientific TSQ Duo User Guide 39
Figure 36. Typical CI- Tune Report with Methane as a CI Reagent Gas
Typical results for a CI- Tune using methane as the reagent gas are listed below.
• Peak Intensities:
– Base Peak: 452 or 633
– Base Peak ≥ 6,000,000
• CI Gas Flow: 1.0–4.0 mL/min Methane
• Emission Current: 50–100 μA
•Multiplier Voltage
– Normal Performance: < 2200 V
– Replace Multiplier: ≥ 2200 V
• Foreline Pressure: < 400 mTorr
Note Emission current is an input value, and it should match the value set in the tune.
3 Tuning
Tune Types
40 TSQ Duo User Guide Thermo Scientific
•Ion Gauge Pressure: < 1e-4 Torr
• Isotope Ratios: m/z 453:452 = 5.8–11.8%
Positive CI Tune
CI+ Tune—Used to analyze samples with positive CI. The standard PCI tune performs a
mass calibration, then tunes the lenses and sets the resolution. This type of tune assumes you
are using methane as the CI reagent gas and tunes the system with a 1.5 mL/min flow. This
tune does not set the detector gain. The built-in CI+ tune will start with the most recent
AutoTune_PCI tune file, so have an appropriate tune file saved on the instrument's PC.
Figure 37 shows a typical CI+ Tune report where methane is the CI reagent gas.
Note Foreline pressure fluctuates with CI reagent gas flow rate. As the CI reagent gas flow
rate increases, the foreline pressure also increases. Ion gauge pressure also increases if an
ion gauge is installed on the system.
Note Chemical ionization tunes are very different from the electron ionization tunes. Do
not use a CI tune unless your instrument has a CI ion volume and CI reagent gas installed.
Note If the instrument was last used in EI mode and tuned with a high repeller voltage
before switching to a clean CI ion Source, a tune file with a low repeller voltage should be
loaded in manual tune and saved to the instrument before tuning in CI mode.
3 Tuning
Tune Types
Thermo Scientific TSQ Duo User Guide 41
Figure 37. Typical CI+ Tune Report with Methane as a CI Reagent Gas
Typical results for a CI+ Tune using methane as the reagent gas are listed below.
• Peak Intensities:
– Base Peak: 414
– Base Peak ≥ 1,000,000
• CI Gas Flow: 1.5–4.0 mL/min Methane
• Emission Current: 25–50 μA
•Multiplier Voltage
– Normal Performance: < 2200 V
Tip If you intend to use ammonia reagent gas, attach methane to one CI reagent gas port
and ammonia to the other port. Tune the instrument using methane, then switch to the
ammonia port. Allow plenty of time for the new reagent gas to purge the CI tubing before
starting your analysis.
Note Emission current is an input value, and it should match the value set in the tune.
3 Tuning
Tuning the Mass Spectrometer
42 TSQ Duo User Guide Thermo Scientific
– Replace Multiplier: ≥ 2200 V
• Foreline Pressure: < 400 mTorr
•Ion Gauge Pressure: < 1e-4 Torr
• Isotope Ratios:
•m/z 415:414 = 5.8–11.8%
Tuning the Mass Spectrometer
To tune your mass spectrometer
1. In the Tune Types field, select EI, CI, or Both, depending upon which ionization mode
you are using.
2. Select a tuning category. See Figure 38.
Figure 38. Tuning Categories
3. Select the tune type you want to use:
Note Foreline pressure fluctuates with CI reagent gas flow rate. As the CI reagent gas flow
rate increases, the foreline pressure also increases. Ion gauge pressure also increases if an
ion gauge is installed on the system.
Note To add a tune type to the list, see Modifying an Automatic Tune.
3 Tuning
Tuning the Mass Spectrometer
Thermo Scientific TSQ Duo User Guide 43
Figure 39. Tune Types
4. Select the Display Report When Complete check box so that you can view the tune
report after running the tune.
Figure 40. Displaying a Report
5. Select the Show Spectra check box to show the spectra while the system is tuning.
6. Click the Start button to begin tuning.
Once the tune completes, your tune report opens in the Tune Results Viewer. If you did
not select the Display Report When Complete check box, you can click View Tune
Report on the dashboard and view the report.
Figure 41. Sample Tune Report
7. Click Report Options. In the dialog box, select the charts and reports you want to
display and change the name of your instrument.
8. Select a mass for Calculate Relative Abundance Using. The default is mass 69, which
will reference all masses to mass 69. Some masses may have over 100% abundance. If you
do not wish to have a relative abundance above 100%, select Base Peak. This option will
select the reference mass as the highest abundance mass in the tune.
9. Click OK.
Note Make sure the power options on your computer are not set to go into Standby
mode while you are acquiring data for your tune. Otherwise, it will interrupt your
tune.
3 Tuning
Tuning the Mass Spectrometer
Thermo Scientific TSQ Duo User Guide 45
Figure 42. Tune Report Options
10. To print your tune report, click Print Report to open a print dialog box and print your
report.
Note Only tune the system as often as your application requires. Repeated tuning on an
otherwise functioning system can cause abnormalities as each tune reoptimizes all
parameters affecting the signal.
3 Tuning
Tuning the Mass Spectrometer
46 TSQ Duo User Guide Thermo Scientific
Figure 43. Printing a Tune Report
In the Tune Results window, you can open tune results, print reports, or change the way
you view the report.
11. To save the report, click the Save icon and save it as a Microsoft Excel™ file or an
Adobe™ Acrobat™ PDF file.
You may find it useful to compare this tune with a previous tune report of the same tune
type. Some changes in peak height are normal, but if the difference is significant, see
Troubleshooting.
12. To browse to another tune report on your computer, click Open Tune Results in the top
of the window.
13. Click Open to open a previously saved tune report.
3 Tuning
Updating Tunes for New RF Lens
Thermo Scientific TSQ Duo User Guide 47
Figure 44. Loading Tune Results
If the sensitivity and resolution are adequate for running your samples, you are ready to
develop or run a method.
Updating Tunes for New RF Lens
If you have purchased a new lens 3/RF lens (PN 1R120574-0103), you must update the ion
guide frequency in the Manual Tune utility and retune your instrument.
To update the ion guide frequency using the Manual Tune utility
1. Open the TSQ Series Dashboard.
2. Click Manual Tune on the dashboard. See Figure 45.
3 Tuning
Updating Tunes for New RF Lens
48 TSQ Duo User Guide Thermo Scientific
Figure 45. Opening Manual Tune on the TSQ Series Dashboard
3. The Manual Tune utility opens.
4. Select Frequency Tune on the top menu. See Figure 46.
Figure 46. Accessing Frequency Tune
5. From the Device drop-down menu, select Ion Guide. See Figure 47.
Manual Tune
Frequency Tune
3 Tuning
Updating Tunes for New RF Lens
Thermo Scientific TSQ Duo User Guide 49
Figure 47. Locating the Device Menu
6. Click Start. The system will detect the ion guide frequency.
7. When the instrument has finished detecting the ion guide frequency, go to Save | To
Instrument on the top menu. A dialog box confirming that the tune settings have been
saved to the instrument will open. See Figure 48.
Figure 48. Saving the New Ion Guide Frequency to the Instrument
8. To confirm that the intensities are still correct, select Mass & Resolution Tune on the
top menu to go back to the Manual Tune home page.
Device Menu
3 Tuning
Updating Tunes for New RF Lens
50 TSQ Duo User Guide Thermo Scientific
9. Choose 3 from the Spectra drop-down menu. See Figure 49.
Figure 49. Selecting the Correct Number of Spectra to Scan
10. Select EI from the Cal. Gas Level menu. See Figure 50.
Figure 50. Setting the Calibration Gas Level to EI
11. Click Start Scan. Check the intensities for the masses 69, 219, and 502. Set the masses
using the Mass drop-down menu below each spectrum. See Figure 51.
3 Tuning
Updating Tunes for New RF Lens
Thermo Scientific TSQ Duo User Guide 51
Figure 51. Checking the Mass Intensities
12. Once you have confirmed the intensities are sufficient for tuning, retune the system.
Note The intensities might be lower than they were at the previous frequency set for the
ion guide until the lenses are tuned in AutoTune.
3 Tuning
Updating Tunes for New RF Lens
52 TSQ Duo User Guide Thermo Scientific
Thermo Scientific TSQ Duo User Guide 53
4
Creating a Method
Once you have tuned the TSQ Duo system, you can create a method for each of its
components. Use these methods to indicate to the GC/MS system how to collect your data.
Accessing the Method Editor
To create a method for the TSQ Duo mass spectrometer, the TRACE 1300 or 1310 GC, and
your autosampler, go to Start > Thermo Chromeleon > Chromeleon 7 and open the
Chromeleon software application The Chromeleon Console opens to the Thermo Scientific
GCMS Home Page. See Figure 52.
Contents
•Accessing the Method Editor
•Creating a GC-MS method
•Running a Sequence
4 Creating a Method
Creating a GC-MS method
54 TSQ Duo User Guide Thermo Scientific
Figure 52. Chromeleon Console: Thermo Scientific GCMS Home Page
Creating a GC-MS method
To create a GC-MS method
1. Open the Chromeleon Console. Select TSQ Duo from the left menu. The TSQ Duo
window opens. See Figure 53.
Note All of the configured instruments are shown in the left pane of the Chromeleon
Console window under Instruments > TSQ-PC. If your instruments are not shown, you
must configure them. See “Configuring Your Instrument” for instructions.
4 Creating a Method
Creating a GC-MS method
Thermo Scientific TSQ Duo User Guide 55
Figure 53. MS Device Window
2. Go to Create > Instrument Method.
Note Instructions for setting the most common parameters for the TriPlus RSH Sampling
System follow. Refer to your autosampler documentation for more detailed information
about settings.
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Creating a GC-MS method
56 TSQ Duo User Guide Thermo Scientific
Figure 54. Creating an Instrument Method
3. The Instrument Method Wizard – Select Instrument window opens. See Figure 55.
Figure 55. Instrument Method Wizard – Select Instrument
4. Select the instrument you want to configure and click Next.
5. The Instrument Method Wizard – System: General Settings window opens. See
Figure 56.
4 Creating a Method
Creating a GC-MS method
Thermo Scientific TSQ Duo User Guide 57
Figure 56. Instrument Method Wizard – System: General Settings
6. You can set the GC Run Time for the method here, or load it with the other GC settings
later. Click Next.
7. The Instrument Method Wizard – TriPlusRSH: Settings window opens. See Figure 57.
4 Creating a Method
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58 TSQ Duo User Guide Thermo Scientific
Figure 57. Instrument Method Wizard – TriPlus RSH: Settings
8. Choose one of these three options: GC Liquids, GC Headspace, or SPME.
9. Enter the ID information for your samples. You must fill in any field with an asterisk (*)
a. Injectors—Enter the injection ID into the corresponding injector port.
b. Syringes—Enter the syringe ID information.
c. Wash Station—Enter the wash station ID information.
d. (Optional) Internal Standard/Solvent Stations—Enter ID information for your
solvent station or interval standard station.
e. (Optional) Cooled/Heated Trays—Enter ID information for your primary and, if
used, secondary trays.
10. Click Create New Method.
11. Use the following instructions to configure the GC Liquids general method settings. See
Figure 58.
4 Creating a Method
Creating a GC-MS method
Thermo Scientific TSQ Duo User Guide 59
Figure 58. General GC Liquids Settings on the TriPlus RSH Sampling System
a. Injector Type—Choose Single or Double for each injector.
b. Injection Mode—Choose Basic, Enrichment, Enrichment Needle Solvent Option,
Internal Standard Double, Internal Standard Post, Needle Solvent Wash, Solvent
Flush Double, or Solvent Flush Post.
c. Rapid Mode—Choose Disable, After Sample Rinse, After Bubble Elimination, or
After Sample Asp. in Home.
d. Syringe Type—Enter your syringe volume in μL. Enter the syringe needle length in
mm.
e. Sample Volume—Enter the sample volume to be injected into the GC. Typical values
are between 0.5 and 5 μL.
f. Plunger Strokes—Select the number of plunger strokes to use when drawing up the
sample. Air bubbles in the syringe change the amount of sample injected, which can
cause signal variation in different runs. To prevent this from occurring, increase the
number of plunger strokes to reduce the chance of an air pocket in your syringe.
Typical values are between 3 and 10.
g. Air and filling mode—Choose Auto to use the default or Custom to change the
parameters.
h. Sample Viscosity—Select Viscous if your sample is viscous or Non Viscous if your
sample is non-viscous. With a viscous sample, the syringe is filled more slowly than if
it was non-viscous. Since the amount of time saved is so small, setting this option to
Yes might be easier.
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60 TSQ Duo User Guide Thermo Scientific
i. Sampling Depth in Vial—Select the Bottom Sense check box and enter the height
from the bottom of the vial (in mm) at which the tip of the syringe needle will be
placed in the sample vial when it is being filled.
j. Injection Depth—Select Standard or Minimum to indicate how the sample is
introduced into the GC. If you select Standard, the autosampler inserts the needle all
the way into the injection port. If you select Minimum, the autosampler barely enters
the injection port.
k. Pre-inj Dwell Time(s)—Use this field to enter the time (in seconds) that the needle
will be in the injection port before the plunger injects the sample.
l. Post-inj Dwell Time(s)—Use this field to enter the time (in seconds) that the needle
will be in the injection port after the plunger injects the sample.
12. Configure the settings under the Washes tab (see Figure 59):
Figure 59. GC Liquids Washes Settings
a. Number of Solvents—Choose Single or Multiple depending on the number of
solvents you will use for your method. You may choose up to four solvents: A, B, C,
or D.
b. Wash Station—Choose Standard Wash Station or Large Wash Station. Refer to the
autosampler documentation for more information about the wash stations.
c. Pre-injection—Use the Solvent and Cycles fields to set the number of solvent purges
that will occur before the autosampler touches your sample. Always include some
sample rinses, either before or after injection, to make sure you do not have sample
carryover from one injection to the next. Configure the settings so that the syringe is
4 Creating a Method
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Thermo Scientific TSQ Duo User Guide 61
purged with the same solvent that was used in location A, B, C, or D or with solvents
A and B or C and D. Typically, there is 0 or 1 cycles of pre-injection purges.
d. Rinse—Use the Rinses list to select the number of times the syringe is rinsed with
your sample before each injection. Rinses help ensure the sample being injected is not
diluted by the residual rinse solvents. By purging the syringe with your sample before
injection, the dilution is minimal. The standard setting is between 1 and 3 rinses. If
you have a very limited amount of sample, however, you may want to set this field to
0 to conserve the sample.
e. Post-injection—Use the Solvent and Cycles fields to set the number of solvent purges
that will occur after the autosampler touches your sample. You should always have
some sample rinses, either before or after injection, to make sure you do not have
sample carryover from one injection to the next. You can have the syringe purged
with the same solvent that was used in location A, B, C, or D or with solvents A and
B or C and D. Typically, there are 1 to 5 cycles of post-injection purges.
13. Click Next. The Instrument Method Wizard – GC Inlets(TRACE1300Series):
FrontInlet Flow/Pressure Options window opens.
Figure 60. Instrument Method Wizard – Front Inlet Flow/Pressure Options
14. Set the Mode to Constant Flow, Constant Pressure, Programmed Flow, or
Programmed Pressure. The gas flow and the oven temperature work together to
determine how well the analytes are separated and how long the analysis will take. If you
use constant pressure, as the column is heated in the oven, the flow rate will fall as the
viscosity of the carrier gas increases. If you use constant flow, the carrier gas pressure will
increase as the column temperature increases to keep the flow constant. Constant flow is
more common. Typical flow rates are 1-3 mL/min. The pressure depends on the column
Carrier Gas
Mode
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62 TSQ Duo User Guide Thermo Scientific
length and internal dimensions, so there is not a typical value. Because the outlet of the
column is in the TSQ Duo instrument, which is under vacuum, be sure the vacuum
compensation is on to ensure accurate flow rates.
15. Click Next. The Instrument Method Wizard – GC Inlets(TRACE1300Series):
FrontInlet Options window opens. See Figure 61.
Figure 61. Instrument Method Wizard – GC Inlets(TRACE1300Series): Front Inlet Options
16. If you have a split/splitless inlet (SSL) injector, click the S/SL-Front or S/SL-Back tab to
configure the injector port settings. In the inlet area, do the following:
a. Select the Enable Temperature Control check box and set the temperature high
enough to volatize all the analytes in your sample. The material should be injected
into the port to vaporize and move into the GC column quickly. Higher temperatures
can lead to thermal decomposition of some analytes, so you must optimize the
injector temperature for your analysis. The SSL temperature can be set up to 400 °C
(752 °F). A typical value would be 250 °C (482 °F).
b. Select the Split Flow Control check box to dilute high concentrations of sample.
The split flow is the amount of gas that is swept through the injector to the exhaust
port. Higher values will give more dilution. The split flow reduces the amount of
contamination that builds up in your system. The split flow ratio is the ratio of the
split flow to the carrier gas flow. It is effectively the dilution ratio of the sample. This
setting is typically turned on and set to a flow of 50 mL/min. However, more carrier
gas is used, so for your analysis, lower split flows may be more acceptable. If you set
the split ratio, the software calculates the correct split flow. The reverse is true also.
c. For best results, check the Constant Septum Purge box to use the septum purge,
which means additional carrier gas will go through the injector. The default purge
4 Creating a Method
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Thermo Scientific TSQ Duo User Guide 63
flow value is 5 mL/min. This reduces the buildup of contaminants in the injector, on
the column, and in the TSQ Duo instrument. If you perform a splitless injection,
even if the split flow is set, the split flow turns off for the splitless time. The septum
purge turns off for the stop purge time. After these times, the split flow and septum
purge are reactivated.
d. If your analysis requires a higher flow to quickly sweep the analytes into the column,
which may be needed with high temperature injectors and thermally labile
compounds, use the surge pressure to increase the column flow for the surge duration
time.
e. Because the outlet of the column is in the TSQ Duo instrument, which is under
vacuum, be sure the vacuum compensation by checking the Vacuum Compensation
checkbox is on to ensure accurate flow rates.
f. In an effort to reduce the amount of carrier gas used, select the Enable Gas Saver
Mode. When used, the split flow is reduced to the gas saver flow after the gas saver
time. It is not recommended to use a flow of less than 20 mL/min because
contaminants can build up in the injector, column, and TSQ Duo instrument, which
can affect the system performance.
17. Click Next. The Instrument Method Wizard – GC Inlets(TRACE1300Series): GC
Oven Settings window opens. See Figure 62.
Figure 62. Instrument Method Wizard – GC Inlets: GC Oven Settings
18. Set the oven temperatures in this window. There is always at least one temperature and
time in any GC temperature program. In the Initial row, enter the initial temperature,
which must be 4 °C (7 °F) above room temperature and less than the maximum operating
temperature of your GC column. If you set the initial temperature to a value below this
limit, the GC will not reach the initial temperature. If you set the temperature above the
limit, the GC column will be damaged. You can set the initial hold time to a value
between 0 and 999.99 minutes. The typical initial temperature is at least 10 °C (18 °F)
4 Creating a Method
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64 TSQ Duo User Guide Thermo Scientific
above the boiling point of your sample solvent, and the initial time is usually long enough
for the solvent to move through the column.
19. Select a maximum of 32 temperature ramps, each with its own ramp rate, final
temperature, and hold time. Each temperature ramp begins at the previous ramp's
temperature after the hold time has expired. A typical program has one or two ramps. The
GC temperature profile is the primary method for separating your analytes from each
other, the solvent, and the matrix. Your temperature profile must be optimized for your
analysis needs.
20. Select the prep-run timeout. The prep-run timeout is the maximum amount of time that
the GC will wait before it gives up on an injection. As an example, with the default value
of 10 minutes, if the GC is ready to receive an injection, but does not receive it after ten
minutes, the GC will stop waiting. This usually occurs in case of an error.
21. Set the oven equilibration time. The equilibration time is a delay between when the GC is
at temperature and when the GC reports as being ready. The equilibration time is
typically set to 0.5 minutes.
22. (Optional) Enable the cryogenic option to cool the oven. If this option is selected, then
the minimum allowed temperature in a temperature ramp will fall from 0 to -99 °C
(32 to -146 °F). The GC also allows the use of a post-run column cleaning. This is not
typically used because the material that is purged from the column in this step would go
into the TSQ Duo, which can lead to contamination. If you want to use this feature, set
the GC oven temperature, as well as the amount of time to remain at that temperature
after the analytical run is complete. You can also set the amount of pressure used to push
the carrier gas through the column. Refer to the TRACE 1300/1310 Series GC User Guide
for more information.
23. If you have a Programmable Temperature Vaporizer (PTV), click the PTV-Front or
PTV-Back tab to configure it. The PTV is a low thermal mass injector that allows the
instrument to rapidly heat or cool the inlet. You can use the PTV page to program the
temperature of the injector. Refer to the GC documentation for details about the PTV or
other types of injectors.
24. To add an inlet or detector to the Method editor user interface:
a. Attach the inlet or detector to the GC. Refer to the GC documentation for
instructions.
CAUTION INSTRUMENT DAMAGE. Be sure not to overheat the GC column or it
may contaminate the instrument.
Note The user interface reflects the current configuration of your GC. If you add,
remove, or change inlets or detectors, redo your instrument method according to the
new GC configuration.
4 Creating a Method
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Thermo Scientific TSQ Duo User Guide 65
b. Add the inlet or detector to the current instrument configuration. See Chapter 1,
“Introduction.” for instructions to configure the GC.
25. Click Next.
26. From the Method Type list, select Acquisition-General or Acquisition-Timed. See
Figure 63. An Acquisition method is used to collect data.
Figure 63. TSQ Series Method Type Setup
27. Use the Method Setup pane to set the temperatures and acquisition threshold in General
Acquisition mode. See Figure 64 on page 66.
Note The Maintenance method is used to bake out or cool down the instrument during
a sequence. This can be useful if you know you want to perform these tasks and you want
to do them in an automated way as part of your sequence.
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66 TSQ Duo User Guide Thermo Scientific
Figure 64. General Acquisition: Setting Temperatures and Acquisition Threshold
a. Set the MS Transfer Line Temperature. This field represents the temperature of the
transfer line, which is the tube that contains the column as it leaves the GC oven and
enters the TSQ Duo system. The maximum allowable temperature is 350 °C.
b. Set the Ion Source Temperature. You can enter a value between 0 and 350 °C. The
optimal temperature depends on the analyte. Higher temperatures will keep the ion
source cleaner, but will lead to increased fragmentation, which may reduce sensitivity.
c. (Optional) Select the Acquisition Threshold check box and enter a value for the
minimum peak height for the data file, if needed. If your peak has an intensity that is
below this threshold, it will not be stored. This setting may help reduce noise, but it
may also alter the reported isotope ratios because the smaller isotope signals will be
preferentially reduced.
d. Select EI from the Ionization Mode pull-down menu.
Method Setup
Pane
CAUTION You will damage the column and contaminate the TSQ Duo
instrument if you set the transfer line temperature above the maximum allowed
temperature for the column.
Note Although CI settings are present in the TSQ Series software, chemical
ionization is not available on the TSQ Duo, and the CI settings are inactive.
4 Creating a Method
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Thermo Scientific TSQ Duo User Guide 67
28. For Acquisition-General methods only, do the following:
a. In the Run Completion group, select the condition under which the run will end.
–GC Run Time—Select this option if you want the MS run to end when the GC
run is complete.
–Probe Run Time—Select this option if you have a probe controller installed and
you want the MS run to end with the probe run is complete.
–Stop After—Select this option to set the number of minutes you want the MS to
run. The end of the run can be between 0 and 1000 minutes. With this option
you can stop the acquisition when all the compounds of interest have eluted, but
the GC is still at an elevated temperature to keep the column clean. Thermo
Fisher Scientific recommends that you select this option to save burn time on the
filament.
b. In the Scans pane, click a scan row to enter scan information under each column. See
Figure 65.
Figure 65. Setting Acquisition-General Scan Information
Note The following parameters apply only to the Acquisition-General method type
only. Acquisition-General is the recommend setting for full-scan only MS methods,
or simple SIM or SRM methods. If you need to develop a complex SIM or SRM
method with a large compound list or overlapping retention times, refer to the
instructions for Acquisition-Timed.
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68 TSQ Duo User Guide Thermo Scientific
i. Use the Time (min) column to set the time that the MS begins to acquire the
scan group. Set the time for the first group late enough to allow the solvent to
move through the system, and early enough to ensure the first analyte will be
captured in the segment. Set subsequent segment times so that the start time will
occur between compounds of interest. You may set up different types of scans in
a single group. The scans will occur in descending order.
Your method may allow sequential full scans and SIM scans of a compound. As
an example, in this method, the mass range of 50–300 will be scanned in
0.2 seconds. Immediately after the full scan finishes, the SIM scans begin. The
SIM scans occur sequentially. Two different SIM masses, at 43 and 44, will be
looked at for 0.05 and 0.08 seconds, sequentially. These simultaneous full scan
and SIM scans will begin 2.5 minutes into the GC run. You will get a complete
set of scans every 0.337 seconds. At 5 minutes into the GC run, the scans change
to a set of SRM scans. The first SRM transition is 292.9 to 257.91 with a
collision energy of 20 eV. The second SRM transition is 262.91 to 192.93 with a
collision energy of 32 eV. Both SRM scans have a dwell time of 0.05 seconds.
You will get a complete set of scans every 0.105 seconds.
All of these scans use the most recent AutoTune_EI file. You can also use a
specific tune file for each of the scans.
ii. Use the SRM, SIM, or Scan Masses column to tell the MS which masses to
scan.
– In full-scan mode, enter the start and end mass separated by a dash. You
must put each full-scan range on a separate line.
– For SRM methods, enter precursor masses, product masses, and collision
energies of the ions you wish to monitor. Separate scan filters will be created
for each SRM transition during acquisition.
– If you would like to combine multiple SRM transitions in a single scan filter,
highlight the rows you want to combine and then right-click and select
Group SRM Scans | Replace Selected Scans. See Figure 66. You can also use
this function to ungroup a group of SRM scans into individual rows.
Note If some of the following columns are not shown in the Scan pane, you can
right-click and display them. You can also reorganize the columns by clicking the
heading of a column and dragging it to the left or right.
Note The faster the MS scans, the more data points across a peak it will
acquire. However, the precision of individual scans may be reduced.
Note Each line in a scan must only contain a full-scan range, individual SIM
masses, or an SRM transition. Scan types cannot be mixed in a single line. Set
up simultaneous scans by giving them the same time in the Time (min)
column.
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Thermo Scientific TSQ Duo User Guide 69
Figure 66. Grouping SRM Scans
iii. Enter the product ion mass (for SRM methods) in the Product Mass column.
The product ion mass is the result of fragmenting the precursor ion with
collision gas. If you want to perform a precursor ion scan, enter the mass of the
target precursor ion into this column.
iv. Use the Neutral Loss Mass column when you want to perform a neutral loss
scan. Enter the mass of the target precursor ion in this column. The scan mass
range must be at least 2.5 amu wide and must begin at 1 + the precursor ion
mass.
v. In the Collision Energy column, enter the collision energy (for SRM methods)
in eV. The collision of a precursor ion with the collision gas at a particular energy
fragments the precursor ions into product ions. By varying the collision energy, a
single precursor ion can be fragmented into several product ions. An SRM
transition is defined by a precursor ion being fragmented into a particular
product ion mass using a certain collision energy. The Collision Energy column
is unusable unless you define a precursor and product ion mass.
vi. In SIM or SRM mode, use the Dwell or Scan Times column to define the
amount of time (in seconds) that the MS will look at your SIM ion mass or your
SRM product ion mass. If you are in full-scan mode, the Dwell or Scan Times
column determines the amount of time to scan across the designated range. Set
this value to have 5–20 scans across your GC peak. If you have too few scans, the
Note Entering a product ion mass changes a scan to SRM.
Note The system controls the collision gas so it will be ready when an
MS/MS scan is requested.
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GC peak area is inaccurate. If you have too many scans, the MS signal becomes
less precise. This column must be set to a value between 0.0005 and 5 s for SRM
and SIM methods. The default is 0.2 s. For full scan methods, the minimum
scan time depends on the mass range so that the scan rate does not exceed
13,000 amu/s.
vii. Use the Tune File Name to select a tune file to be used for this scan. Select the
autotune file you created in Chapter 3, “Tuning,” . If you wish to use the same
tune file for multiple scans, you can fill down this column by right-clicking on a
tune file name.
viii. (Optional) Use the Scan Name column to enter a description of the scan. You
may use the name as a label to indicate the compound used with the scan.
ix. Use the SIM Widths column to set the width range of the SIM window. The
range of values can be between 0.01 and 10. The default is 1 amu, which means
the MS will collect all the ions from your SIM mass ±0.5 amu.
x. Use the Data Type column to select whether you want to collect Profile,
Centroid, or Nominal mass spectra. Centroided mass spectra are the most
common because they are used by most of the libraries and provide the smallest
data files. Profile mass spectra provide detailed mass spectral peaks, which result
in large data files. Profile mass spectra are not available for SRM scans. when you
want to perform fast scanning (up to 20,000 amu/s), select Nominal from the
drop-down list under Data Type.
xi. Use the Precursor (Q1) Resolution column to open the peak width of the
precursor mass for SRM scans. The options are Normal, Wide (1.5 at 50%), or
Widest (2.5 at 50%). The default setting is Normal, which uses the tuned
resolution values from the tune file specified in the Tune File Na m e column.
Selecting Wide or Widest increases the precursor peak width to 1.5 and 2.5 amu
(at 50%) respectively. Opening the precursor peak width will increase the ion
signal into the collision cell and may improve the sensitivity of your method;
however, it may also increase the background noise level.
xii. Use the Product (Q3) Resolution column to open the peak width of the
precursor mass for SRM scans. The options are Normal, Wide (1.5 at 50%), or
Widest (2.5 at 50%). The default setting is Normal, which uses the tuned
resolution values from the tune file specified in the Tune File Na m e column.
Note Selecting a tune file to open without a date-time stamp opens the most
recent tune of the tune type selected. To use a specific tune file, select a tune
file of that prefix with the date-time stamp that you want.
Tip Use a tune file without the date-time stamp to create your method.
Note Scan Name, SIM Widths, Data Type, and Q1 Resolution columns are
not shown by default. To view them, right-click one of the column headers to
pull up the menu to display the hidden columns
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Thermo Scientific TSQ Duo User Guide 71
Selecting Wide or Widest increases the precursor peak width to 1.5 and 2.5 amu
(at 50%) respectively.
c. In the Groups pane on the right, review the information in each row. See Figure 67.
As you create scans in the Scans pane, information in the groups pane is
automatically displayed.
Figure 67. Accessing the Groups Pane
i. The Time (min) column indicates the time that the MS begins to acquire data
after the GC starts for that group. It is typical to have enough of a time delay for
the start of the first group to allow the solvent to get through the column before
starting acquisition. The Time column in the group pane cannot be modified. If
necessary, modify the scan time in the Scans pane.
ii. The Tota l S c an Time ( s e c) column indicates the sum of all the scans in each
segment. See Figure 68. The total scan time also contains the stabilization time
that occurs between each scan. This method, beginning 2.5 minutes into the GC
run, gives you a complete set of scans every 0.337 seconds. At 5 minutes into the
GC run, the scanning completely changes. Now the scans will repeat every
0.105 seconds until the GC run is complete. As the total scan time is a calculated
value, it is not editable.
Note By default not all columns are displayed in the Groups pane. Right-click a
heading to display them. You can also reorganize the columns by clicking the
heading of a column and dragging it to the left or right.
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72 TSQ Duo User Guide Thermo Scientific
Figure 68. Determining Groups Total Scan Time
iii. Use the Chrom Filter On column to enable the chromatographic filter. This
filter smooths spectral data as it is acquired, which may increase the
signal-to-noise ratio by a factor of two or more. The chromatographic filter is
most useful when at least four full scans are acquired across a GC peak. This
setting is typically left on.
iv. Use the Chrom Filter Peak Width column to set the peak width to match the
width of the GC peak (in seconds). If the peak width is set too large, signal
intensity may be reduced. The default value is 1 s.
v. Use the Filament On column to turn the filament on and off in the selected
segment. Turning off the filament increases the lifetime of the filament and keeps
the ion source clean longer. However, no data is collected. Use this column if you
had analytes eluting before the solvent peak. You can create a segment to turn off
the filament during the solvent peak to preserve the filament.
vi. Use the Emission Current column to set the emission current used during the
acquisition. For optimal analytical performance and stability, use the emission
current at which the system was tuned. However, if you want to use a different
emission current, clear the Use Tune File Emission Current check box and enter
a value in the Emission Current (μA) column. A high emission current will lead
to the production of more ions, but the interaction of too many ions in the
source can cause a degradation in the resolution and signal. The margin of error
is ± 0.5 μA.
vii. Use the Use Last Tuned Detector Gain column to indicate that you want to use
the detector gain set in Auto Tune. If you do not need to use the gain set in Auto
Tune or saved to the instrument in Manual Tune, then you can set the gain
manually. Higher gains give larger signals, but may shorten the lifetime of the
detector when concentrated samples are detected.The MS/MS Gain Multiplier
4 Creating a Method
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Thermo Scientific TSQ Duo User Guide 73
column only applies to groups with MS/MS events. The MS/MS gain multiplier
only applies if the Use Last Tuned Detector Gain column is selected. The
default MS/MS Gain Multiplier is 7 and is intended to give similar signal levels
as a SIM scan on the precursor ion. If you enter a specific gain, the MS will use
that gain for the SRM scan without the multiplier.
29. The following settings apply to Acquisition-Timed methods only.
Figure 69. Acquisition-Timed Method Settings
a. In the Scans pane above list of scans, select SIM or SRM from the Scan Type list. If
you want to link to an external method, click Link to External File. You may link to
a .csv or .xml method file.
b. After clicking Link to External File, the SIMBridge dialog box opens. Choose the
language of your method file from the Source Locale drop-down menu. See
Figure 70.
Note In order to edit the scans within the TSQ Duo method editor, clear the
Link to External File.
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Creating a GC-MS method
74 TSQ Duo User Guide Thermo Scientific
Figure 70. Setting the Source Language of Method Files using SIMBridge
c. Browse to your file. See Figure 71.
Figure 71. Linking to an External File using SIM Bridge
d. Click Open to open the method in SIMBridge.
e. If necessary, change the method headings in your original file to match those in the
method editor. A green check mark appears when your method is validated. See
Figure 72.
4 Creating a Method
Creating a GC-MS method
Thermo Scientific TSQ Duo User Guide 75
Figure 72. Changing Method Headings in SIMBridge
f. Click Open and the external method will be opened in the method editor. See
Figure 73.
Figure 73. Viewing a Linked File in the Method Editor
g. If you open an older model TSQ 8000 or a TSQ 8000 Evo (if you have a TSQ Duo
system) method, the Instrument Model for Method box appears.
h. Select your model from the drop-down menu in Instrument Model for Method in
order to make the imported method compatible with your model.
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76 TSQ Duo User Guide Thermo Scientific
i. In the Name column, enter the analyte name. If you have linked to an external file,
the analyte name located in the first column of your linked file will appear in the first
cell in the Name column. Right-click this window to search for an analyte within
your method. See Figure 74. This function is useful if you need to edit an analyte in a
complex method.
Figure 74. Finding an Analyte in a Method
j. In the RT column, enter retention times for SRM methods. The retention time is the
time it takes an analyte to pass from the column inlet to the detector.
k. In the Window (min) column, set the acquisition times. Smaller acquisition
windows increase sensitivity but can cause you to miss your peak if set too small.
Changing the window size only affects sensitivity if it reduces the number of
compounds analyzed in a segment. If the windows do not overlap, you will not notice
an improvement by reducing the acquisition window.
l. In the Mass column, enter the precursor ion mass for SRM methods. For SIM
methods, enter the mass of the ion you wish to monitor.
m. In the Product Mass column, enter the product ion mass (for SRM methods). The
product ion mass is the result of fragmenting the precursor ion with collision gas.
30. In the Collision Energy column, enter the collision energy (for SRM methods) in eV.
The collision of a precursor ion with the collision gas at a particular energy fragments the
precursor ions into product ions. By varying the collision energy, a single precursor ion
can be fragmented into several product ions. An SRM transition is defined by a precursor
ion being fragmented into a particular product ion mass using a certain collision energy.
Note The Window (min) column does not appear by default. The Method
Editor displays it only when the window optimizer is not active.
Right-click the
Name Column
to Find an
Analyte in a
Method
4 Creating a Method
Creating a GC-MS method
Thermo Scientific TSQ Duo User Guide 77
31. Use the right-side panel in Acquisition-Timed mode to make the following adjustments
to your method.
a. Use the Scan Settings panel to adjust the following settings. See Figure 75.
Figure 75. Acquisition-Timed Scan Settings
i. The Window Optimization pane allows access to the window optimizer
settings. When the optimize button is checked, acquisition windows will be set
automatically based on the acquisition window and dwell time targets set in this
pane. For complex SRM or SIM methods, such as a method containing more
than three hundred SRM transitions, this option will help insure a method is
created that can achieve the requested scans per peak.
Algorithm Details: If the Optimize checkbox is checked, the SRM acquisition
windows in the method are set to the Desired Window unless the Desired Min
Dwell Time cannot be met with the number of Requested Scans Per Peak. If
this occurs, then the acquisition windows are reduced until either the Desired
Min Dwell Time is met, or the Minimum Window is reached. If the Minimum
Window is reached first, the Minimum Dwell Time is reduced until the
Requested Scans Per Peak is achievable. If the absolute minimum dwell time on
the instrument, which is 0.5 ms, is reached before the requested points across the
peak are achieved, the Minimum Window is lowered until the Desired Scans
Per Peak criteria are met or until the absolute allowed minimum window on the
Scan Settings
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78 TSQ Duo User Guide Thermo Scientific
instrument is reached, which is 0.24 min. In this very rare case you must reduce
the number of Desired Scans Per Peak, increase the Min Baseline Peak Width,
or reduce the number of transitions contained in your method before you will be
allowed to save your method (see Chapter 7, “Troubleshooting.” ).
Settings: Optimize is checked by default. When Optimize is checked, you can
adjust the settings in the pane to optimize your method. See Figure 75 on
page 77. Remove the check from the box if you want to manually input your
acquisition windows. The default values for the window optimizer should give
reasonable results for normal methods. The default values are:
Desired Min Dwell Time—10 ms
Desired Window—0.6 min
Minimum Window—0.3 min
– Change the minimum dwell time using the Desired Min Dwell Time
combo box. If your method has many transitions, you may want to reduce
the desired minimum dwell time. Note that the wider the acquisition
windows in your method, the shorter the average dwell time will be.
– Change the desired acquisition window in the Desired Window combo box.
The desired window is the amount of time to scan for a transition around a
given retention time to ensure that compound will be observed. The desired
window can be set from 0.24–5 min. Set the window wide enough so that a
retention time shift will not cause you to miss any compounds. Include extra
time in this window if there is any uncertainty in compound retention times
in the method. Note that the longer the dwell time for your compounds, the
narrower your acquisition windows will be.
– Change the minimum acquisition window in the Minimum Window
combo box. The minimum window can be set from 0.24–5 min. This is the
smallest amount of time that should be scanned for a transition around a
given retention time so that you are confident the compound will be
observed. Set the minimum window to the lowest safe value to prevent
compound retention times from drifting outside the acquisition window.
ii. The Time Summary section reports the resulting total scan time, the SRM/SIM
time, and lowest dwell time for you method. These values are for information
only and not editable.
–The Resulting Total Scan Time is the baseline peak width divided by the
number of points desired across the peak. These values should be updated if
your method requirements are different from the defaults.
Note If the dwell time limit is reached and the minimum acceptable window
is forced below the 0.24 min limit, the method will fail, and a smaller list
must be used.
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Thermo Scientific TSQ Duo User Guide 79
–The SIM/SRM time is the total length of all SIM or SRM scans for each
compound in your list. This will match the total scan time unless the
method also has a full scan event.
–The Lowest Dwell Time is the actual lowest dwell time achieved by the
method settings. When the Optimize check box is selected, if the actual
lowest dwell time is considerably lower than the requested dwell time, then
the minimum window has been reached, and if the actual lowest dwell time
is considerably higher than the requested dwell time, then the requested
window has been reached.
iii. Under Peak Width, you can change the minimum baseline peak width and
desired scans per peak. These values are used to calculate the SRM/SIM Time.
The minimum baseline peak width should be set roughly to the shortest
chromatographic peak time in your analysis.
iv. Under SRM Resolution, check the Set Resolution for Each Unique Transition
Scan checkbox if you want to adjust the Precursor (Q1) Resolution or Product
(Q3) Resolution for individual analytes. If this box is not checked, the settings
apply to all compounds in the method.
–Use the Precursor (Q1) Resolution column to set the full width at 50%
(FWHM) of the precursor mass for SRM scans. The combo-box options are
Normal, Wide (1.5 FWHM), or Widest (2.5 FWHM) for each scan after a
precursor mass has been entered. The default setting is Normal, which uses
the tuned resolution values from the tune file specified in the Tun e File
Name column. Opening the precursor peak width increases the ion signal
into the collision cell, which might improve the sensitivity of your method;
however, it may also increase the background noise level.
–Use the Product (Q3) Resolution column to set the full width at 50%
(FWHM) of the product mass for SRM scans. The combo box options are
Normal, Wide (1.5 FWHM), or Widest (2.5 FWHM) for each scan after a
product mass has been entered. If the product mass is removed from a scan
to run a SIM or FS scan event, the Product (Q3) Resolution column returns
to the default value of Normal, which uses the tuned peak width at 10% or
50% as specified in the Tune File Name column. Selecting Wide (1.5
FWHM) or Widest (2.5 FWHM) increases the product ion peak width to
1.5 and 2.5 amu FWHM respectively, resulting in an increase of ions
reaching the detector. The increase in ions at the detector may improve the
sensitivity of your method; however, it may also increase the background
noise level, as well as introduce isotopic interference from +/- 1 amu ions.
Note To achieve the highest transition speeds capable on the instrument,
the resolution of all transitions must be set to Wide or Widest for both
Q1 and Q3 resolution.
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80 TSQ Duo User Guide Thermo Scientific
v. Under Acquisition Options, select the Allow for Asymmetric Acquisitions
check box to add extra time to the beginning or end of an acquisition window
without affecting other timing in your scan. When you select this option,
Pre-width and Post-width columns are added to your method. Enter the extra
times in these columns.
Select the Allow Dwell Time Prioritization check box to increase the dwell
times for selected scans. The choices for each scan are Normal or High. Giving a
scan high priority increases its dwell time by the value you set in the High
Priority Multiplier box.
vi. Under Full Scan, you indicate if a Full Scan is to be run along with SIM and
SRM. The Mass Range, Scan Time, Start and End Time can be set after the Use
Full Scan box is checked. The full scan time will reduce the SRM/SIM time
without increasing the total scan time. If you only want to use full scan for part
of your method, you can enter full-scan start and end times.
b. Use the options in the Instrument Settings panel to further adjust your method.
i. Use Tune Fi l e to select a tune file or files to be used for this scan.
ii. In the Detector Gain area, set the detector gain. Select the Use Last Tuned
Detector Gain option to indicate that you want to use the detector gain set in
Auto Tune. If you do not need to use the gain set in Auto Tune, then you can set
the gain manually. Higher gains give larger signals, but may shorten the lifetime
of the detector when concentrated samples are detected. To manually set the
detector gain, select the Use Specified Detector Gain radio button and enter the
desired value in the Detector gain box.
iii. Use the Emission Current box to set the emission current used during the
acquisition. For optimal analytical performance and stability, use the emission
current at which the system was tuned. However, if you want to use a different
emission current, select the Use Specified Emission Current radio button and
enter a value in the Emission Current (μA) box. A high emission current will
lead to the production of more ions, but the interaction of too many ions in the
source can cause a degradation in the resolution and signal. The margin of error
is ± 0.5 μA.
Note When the window optimizer is activated the Window, Pre-width, and
Post-width columns are no longer available in the compound list editor. If your
method is linked to a file or imported from a file with values in these columns, the
values are stored in memory and can be recovered by deactivating the window
optimizer.
Note This option is only available when the method optimizer is not active.
Tip Click the arrow at the top right of the Scan Settings panel to collapse or
expand the panel.
4 Creating a Method
Creating a GC-MS method
Thermo Scientific TSQ Duo User Guide 81
Figure 76. Acquisition-Timed Instrument Settings
32. Click Next. The Instrument Method Wizard – Completion page opens. See Figure 77.
Figure 77. Instrument Method Wizard – Completion
33. Enter any comments or notes for your method and click Finish.
Tip Click the arrow at the top right of the Instrument Settings panel to
collapse or expand the panel.
Instrument
Settings
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82 TSQ Duo User Guide Thermo Scientific
34. The New Instrument Method (Instrument Method) Chromeleon Chromatography
Studio window opens. Click the Save icon to save your method. See Figure 78.
Figure 78. Saving Methods
35. The Save Instrument Method dialog box opens. Save your method in Chromeleon Local
> Instrument Method. See Figure 79.
Figure 79. Finding the Instrument Method Folder
36. Enter your method in the Object Name box and click Save. Your method is now saved.
4 Creating a Method
Creating a GC-MS method
Thermo Scientific TSQ Duo User Guide 83
37. You can view all instrument methods on your system by opening the Chromeleon
Console and selecting Data from the left menu. See Figure 80.
Figure 80. Viewing all Instrument Methods
38. To edit a method, select it from the list. The method opens in the Chromatography
Studio. See Figure 81.
Figure 81. Editing a Method
39. Select a device from the left menu and edit its parameters as described in this chapter.
Running a Sequence
This section provides a quick introduction to running a sequence on a TSQ Duo MS. For
detailed information, refer to the Chromeleon document set or help file.
To create and run a sequence
1. Go to Start > All Programs > Thermo Chromeleon. The Chromeleon Console opens.
From the top menu, choose Create > Create New Sequence. See Figure 82.
Figure 82. Creating a New Sequence in the Chromeleon Console
2. The New Sequence Wizard opens. In the Pattern for Injection Name box, enter your
sequence name. See Figure 83.
4 Creating a Method
Running a Sequence
Thermo Scientific TSQ Duo User Guide 85
Figure 83. Entering the Sequence Name
3. Click Next. The Methods & Reporting window opens. Browse to the instrument
method you want to associate to your sequence. See Figure 84.
Figure 84. Associating an Instrument Method to a Sequence
4. Click Next. The General Sequence Setting window opens. Add comments about your
new sequence if desired and click Finish.
5. The Save Sequence window opens. See Figure 85.
4 Creating a Method
Running a Sequence
86 TSQ Duo User Guide Thermo Scientific
Figure 85. Saving a Sequence
6. Navigate to ChromelonLocal > Instrument Sequence. Enter your sequence name in the
Object Name box and click Save. See Figure 86.
Figure 86. Naming a Sequence
7. Open the Chromeleon Console and click Data form the left menu and choose your
sequence from the Chromeleon Local > Instrument Sequence folder in the left menu.
See Figure 87.
4 Creating a Method
Running a Sequence
88 TSQ Duo User Guide Thermo Scientific
Figure 89. Starting a Sequence
10. The Save Modifications dialog box opens. If you are satisfied with your sequence, click
Save.
Figure 90. Saving Changes to the Sequence
11. Your run begins. You can click Stop if you want to stop the run. See Figure 91.
Start Button
4 Creating a Method
Running a Sequence
Thermo Scientific TSQ Duo User Guide 89
Figure 91. Stopping a Run
12. When the run is complete, refer to the Chromeleon user documentation or help files for
instructions on analyzing your data.
Thermo Scientific TSQ Duo User Guide 91
5
Optimizing Your Method
If you are not getting the expected results from your method, you can modify it using the
following procedures for better results.
Changing the Chromatographic Separation
Peak shapes are defined by the chromatographic conditions. If your peak is too wide, too
narrow, or not symmetrical enough, then changing the chromatographic conditions are the
best way to improve your method. Start by changing the GC carrier gas flow or oven
temperatures (the initial temperature, initial hold time, ramp temperature, final temperature
for that ramp, and hold time at that final temperature). These temperatures can be adjusted
for each ramp.
Oven changes are strongly dependent on the nature of the compounds you are analyzing. At
some point, the GC oven has to be above the boiling point of the compounds you are looking
for. If the GC oven is not at the boiling point, the compounds will not volatilize and they will
become immobilized. You can change ramp rates to separate coeluting peaks. Refer to the GC
user documentation for further suggestions on optimizing chromatographic separation.
Contents
•Changing the Chromatographic Separation
•Finding the Best Way to Make an Injection
•Improving the Way You Prepare Samples
•Changing the Dwell Time or Scan Rate
•Narrowing the Mass Range
•Adjusting the Transfer Line and Ion Source Temperature
•Modifying an Automatic Tune
5 Optimizing Your Method
Finding the Best Way to Make an Injection
92 TSQ Duo User Guide Thermo Scientific
Finding the Best Way to Make an Injection
Adjusting the way you get the sample from the needle into the column can sometimes
improve the results of your data. Try modifying the autosampler method, injecting a different
amount of liquid, adjusting the injector port temperature or flow, or changing the speed of
your injection. You can also try using a hot or cold needle injection. In some cases, adjusting
your injection port liners may give you better results. (For detailed instructions, refer to the
user guide for your autosampler.)
Improving the Way You Prepare Samples
Although sample preparation adds time and expense to the overall analysis, a more focused
method can give you better results. Try extracting your sample in a solvent that increases the
solubility of the analytes of interest, but does not increase the solubility of the other
compounds. If your method allows it, try switching solvents.
You can also use or change the phase of a solid phase extraction cartridge, which gives you
similar results as changing a solvent. You can affect the way you prepare samples by changing
the type of cartridge you are using.
Changing the Dwell Time or Scan Rate
The precision of your data depends on how well you define your chromatographic peak.
Typically, you get good precision when sampling ten times across the chromatographic peak.
In a full scan analysis, increasing the scan rate increases the number of times you have sampled
across the peak. However, increasing the scan rate too much results in mass spectral noise,
which decreases your analytical precision.
In a SIM or SRM analysis, reducing the dwell time will have a similar effect to increasing the
scan rate in full scan. The dwell time is a measure of how long the instrument will average a
SIM or SRM event.To optimize your scan rate or dwell time, select a value that gives you
8-12 points across a chromatographic peak. In timed acquisition mode this optimization is
done automatically, providing you with the longest dwell time or slowest scan rates possible
such that all compounds receive the desired scans across a chromatographic peak.
To prioritize the dwell times of the problem analytes
1. In the Acquisition Options area, check Allow Dwell Time Prioritization. See Figure 92.
2. Set the High Priority Multiplier to the desired value.
3. A new Dwell Time Priority option appears in your scan list. The choice are Normal or
High. Choosing High multiplies the dwell times by the value set in the previous step.
5 Optimizing Your Method
Narrowing the Mass Range
Thermo Scientific TSQ Duo User Guide 93
Figure 92. Setting the Dwell Time Prioritization
Narrowing the Mass Range
In a full scan analysis, by narrowing your mass range, you can look directly at the compounds
of interest. However, if you are looking at a large number of compounds that have a broad
range of mass fragments, a wide mass range makes sense. To narrow the mass range, refine
your scan parameters to a smaller number. A narrower mass range also allows you to decrease
the scan rate and get the same chromatographic peak sampling. By breaking your MS method
into groups, you can create compound-specific MS settings to optimize your data.
Adjusting the Transfer Line and Ion Source Temperature
If your transfer line temperature is set too low, the less volatile compounds may get stuck in
the transfer line and never make it into the ion source. On the other hand, if your transfer line
is too hot, you could damage the column or cause a thermal breakdown in the compounds
you are analyzing. Typically, aim for the transfer line temperature to be 10 °C (18 °F) over the
highest boiling point of the compounds of interest, but no higher than the maximum safe
operating temperature of the column.
Note The total scan time does not change. If prioritizing some dwell times reduces others
to less the lowest allowed dwell time for your method, try increasing the acquisition
windows.
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Optimizing an SRM Method
94 TSQ Duo User Guide Thermo Scientific
Use the highest ion source temperature setting that allows adequate response for targeted
analytes in order to improve response for high-boiling compounds and prevent column bleed
and matrix compounds from dirtying the ion source.
Optimizing an SRM Method
The following actions might improve your results when using an SRM method:
• Use timed SRM to optimize segments automatically and possibly improve dwell time and
number of points across the peak.
• Reduce the Retention Time window if possible. If your sample's retention time is well
known the scan window can be reduced. If this is in a high-density compound area it can
dramatically improve the ion signal and number of points across the peak.
• Use AutoSRM to optimize collision energy and retention times. This can reduce errors in
collision energy and improve confidence in retention times to allow shorter windows.
• Choose the optimum fragment ion for study if allowed by your method. Some fragments
are higher in intensity and have less interference associated with their transition.
Note The transfer line temperature and ion source temperature should be similar to avoid
contaminating the ion source.
5 Optimizing Your Method
Modifying an Automatic Tune
Thermo Scientific TSQ Duo User Guide 95
Modifying an Automatic Tune
The MS instrument control software includes a utility that uses certain parameters in the tune
types to optimize system performance when generating a tune file. Follow these procedures:
•To modify an automatic tune
•To modify advanced tune settings
To modify an automatic tune
1. Open the TSQ Series Dashboard and click Tune Ty p es.
2. In the Tune Types dialog box, select a tune type to edit and click Copy. See Figure 93.
Figure 93. Tune Types Dialog Box
3. The Tune Type Editor opens. Configure the parameters under the General tab in the
Tu n e Ty p e E d i t or.
Figure 94. Configuring General Tuning Parameters
a. Name—Enter a name for your tune type.
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Modifying an Automatic Tune
96 TSQ Duo User Guide Thermo Scientific
b. Description—Enter details or notes about your tune type.
c. Categories—This is an optional field that allows you to display a subset of tunes
under Auto Tune on the dashboard. This is convenient for separating your most
frequently used tunes.
d. Type—Select the Tune and Diagnostics option to run a tune with diagnostics or
select the Diagnostics Only option if you are creating a diagnostics test.
e. Output Tune Filename Prefix—Enter a prefix to be added to the title of your tune
report. It is a good idea to use a descriptive prefix for your tune type. For example, if
you are always running BFB reports, you could enter BFB here to distinguish it from
other reports you are generating.
f. Starting Tune File—Select a tune file that your tune type will be based on:
•Select Factory to use a default factory-made file on the instrument that can be
used to begin tuning an instrument with a clean ion source.
•Select Last Saved to use a tune file saved on the instrument by the most recent
successful automatic tune.
• Select a specific tune file if you have a reliable tune file you want to use as a
starting point for a new tune file.
g. Perform Mass Calibration—Select this to enable the system to recalibrate all of the
masses during a tune.
h. Check Mass Calibration—Select this to enable the system to confirm that your mass
calibration is correct rather than performing a mass calibration.
4. Select the Ion Source tab to configure the ion source as follows:
Note Create the new tune type name now. You will not be able to edit the tune
type name later. Also, you will not be able to save new parameters to a built-in
tune.
Note If you select a tune file with a prefix-only name rather than a tune file with
a date-time stamp, the most recent tune file of with that prefix name will be
loaded at the start of each tune.
Note If Tune and Diagnostics is selected, you can select only one Mass
Calibration option.
5 Optimizing Your Method
Modifying an Automatic Tune
Thermo Scientific TSQ Duo User Guide 97
Figure 95. Configuring the Ion Source Parameters
a. Ionization Mode & Ion Polarity—Use this pull-down menu to select a mode:
•Select EI + to run a tune in Electron Ionization (EI) mode.
b. Emission Current—Defines the emission current that you use to run subsequent
tunes, but not the emission current that is used for data acquisition.
•Tu n e File—Select this option to use the value in the tune file that you selected
on the General tab.
•Default—Select this option to use the default emission current, which is 50 μA.
•Custom—Select this option if you want to use a value other than 50 μA when
increasing or decreasing the sensitivity of the instrument. For the emission
current, the default is 50 μA. Tune with the same value you are planning to use
for your analysis. The use of emission currents above 100 μA may lead to the
generation of too many ions in the source and a degradation in resolution.
c. Electron Energy—Indicates the energy of the electrons that come off the
filament.Lowering the electron energy will extend the lifetime of your filament.
•Default—Select this option to use the default electron energy, which is 70 eV.
•Tu n e File—Select this option to use the value in the tune file you selected in the
General tab.
•Custom—Select this option to set the energy of the electrons emitted by the
filament. For example, you could change the voltage if you wanted to change the
ionization efficiency and fragmentation of the sample. This is typically set to
70 V because the standard EI libraries are based on 70 eV electron beams.
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98 TSQ Duo User Guide Thermo Scientific
d. Electron Lens Positive Voltage—Allows the electrons to enter the ion volume.
•Default—Select this option to use the default electron lens positive voltage,
which is 15 V.
•Tu n e File—Select this option to use the value used in the tune file that you
selected on the General tab.
•Custom—Select this option if you do not want to use the default value for the
tune. For the electron lens positive voltage, the default is 15 V. You should tune
with the same value you are planning to use for your analysis. This value affects
the focusing of the electron beam into the source. If you change your electron
energy from 70 eV, this value also changes. This voltage must always be at least
45 V above the voltage applied to the filament. The voltage applied to the
filament is the same number, but the opposite sign, of the electron energy.
e. Electron Lens Negative Voltage.
•Default—Select this option to use the default electron lens negative voltage,
which is –75 V.
•Tu n e File—Select this option to use the value used in the tune file that you
selected on the General tab.
•Custom—Select this option if you do not want to use the default value for the
tune. For the electron lens negative voltage, the default is –75 V. Tune with the
same value you are planning to use for your analysis. This value affects how well
the electrons are kept from entering the ion source when they are not supposed
to. If you change your electron energy from 70 eV, this value also changes.
Ensure this voltage is at least 5 V below the voltage applied to the filament.
f. Set Ion Source Temperature—Select this check box to enable the temperature field.
Then enter a value between 0 and 350 °C. The default is 200 °C. The optimal
temperature is determined by the molecular structure and weight of the compounds
you are analyzing. Heavier compounds require a higher temperature. Tune at the
same temperature you will use to run your samples. You should set the temperature as
high as possible to keep the ion source clean and maintain the right amount of
sensitivity.
Note Avoid reducing the electron energy to less than 70 eV. The calibration
compound will not be sufficiently ionized for tuning or calibrating at low
electron energies.
Note A custom electron energy can be selected in the instrument acquisition
method even if it is not used for tuning.
Tip If you tune regularly between running sample sets, you can save time waiting
for the temperatures to equilibrate by setting the tune temperatures to the same
temperature used in your acquisition method.
5 Optimizing Your Method
Modifying an Automatic Tune
Thermo Scientific TSQ Duo User Guide 99
5. Click the Targets tab to configure how you want to tune your targets. Target tuning is
used to adjust the way the mass spectrometer tunes to meet regulatory requirements.
Otherwise, this is an optional setting.
Figure 96. Configuring Tuning Targets
Tu n e Ta r g e t Io n R a t i os—Select this check box to adjust the ratios based on the results
from an injection of tuning compound.
6. Click the Detector tab to configure the detectors. See Figure 97.
Figure 97. Configuring the Detectors
a. Set Initial Detector Gain—Select this option to set the electron multiplier gain that
will be used in tuning the instrument. The gain is the number of electrons generated
for every ion that strikes the detector. This is typically set at 3 × 105 electrons per ion.
Gains larger than this will generate more electrons per ion, but both the analyte ion
and the noise ion signals will be larger. You can also tune to lower gain values, which
5 Optimizing Your Method
Modifying an Automatic Tune
100 TSQ Duo User Guide Thermo Scientific
decreases the signal strength. Lower values also increase the chance that an ion will
not be detected.
b. Tu n e D e t e c t o r —Select this check box to tune the detector. As the electron multiplier
ages, the voltage required for a given gain increases. Depending on your sample load
and if your system is leak tight (oxygen is bad for the detector), you should not have
to perform this tune very often. Limit to 1–2 times a year.
c. Adjust Detector Sensitivity—Select this check box to tune the detector to generate a
consistent area count of a calibration gas ion for the tune report. Because the intensity
of the cal gas varies depending on the atmospheric pressure and temperature of the
lab, this option results in larger variation in the analytical runs, as compared to using
a fixed detector gain. If you use this function, set the initial detector gain to 3 × 105
electrons per ion.
•Mass—Select the calibration gas mass you want to use.
•Intensity—Enter the intensity you want to see on the tune report.
7. Click the Diagnostics tab and select a test to confirm the operational ability of the
system. See Figure 98.
Figure 98. Setting Diagnostics
5 Optimizing Your Method
Modifying an Automatic Tune
Thermo Scientific TSQ Duo User Guide 101
8. Click the Report tab configure how you want to view your data
Figure 99. Selecting Data Report Options
.
a. Acquire Full-Scan Spectrum—Select this check box to display the full spectrum on
your tune report.
b. Acquisition Threshold—Enter a minimum peak height for the full scan spectrum
on the tune report. If your peak has an intensity that is below this threshold, it will
not be stored.
c. SIM Masses—Select masses to be displayed on your tune report. You can select a
maximum of five masses, one from each list. At least one mass must be displayed on
the report.
9. Once you are finished configuring all the tabs, click Save to save the tune type. Your new
tune type appears in the Tune Types window.
10. Click Close to return to the dashboard. You can select the tune type in the automatic
tune window.
11. If you want to rename a tune you created, open the Tune Types dialog box by clicking
Tu n e Ty p e s on the TSQ Series Dashboard.
a. Select Rename in the Tune Types dialog box.
Tip Factory tunes cannot be altered. If a newly created tune does not perform as
expected, you can always go back to a factory tune, copy it, and change the
settings as described above. Save the new tune with a new name before closing the
Edit Tune Type dialog box.
Note You cannot rename a factory tune.
5 Optimizing Your Method
Modifying an Automatic Tune
102 TSQ Duo User Guide Thermo Scientific
Figure 100. Renaming a Tune Type
b. The Rename Tune Type dialog box opens. Assign a valid new name to your tune.
You will not be able enter a name that is an invalid file name or already in use. See
Figure 101.
Figure 101. Changing a Tune File Name
c. Click OK.
To modify advanced tune settings
1. To configure the Q1 Lenses, you must select the Show Advanced Settings check box.
The lens tune is the main portion of the tune algorithm. In this section you can choose
which components to tune, which mass to optimize for the tune, what the range of
allowed values is, how to move through the range, how much the signal must change for a
new value to be selected, and what (if anything) can be done about the resolution of the
peak and any errors that occur. Select the Tune Lenses check box to access the data table.
See Figure 102.
Note The following instructions refer to advanced tuning settings that most users will
never need to access. Contact your local Thermo Fisher Scientific service organization
before adjusting these settings.
5 Optimizing Your Method
Modifying an Automatic Tune
Thermo Scientific TSQ Duo User Guide 103
Figure 102. Tuning the Q1 Lenses
a. Device—Click in this box to select the component you want to tune according to the
settings in the other columns.
i. Repeller—Controls how the repeller pushes the ions out of the ionization
region. The voltage applied to this component has a very strong effect on the
energy of the ion beam, which has a strong effect on the resolution and the
intensity. The lower the voltage, the better the resolution. However, higher
voltages will prevent ions from striking the repeller surface, which leads to better
robustness. A clean system typically tunes from 3 to 8 V, although a dirty system
may have the repeller climb as high as 12.5 V. Do not set the repeller any higher.
ii. Lens 1—Controls Lens 1, which is the first of three lenses that the ions see as
they leave the ionization region. These three lenses act as a focusing element to
maximize the ion beam intensity that is entering the ion guide. This field is
typically set between –35 and –50 V.
iii. Lens 2—Controls Lens 2, which is the second of three lenses that the ions see as
they leave the ionization region. These three lenses act as a focusing element to
maximize the ion beam intensity that is entering the ion guide. This field is
typically set between 0 and –15 V.
iv. Lens 3—Controls Lens 3, which is the last of three lenses that the ions see as
they leave the ionization region. These three lenses act as a focusing element to
maximize the ion beam intensity that is entering the ion guide. This field is
typically set between -30 and -35 V.
v. Ion Guide Voltage—Controls the ion guide’s DC offset voltage. It can
potentially help focus the ions into the quadrupole while ensuring that neutral
noise is eliminated. The voltage on this component is mass dependent and
5 Optimizing Your Method
Modifying an Automatic Tune
104 TSQ Duo User Guide Thermo Scientific
should be set at several different masses. This field is typically set between +1 and
–15 V, depending on the mass of the ion.
vi. Ion Guide RF q—Controls the ion guide's RF q (amplitude). This device is
mass dependent and should be set at several different masses. This field can be
tuned between 0 and 2. This device determines the ion guide RF amplitude tune
value which is given as the RF q * (m/z).
vii. Ion Guide RF—(This setting is maintained for compatibility with legacy tune
types. For new tune types, Ion Guide RF q is the recommended setting.)
Controls the ion guide’s RF voltage. It can potentially help focus the ions into the
quadrupole while ensuring that neutral noise is eliminated. The voltage on this
component is mass dependent and should be set at several different masses. This
field is typically set between 0 and +5 V, depending on the mass of the ion.
viii. Q1 Voltage—Controls the voltage that pulls the ions into the quadrupole. The
voltage applied to this component has a very strong effect on the energy of the
ion beam, which has a strong effect on the resolution and the intensity. The
lower the voltage, the better the resolution. However, higher voltages will pull
more ions into the quads, which leads to better signal. This field is typically set
between 0 and –5 V.
ix. Q1 Resolution—Adjusts the ratio of the quadrupole DC and RF voltages to
create the resolution required for your analysis. You can set the desired peak
width at a given mass and whether you measure the width at 10% or 50% of the
peak height. Because there is no static DC voltage involved, the start, stop, and
step values are not used.
b. Mass—Click in this box to select the ion to be used for tuning.
c. Start—Enter the starting voltage for the tune. The start voltage must always be less
than the stop voltage. For example, –35 is smaller than 0.
d. Stop—Enter the final voltage for the tune.
e. Step—Enter the increment for the tuning range. For example, if you tune from 0-50
in increments of 10 V, then you would set the Step field to 10.
f. Max Width—Enter the maximum allowable width of the ion during the tune.
g. Measure at %—Click in this box to select the location on the peak where you want
to measure the maximum width.
•10—Measures the width at 10% of the peak height.
•50—Measures the width at 50% of the peak height.
Note If the start and stop values are the same value, the device will be set to that
value and ignore the step size. In some tunes, devices are set to a value before
tuning them in another line. This presetting is done because ramping devices do
not allow the tune to run at values higher than those chosen for higher masses for
the same device.
5 Optimizing Your Method
Modifying an Automatic Tune
Thermo Scientific TSQ Duo User Guide 105
h. Threshold—Enter the change in intensity that has to occur when the tune selects a
new voltage. For example, if you set this field to 1.1, the tune will not select a new
voltage for that component unless the intensity is 110% of the old intensity. If you set
this field to 1, anytime the new voltage has an intensity larger than the old intensity,
the tune will select the new intensity.
i. On Error—Click in this box to select how to handle an error in the tune.
•Fail—Stops the tune when an error occurs or if no tune points are found
meeting the tune criteria.
•Continue—Allows the tune to continue on to the next device when an error
occurs.
j. Entrance lens offset and Exit lens offset—Changing these voltages affects ion
acceleration. The default levels will give the best performance; changing the voltages
will affect peak resolution.
2. Click the Q1 Resolution tab to configure the resolution of your tune. You must select the
Show Advanced Settings check box to access this tab. Selecting this option tunes the
resolution of Quadrupole 1 by itself. This resolution tunes the system at 100 and
1000 amu/s scan rates. You can tune the resolution during a lens tune or you can tune the
resolution by itself.
Figure 103. Configuring Q1 Resolution
a. Mass—Click in this box to select the ion to be used for tuning.
Note If you choose a value less than 1 for ramped devices, the tune steps back in
energy until the lower intensity is detected. For example, if you choose 0.8, the
device value lower in energy than the device value with the maximum response
that gives an intensity closest to 80% of the maximum intensity is chosen.
Note Changing the Q1 lenses or resolution affects the Q3 lenses and resolution.
5 Optimizing Your Method
Modifying an Automatic Tune
106 TSQ Duo User Guide Thermo Scientific
b. Peak Width—Enter the target peak width.
c. Measure at %—Click in this box to select the location on the peak where you want
to measure the target peak width.
•10—Measures the width at 10% of the peak height.
•50—Measures the width at 50% of the peak height.
d. Lens Tune Relation—Click in this box to set the occurrence of the resolution tune
parameters before or after a lens tune.
•Before and After—Uses the same resolution parameters before and after a lens
tune.
•Before—Uses the resolution parameters before a lens tune.
•After—Uses the resolution parameters after a lens tune.
3. Select the Q3 Lenses tab to configure the Q3 lenses. You must select the Show Advanced
Settings check box to access this tab. The lens tune is the main portion of the tune
algorithm. In this section you can choose which components to tune, which mass to
optimize for the tune, what the range of allowed values are, how to move through the
range, how much the signal must change for a new value to be selected, and what (if
anything) must be done about the resolution of the peak and any errors that occur.
Figure 104. Tuning the Q3 Lenses
5 Optimizing Your Method
Modifying an Automatic Tune
Thermo Scientific TSQ Duo User Guide 107
a. Q3 Voltage—Controls the voltage that pulls the ions into the quadrupole. The
voltage applied to this component will have a very strong effect on the energy of the
ion beam, which will have a strong effect on the resolution and the intensity. The
lower the voltage, the better the resolution. However, higher voltages will pull more
ions into the quads, which leads to better signal. This field is typically set between
0and –5V.
b. Resolution—Adjusts the ratio of the quadrupole DC and RF voltages to create the
resolution required for your analysis. You can set the desired peak width at a given
mass and whether you measure the width at 10% or 50% of the peak height. Because
there is no static DC voltage involved, the start, stop, and step values are not used.
c. Mass—Click in this box to select the ion to be used for tuning.
d. Start—Enter the starting voltage for the tune. The start voltage must always be less
than the stop voltage. For example, –35 is smaller than 0.
e. Stop—Enter the final voltage for the tune.
f. Step—Enter the increment for the tuning range. For example, if you tune from 0-50
in increments of 10 V, then you would set the Step field to 10.
g. Max Width—Enter the maximum allowable width of the ion during the tune.
h. Measure at %—Click in this box to select the location on the peak at which you
want to measure the maximum width.
•10—Measures the width at 10% of the peak height.
•50—Measures the width at 50% of the peak height.
i. Threshold—Enter the change in intensity that has to occur when the tune selects a
new voltage. For example, if you set this field to 1.1, the tune will not select a new
voltage for that component, unless the intensity is 110% of the old intensity. If you
set this field to 1, anytime the new voltage has an intensity larger than the old
intensity, the tune will select the new intensity.
j. On Error—Click in this box to select how to handle an error in the tune.
•Fail—Stops the tune when an error occurs.
•Continue—Allows the tune to continue on to the next device when an error
occurs.
k. Entrance lens offset and Exit lens offset—Changing these voltages affects ion
acceleration. The default levels will give the best performance; changing the voltages
will affect peak resolution.
l. MS/MS Voltages—These overwrite the Q3 voltage tune values when the instrument
is in SRM mode. These values are not tuned and are added to the collision energy
used in the SRM scan.
4. Click the Q3 Resolution tab to configure the resolution of your tune. You must select the
Show Advanced Settings check box to access this tab. Select this option to tune the
resolution of Quadrupole 3 by itself. This resolution will tune the system at 100 and
1000 amu/s scan rates. You may also tune at a higher scan rate. You can tune the
resolution during a lens tune or you can tune the resolution by itself. See Figure 105.
Figure 105. Configuring the Q3 Resolution
a. Mass—Click in this box to select the ion to be used for tuning.
b. Peak Width—Enter the target peak width.
c. Measure at %—Click in this box to select the location on the peak at which you
want to measure the target peak width.
•10—Measures the width at 10% of the peak height.
•50—Measures the width at 50% of the peak height.
d. Lens Tune Relation—Click in this box to set the occurrence of the resolution tune
parameters before or after a lens tune.
•Before and After—Uses the same resolution parameters before and after a lens
tune.
•Before—Uses the resolution parameters before a lens tune.
•After—Uses the resolution parameters after a lens tune.
5. Tune High Scan Rate—Select this check box to tune the resolution at a scan rate in
addition to the 100 and 1000 amu/s default scan rates.
Thermo Scientific TSQ Duo User Guide 109
6
Computer Settings
Your TSQ Duo system includes a computer with all the software needed to operate the
instrument.
If you replace the computer in the future, use the information in this chapter to change the
computer settings so your TSQ Duo system and the associated Thermo Scientific software
will run correctly. Instructions for installing Thermo Scientific software are included on the
software CD shipped with your instrument.
System Requirements
The TSQ Duo system requires a Windows 7 32-bit or 64-bit operating system. See “System
Requirements” on page xi for a complete list of system requirements.
Computer Settings
The following computer settings will help prevent communication interruptions in your
TSQ Duo system.
To use the power save feature
1. From the Start menu choose Control Panel | System and Security | Power Options.
2. On the left side, click Change When the Computer Sleeps.
3. For Put the Computer to Sleep, select Never. See Figure 106. You may set the display to
turn off at any time. It will not affect the performance of your TSQ Duo system.
Contents
•System Requirements
•Computer Settings
•Excluding the Xcalibur Directory from Virus Scan
6 Computer Settings
Computer Settings
110 TSQ Duo User Guide Thermo Scientific
Figure 106. Power Settings for the Computer
To use the virtual memory feature
1. From the Start menu, choose Control Panel | System and Security | System.
2. On the left side of the window, click Advanced System Settings.
3. In the System Properties dialog box, click Settings.
4. In the Performance Options dialog box, click the Advanced tab, and then click Change
to open the Virtual Memory window.
5. Confirm that Automatically Manage Paging File Size for All Drives check box is
selected. See Figure 107.
Figure 107. Virtual Memory Settings
6 Computer Settings
Computer Settings
Thermo Scientific TSQ Duo User Guide 111
To confirm the network card firewall settings
1. From the Start menu, choose Control Panel | Network and Internet | System and
Security | Windows Firewall | Advanced Settings.
2. In the Actions Panel on the right, (see Figure ), select Properties.
3. In the Windows Firewall with Advanced Security on Local Computer Properties
window, select Domain Profile | State | Customize.
Figure 108. Firewall Settings for the TSQ Duo System Computer
4. In the Protected Connections for the Domain Profile window, make sure that any
instrument checkboxes are not checked.
Figure 109. Setting the Network Connections
Actions
Panel
6 Computer Settings
Excluding the Xcalibur Directory from Virus Scan
112 TSQ Duo User Guide Thermo Scientific
Excluding the Xcalibur Directory from Virus Scan
If you are using anti-virus software on your computer, exclude the following folders from
scanning:
• C:\Program Files\Thermo\
•C:\Thermo\
•C:\Xcalibur\
Failure to exclude these folders might cause interruptions in data acquisition. If you must, for
security reasons, scan all system files, set the virus scans so that they occur when you are not
using the instrument to acquire data.
Thermo Scientific TSQ Duo User Guide 113
7
Troubleshooting
This section contains information to help you diagnose problems within your data.
Sometimes, your experience as a scientist will enable you to look at your data and detect that
something is wrong either with the instrument or your sample. This chapter describes the
most common indications of a problem with a baseline, peak or result.
If there is an issue with the hardware, see the troubleshooting section of the hardware manual.
You can begin troubleshooting by running a tune with diagnostics on the instrument. If you
have good ion intensities, good peak shapes, and no air leak, you might want to look first at
the GC, autosampler, or carrier gas.
If you have air leaks, locate and address them. Pay particular attention to the transfer line
ferrule, vent valve knob, front panel, gas quality, carrier gas vacuum compensation, and
vacuum interlock on the mass spectrometer, as well as the inlet on the GC.
If your intensities are too low, make sure carrier vacuum compensation is turned on.
Contents
•Setting Instrument Conditions for Troubleshooting
•Checking Air/Water Spectra
•Diagnostics Checks
•How to Know When Your System Needs Maintenance
•Investigating Baseline Issues
•Investigating Peak Issues
•Investigating Results Issues
CAUTION ELECTRICAL SHOCK HAZARD: When troubleshooting any issue that requires
removing a cover on the instrument, power-off and vent the instrument to avoid possible
injury.
7 Troubleshooting
Setting Instrument Conditions for Troubleshooting
114 TSQ Duo User Guide Thermo Scientific
If you have no ions in full-scan or SIM mode, do the following:
•Switch filaments.
• Confirm the starting tune file is appropriate for ionization mode or source cleanliness
level.
• Confirm the correct ion volume is inserted (EI or CI).
• Verify the ion source is correctly installed.
• Run diagnostic checks (Diagnostics Only tune type)
• Clean the ion source.
If you do not see ions in CI mode:
• Confirm that the CI ion volume is installed.
• Confirm that the reagent gas is connected and turned on.
If you do not see any peaks in SRM scans, do the following:
• Verify the collision gas supply.
• Run diagnostics checks (Diagnostics Only tune type).
• Run a full-scan method to check if your system is functional.
Setting Instrument Conditions for Troubleshooting
Before troubleshooting the TSQ Duo system, set the instrument to the conditions in this
section in order to compare your system more accurately to the values in the section. All
troubleshooting should be performed in EI mode. Once EI mode is working, check CI
conditions if relevant.
• Clean the ion source cartridge. See the TSQ Duo Hardware Manual for instructions.
IMPORTANT When inserting a cold ion source cartridge such as after cleaning or when
switching between EI and CI modes, the ion source and lens stack will expand as the
source cartridge heats, often pushing the ion volume and lenses away from the rear of the
instrument where they are firmly held by the RF Lens spring contacts. To avoid
intermittent electrical contacts to the lenses, you should insert the ion source cartridge,
wait 30 min for it to get to temperature, then remove and reinsert it. See the hardware
manual for instructions on cleaning and inserting the ion source cartridge.
IMPORTANT Use only Nitrile Cleanroom gloves when touching ion source components.
Other types of gloves deposit contaminants on the source components that affect system
performance. See the TSQ Duo Spare Parts Guide for ordering information.
7 Troubleshooting
Checking Air/Water Spectra
Thermo Scientific TSQ Duo User Guide 115
• Install a 15 m × 0.25 mm × 0.25 μm GC column (If using a different column,
pressure readings may vary.)
• Ion Source Temperature — 200 °C
• Transfer Line Temperature — 250 °C
• Vacuum Compensation — On
• Column Flow Rate — 1.5 mL/min
• Foreline Pressure — < 100 mTorr
• Pump down the system according to the time recommended for the turbomolecular
pump installed on it.
• Air/Water Check — Water (m/z 18/69) < 300%
Once you have applied the settings in this section, and have allowed the TSQ Duo system to
equilibrate, run an EI diagnostic tune even if you cannot see any ion intensities.
Checking Air/Water Spectra
Before running additional diagnostics, check the air/water spectra of your TSQ Duo system in
the TSQ Series Manual Tune utility and use the information in this section to troubleshoot
your system.
To check Air/Water spectra on the TSQ Duo system
1. Open the TSQ Series Dashboard. Check that all the Status indicators are green and that
the turbo pump is set at 100%.
2. Select TSQ Series Manual Tune and check the Air/Water spectrum. See Figure 110.
Note Foreline Pressure is a function of how long the interior of the manifold has
been exposed to the atmosphere, the pumping capacity of the turbo pump, length
of the foreline hose, and other criteria. As an example, if the system has been
recently exposed to atmosphere, the foreline pressure will be above the expected
value. Foreline pressure is not set by the user, but the value above needs to be
reached prior to troubleshooting.
7 Troubleshooting
Checking Air/Water Spectra
116 TSQ Duo User Guide Thermo Scientific
Figure 110. Typical TSQ Duo Air/Water Spectrum for a System with Helium Carrier Gas
The correct settings should be:
• Detector Gain = 3e5
• Peak Intensity > 3e6
• Normal ions are present and in acceptable ratios:
– 18 (Water) — 20–300% of N2
–28 (N
2) — Reference (base) Peak
–32 (O
2) — 10–40% of N2
– 40 (Argon) — <10% of N2
3. Using hydrogen as a carrier gas changes the air/water spectrum on the TSQ Duo system.
It general more background peaks due to the increased reactivity of the hydrogen gas with
the components inside of the sample path. See Figure 111 for an image of a typical
TSQ Duo air/water spectrum when hydrogen is used as a carrier gas.
Note Several factors strongly influence the ion ratios listed above: tune file, gas flow, gas
quality, temperature, and time from pump down.
7 Troubleshooting
Checking Air/Water Spectra
Thermo Scientific TSQ Duo User Guide 117
Figure 111. Typical TSQ Duo Air/Water Spectrum for a System with Hydrogen Carrier Gas
The following conditions can cause changes in the air/water spectrum on the TSQ Duo
instrument.
1. Standard detector gain is equal to 3e5, but this can vary depending on customer defined
tunes.
2. As the instrument pumps down over time, the ratio of 18/28 will change as m/z 18
decreases with m/z 28 remaining constant. This eventually changes m/z 28 to the base
peak.
3. Changing components of the system such as the column, ion source, or gas supply affects
the different masses present in the air/water spectra.
4. Maximum intensity may vary based on different instrument parameters, such as changing
the column flow, or accessories.
If any of the previous conditions are not met and a leak is suspected as the root cause, follow
“An air leak has been detected” in the “Investigating Vacuum Issues” section of the TSQ Duo
Hardware Manual or “How to Know When Your System Needs Maintenance” on page 121.
The next several images show a typical air/water spectrum for several common problems.
1. Figure 112 is an example of an air/water spectrum of a system with a potential air leak.
7 Troubleshooting
Checking Air/Water Spectra
120 TSQ Duo User Guide Thermo Scientific
Figure 114. Typical Air/Water Spectrum of a TSQ Duo System with No Column Flow
4. Figure 115 is an example of a spectrum with a CI tune file run with an EI ion source.
Figure 115. Typical Air/Water Spectrum of a TSQ Duo System with an EI Ion Source Run with a CI
Tune File
7 Troubleshooting
Diagnostics Checks
Thermo Scientific TSQ Duo User Guide 121
Diagnostics Checks
The following table provides you with possible corrective actions you can take after failing a
diagnostics check on your system.
How to Know When Your System Needs Maintenance
Typically, you will notice that your instrument needs maintenance when you are analyzing
your data on the computer. Figure 116 shows a normal full scan background on a TSQ Duo
system.
Note If you are unsure about what to do if your system fails a diagnostic, please contact
your field service engineer.
Table 2. Diagnostics and Corrective Actions
Diagnostic Cause of Failure Corrective Action
Communication
Check
Unknown Contact your Field Service Engineer.
Frequency Check RF Dip is not correct Run a full tune that will correct for any RF
dip problems.
Ensure source cartridge is installed.
Contact your Field Service Engineer.
SRM Efficiency
Check
Collision gas is not
supplied correctly
Check collision gas tank and pressure.
Q1 is poorly tuned Run an EI SRM tune (not a quick tune).
Lens Continuity
Check
Ion source not inserted
properly
Remove and reinsert ion source.
Lens plate and/or
springs are damaged
Contact your Field Service Engineer.
A wire is disconnected
or shorted inside the
manifold
Contact your Field Service Engineer.
7 Troubleshooting
How to Know When Your System Needs Maintenance
122 TSQ Duo User Guide Thermo Scientific
Figure 116. Normal Full Scan Spectrum of a TSQ Duo System
A normal system should have the following conditions met;
•Detector gain — 3e5
• Maximum intensity — < 1e6
• There should be exponential decay for background noise.
• There should be no extraneous peaks indicating contamination.
If you run a sample with Perfluorotributylamine (PFTBA), the tuning compound, the
spectrum should look like Figure 117 below.
7 Troubleshooting
How to Know When Your System Needs Maintenance
Thermo Scientific TSQ Duo User Guide 123
Figure 117. Normal PFTBA Profile Spectrum
A normal PFTBA profile spectrum should meet the conditions below.
• All status indicators on the TSQ Series Dashboard are green.
• Turbo Pump = 100%
• Intensity >1.5e7 (15,000,000)
•The ions m/z 69, 131, 219, 414, and 502 are all present and in the correct relative ratios.
–m/z 69 or m/z 219 is the base peak
–m/z 131 and m/z 219 between 60-99%
–m/z 414 and m/z 502 between 2-10%
–m/z 100, 119, and 264 are also present and cleanly separated from any noise.
• Mass assignments are correct. Review the tune report for true mass assignment values.
• No extraneous peaks indicating contamination are present.
Some of the most common reasons and indications that your system needs maintenance are as
follows:
•Contamination—Excessive background in your mass spectra usually indicates that your
instrument is contaminated. Use the mass spectrum in the table below to understand the
origin of the contamination. Cleaning solvent peaks usually indicate that the ion source
cartridge was installed before it completely dried.
•Fingerprints—A series of mass peaks in your data that are 14 amu apart usually indicates
fingerprint or other hydrocarbon contamination. To avoid fingerprints, wear clean,
lint-free gloves when performing any type of maintenance on a component in the vacuum
manifold of the instrument.
•Air Leaks—Higher than normal vacuum pressure or poor sensitivity usually indicates an
air leak. Check the last o-ring or ferrule that you installed.
Figure 118 shows an abnormal PFTBA profile spectrum.
Table 3. Common Contaminants
Ions (m/z) To Monitor Compound Possible Source
13, 14, 15, 16, 17, 29, 41,
57
Methane CI gas
18, 28, 32, 44 or 14, 16, 19 H2O, N2, O2, CO2 or N, O Residual air and water, air
leaks, outgassing from
Vespel ferrules
69, 100, 119, 131, 169,
181, 214, 219, 264, 376,
414, 426, 464, 502, 576,
614
PFTBA and related ions PFTBA (tuning
compound)
31 Methanol Cleaning solvent
43, 58 Acetone Cleaning solvent
78 Benzene Cleaning solvent
91, 92 Toluene or xylene Cleaning solvent
105, 106 Xylene Cleaning solvent
151, 153 Trichloroethane Cleaning solvent
149 Plasticizer (phthalates) Use of vinyl or plastic
gloves
Peaks spaced 14 amu apart Hydrocarbons Fingerprints, foreline pump
oil, or other hydrocarbons
7 Troubleshooting
How to Know When Your System Needs Maintenance
Thermo Scientific TSQ Duo User Guide 125
Figure 118. Abnormal PFTBA Spectrum
In Figure 118, the abnormal results are as follows:
• Maximum intensity < 1.5e7 (15,000,0000)
•m/z 207 is prominent, indicating column bleed
• Many small contamination peaks present
7 Troubleshooting
Investigating Baseline Issues
126 TSQ Duo User Guide Thermo Scientific
Investigating Baseline Issues
Behavior Characteristic Cause Remedy
Drifting Baseline General Stationary phase has
accumulated in column
Replace the column or cut off the end of
the column.
Chromatographic baseline
is high
Replace the column or cut off the end of
the column.
Carrier gas pressure is too
low
Check for leaks in injector or flow path.
Replace the carrier gas cylinder if it is
empty or low. Increase the pressure if
maximum injector pressure in method is
greater than carrier line pressure set by
regulator. Make sure the vacuum
compensation is on.
Carrier gas flow is drifting Check for leaks in injector or flow path.
Check the carrier gas tank.
Impurities have
accumulated in column
Run solvent blank to remove impieties.
If impurities persistent after multiple
solvent blanks: Inject solvent from a
different source. Change syringe, liner
and septum. Clean injector. Check
impurity levels in your gas. Use the
correct gas purity and filter.
Falling Carrier gas leak in the
system
Perform a leak test and tighten the
connections to the carrier gas line if leak
is found.
Column is baking out Wait for the column to stabilize.
Rising Impurities have
accumulated in column
Check impurity levels in the gas source.
Use correct gas purity.
Abnormal rise in
baseline when oven
temperature is high
Impurities have
accumulated in column
Recondition or replace the column.
7 Troubleshooting
Investigating Baseline Issues
Thermo Scientific TSQ Duo User Guide 127
Noisy
Chromatographic
Peaks
General Excessive column bleed
at high oven temperatures
Reduce the column temperature.
Bake out the column.
Install a high-temperature column.
Install oxygen filters in carrier gas line.
Check pneumatic and inlet systems for
leaks.
Use correct gas purity with low oxygen
content.
Column is contaminated
or damaged
Condition or replace the column.
Oven temperature is higher
than column’s maximum
allowable temperature
Reduce oven temperature to the
maximum allowable temperature of the
column.
Leak at column fittings Find leak. Tighten fittings if loose.
Replace ferrule if overtightened.
Transfer line temperature is not set too
low.
Behavior Characteristic Cause Remedy
7 Troubleshooting
Investigating Peak Issues
128 TSQ Duo User Guide Thermo Scientific
Investigating Peak Issues
Table 4. Troubleshooting Peak Issues in Your Data (Sheet 1 of 3)
Behavior Characteristic Cause Remedy
Broadening General Column higher than
optimum of column
Reduce the flow. Make sure vacuum
compensation is turned on.
Column flow lower than
optimum of column
Increase the flow.
Split flow is too low for
split injection
Increase the flow to 40-50 ml/min.
Performance of the column
has degraded
Test the column at the optimum flow
rate.
Injector is dirty Clean or replace the liner.
Ion source is dirty Clean the ion source and tune the
instrument.
Column is not far enough
into the transferline
The GC column does not extend into
the MS source. Use the column
measuring tool to confirm column
length. If the end of the column is inside
the transfer line, an excessive amount of
GC effluent will contact the inside wall.
Fronting General Column is overloaded Decrease the injected amount and/or
analyte concentrations. Increase the split
ratio. Use a column with a thicker film.
7 Troubleshooting
Investigating Peak Issues
Thermo Scientific TSQ Duo User Guide 129
Tailing Sample peaks Column degradation is
causing activity
Inject a test mixture and evaluate the
column. Replace column if necessary.
Liner is dirty Clean or replace the liner.
Ion source is dirty Clean the ion source and tune the
instrument.
Glass wool or inlet liner is
causing activity
Replace wool with fresh silanized wool
and install a clean inlet liner.
Inlet temperature is too low Increase the temperature of the inlet.
Column connections are
poor or obstructed
Reconnect the column inlet.
Stationary phase is not
appropriate for your target
compounds
Replace the column and choose a more
appropriate phase for your analysis.
Final hold oven
temperature is too low
crease the column/oven temperature. Do
not exceed the recommended maximum
temperature for the stationary phase.
Transferline temperature is
too low
If tailing occurs on late eluting
compounds, it is likely the source or
transferline temperature is too low.
Source temperature is too
low
If tailing occurs on late eluting
compounds, it is likely the source or
transferline temperature is too low.
Poor column
characterization
See Changing the Column for
information about checking for leaks
and column flow.
Table 4. Troubleshooting Peak Issues in Your Data, continued (Sheet 2 of 3)
Behavior Characteristic Cause Remedy
7 Troubleshooting
Investigating Peak Issues
130 TSQ Duo User Guide Thermo Scientific
Ghost Peaks General Incomplete elution of
previous sample
Increase the final oven program
temperature or total run time.
Increase the column flow rate.
Carrier gas is contaminated Replace the gas cylinder or filter.
Laboratory glassware has
caused contamination
Ensure the glassware is clean and
contaminant-free.
Injected sample has
decomposed
Decrease the injection port temperature.
Use the on-column injection technique.
Injection solution has
matrix present
Adequately clean up your sample prior
to injection.
Inlet or pneumatics are
contaminated
Remove the column and bake out the
inlet.
Use a high-quality septum.
Replace the split vent filter.
Install an in-line filter between the
pneumatics and the inlet.
Missing Peaks Baseline or background
present
Column is broken Replace the column.
Column flow is incorrect Make sure the septa are sealing. Make
sure vacuum compensation is turned on.
Backflush settings are
incorrect
Set backflush to off until after injection.
Column position in
S/SL injector is incorrect
(too high)
Check the position of the column.
No baseline or
background present
Poor or missing electrical
connection
Check the cable connections.
Mass spectrometer is not
collecting data
Make sure the tune file is correct.
Verify that the Busy light is on during
acquisition.
Make sure the filament is not burned
out.
Close Xcalibur, open Instrument
Configuration, press the Reset button on
the mass spectrometer, wait ten seconds,
close Instrument Configuration.
Table 4. Troubleshooting Peak Issues in Your Data, continued (Sheet 3 of 3)
Behavior Characteristic Cause Remedy
7 Troubleshooting
Investigating Results Issues
Thermo Scientific TSQ Duo User Guide 131
Investigating Results Issues
Behavior Characteristic Cause Remedy
Low
Reproducibility of
Peaks Area
General Detector gain is set too low Retune the gain.
Increase the electron multiplier voltage.
Increase the target ion count.
Concentration is not
compatible with the
dynamic range of the
detection system
Verify that the sample concentration is
suitable for the system.
Chromatogram and
spectrum are blank
Make sure the tune file is correct.
Verify that the Busy light is on during
acquisition.
Make sure the filament is not burned
out.
Injection technique is not
appropriate
Use a different injection technique.
Injection parameters are
not appropriate
Verify the injection temperature and
flow rates.
Sample injection technique
is not reproducible
Evaluate the sample preparation
sequences.
Compare the results with a series of
standard injections.
Syringe or septum is
leaking
Check and replace the syringe and/or
septum at regular intervals.
Injection port is leaking Check the column connections.
Run a leak check.
Injection technique is not
suitable
Carefully meter the injected amount.
Use a clean, good-quality syringe.
Ion source is dirty Clean the ion source and retune the
instrument.
Split flow or ratio control is
inadequate
Monitor the flow.
Replace the in-line filter.
7 Troubleshooting
Investigating Results Issues
132 TSQ Duo User Guide Thermo Scientific
Poor Sensitivity With increased
retention time
Carrier gas flow rate is too
low
Increase the carrier gas flow rate.
Locate and remove possible obstructions
in the carrier gas line.
Check the septum for leaks.
Check the injector/column ferrules for
leaks.
With normal
retention time
GC carrier gas line has leaks Run a leak test and correct leaks.
Syringe is leaking during
injection
Replace syringe or piston seals, if
necessary.
Split injection temperature
is too low
Increase the temperature of the injector.
Voltage is not reaching the
lens.
Replace the lens plate and springs if
damaged.
Remove debris or broken pieces in the
manifold.
Run a lens check diagnostic.
Check the connection by removing or
inserting the ion source.
Retention Times Low reproducibility DCC is drifting or unstable Monitor the column pressure or flow.
Check and replace the controller, if
necessary.
Injection technique is
inadequate
Pick injection technique suitable for the
injector and liner you are using.
Vaporization size of sample
inject larger than volume of
liner
Reduce the injected amount and/or
volume.
Column temperature is
unstable
Check the main oven door and cooling
flap.
Monitor the column temperature.
Behavior Characteristic Cause Remedy
Thermo Scientific TSQ Duo User Guide 133
I
A
acquisition methods, purpose of, 65
AutoTune, modifying, 95
Autotune, using, 31
B
baseline (troubleshooting)
drifting, 126
baseline issues, investigating, 126
C
centroided data, about, 70
chromatographic separation, changing, 91
column
changing, 15
leak checking, 19
temperature, 21
compliance
FCC vi
regulatory v
WEEE vii
Configuring the TSQ Duo, 6
contaminants, common, 124
contamination, indications, 123
D
data result issues, investigating, 131
diagnostics, selecting tests to run, 100
documentation survey xxi
E
electromagnetic compatibility vi
F
FCC compliance vi
filament voltage, setting, 97
filament, turning off and on, 72
fingerprint, indications, 124
full-scan mode, about, 69
G
GC
creating a method, 61
ghost peaks, troubleshooting, 130
I
ion source temperature, setting, 66, 98
L
leak, indications, 124
leaks, checking for, 19
M
maintenance, settings, 10
mass range, narrowing, 93
methods
acquisition, 65
creating, 53
purpose of, 53
P
peak height, minimum, 66
peak issues, investigating, 128
peaks (troubleshooting)
broadening, 128
fronting, 128
ghost, 130
none, 130
tailing, 129
profiled data, about, 70
Index
134 TSQ Duo User Guide Thermo Scientific
Index: R
R
regulatory compliance v
results (troubleshooting)
low reproducibility of peaks area, 131
poor sensitivity, 132
retention times, 132
retention times, troubleshooting, 132
routine maintenance
causes, 121
S
safety standards v
scan rate, optimizing, 92
scans, running, 67
sensitivity, troubleshooting, 132
survey link xxi
T
tailing peaks, troubleshooting, 129
temperature of the ion source, 66
temperature of the transfer line, 93
temperature of transfer line, 66
transfer line temperature, setting, 66
transfer line, about, 66
troubleshooting
about, 113
baseline issues, 126
peak issues, 128
results issues, 131
tune report, 46
TSQ Duo
changing the column, 15
configuring, 6
creating a method, 53
TSQ Series AutoTune, about, 95
tune reports
example report, 46
printing, 46
settings, 46
tune types
adding, 42
CI- tune, 38
daily tune check, 33
Daily Tune, 37
daily tune, 31
EI default tune, 37
EI full tune, 33
tuning
using Autotune, 31
with TSQ Series Autotune, 31
V
voltage of filament, setting, 97
W
WEEE compliance vii
