Thermo Scientific TSQ Altis User manual

TSQ Series II
TSQ Altis, TSQ Quantis,
and TSQ Fortis
Hardware Manual
80111-97047 Revision A June 2018

© 2018 Thermo Fisher Scientific Inc. All rights reserved.
OptaMax NG, TSQ Fortis, and Viper are trademarks; Unity is a registered service mark; and
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Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the
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document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.
The contents of this document are subject to change without notice. All technical information in this
document is for reference purposes only. System configurations and specifications in this document supersede
all previous information received by the purchaser.
This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This
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Release history: Rev. A June 2018
Software version: (Thermo) Foundation 3.1 and later, Xcalibur 3.0 and later, Tune 2.1 and later
For Research Use Only. Not for use in diagnostic procedures.

Regulatory Compliance
Thermo Fisher Scientific performs complete testing and evaluation of its products to ensure full compliance with
applicable North American and European regulations. Your system meets the applicable requirements in the
electromagnetic compatibility (EMC) and product safety standards described in this section.
Unauthorized changes that you make to your system will void regulatory compliance and may defeat the built-in
protections for your instrument. Some examples of unauthorized changes include using replacement parts or adding
components, options, or peripherals that Thermo Fisher Scientific has not qualified and authorized. Unauthorized
changes can also result in bodily injury and/or damage to your system and laboratory.
Ensure continued compliance with regulatory standards:
• Follow all installation instructions provided in the documentation that comes with your system.
• Order replacement parts (as specified in the instrument manual) and additional components, options, and periph-
erals directly from Thermo Fisher Scientific or an authorized representative.
FCC Compliance Statement
Low Voltage Directive 2014/35/EU
This device complies with Low Voltage Directive 2014/35/EU and the harmonized safety standard IEC/EN/CSA/
UL 61010-1, 3rd Edition.
EMC Directive 2014/30/EU
This device was tested by TUV Rheiland in San Jose, CA. and complies with the following EMC standards:
EN 61326-1 and subordinate EMC standards 47 CFR 15, Subpart B, Class A: 2015
RoHS II Directive 2011/65/EU
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.

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: This instrument must be used in the manner specified by Thermo Fisher
Scientific to ensure protections provided by the instrument are not impaired. Deviations from specified instructions on
the proper use of the instrument include changes to the system and part replacement. Accordingly, order replacement
parts from Thermo Fisher Scientific or one of its authorized representatives.
CAUTION Read and understand the various precautionary notes, signs, and symbols contained inside
this manual pertaining to the safe use and operation of this product before using the device.

WEEE Directive
2012/19/EU
Thermo Fisher Scientific is registered with B2B Compliance (B2Bcompliance.org.uk) in the UK and with the
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If this product is located in Europe and you want to participate in the Thermo Fisher Scientific Business-to-Business
(B2B) Recycling Program, send an email request to [e-mail] with the following information:
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• Number of product pieces, and the estimated total weight and volume
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• Appropriate pick-up time
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IMPORTANT This recycling program is not for biological hazard products or for products that have been medically
contaminated. You must treat these types of products as biohazard waste and dispose of them in accordance with
your local regulations.

Thermo Scientific TSQ Altis, Quantis, and Fortis Hardware Manual vii
C
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xv
Suggesting Changes to the Documentation or to the Help . . . . . . . . . . . . . . . . xv
Accessing Documentation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv
Viewing the Product Manuals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv
Viewing the Help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xvi
Viewing User Documentation from the Thermo Fisher Scientific Website . .xvi
Special Notices, Symbols, and Cautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xvi
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xviii
Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Mass Spectrometry Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
TSQ Altis MS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
TSQ Quantis MS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
TSQ Fortis MS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
MS Mass-To-Charge Ratio Ranges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Chapter 2 Principles of Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5
Overview of the MS System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Overview of Ion Optics and Mass Analyzer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Chapter 3 Vacuum System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
Vacuum Pumps. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Vacuum Manifold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Vacuum System Block Diagram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Vacuum Gauges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Chapter 4 Internal Gas Supply. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
Chapter 5 Atmospheric Source Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17
API Source Interface Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Ion Transfer Tube . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
RF and Exit Lens. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Chapter 6 Ion Optics and Detector Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23
MP00 Ion Optics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Contents

Contents
viii TSQ Altis, Quantis, and Fortis Hardware Manual Thermo Scientific
MP0 Ion Optics and Beam Blocker. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Dual-Mode, Discrete-Dynode Ion Detection System . . . . . . . . . . . . . . . . . . . . 24
Chapter 7 Controls and Indicators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .25
LEDs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Power Entry Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Main Power Switch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Electronics Service Switch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
SV65 Pump Enable Connector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Communications Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Cooling Fans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Chapter 8 Using the MS Power Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .31
Turning the MS On . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Placing the MS in Standby Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Shutting Down the MS System in an Emergency . . . . . . . . . . . . . . . . . . . . . . . 32
Chapter 9 Shutting the MS System Down Completely . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33
Shutting the MS Down Completely . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Turning off the LC, Gases, Data System, and Autosampler. . . . . . . . . . . . . . . . 34
Chapter 10 Restarting the MS System After a Shutdown. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .35
Restarting the Data System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Restarting the Data System Using Windows . . . . . . . . . . . . . . . . . . . . . . . . . 35
Restarting the Data System Using the Power Button. . . . . . . . . . . . . . . . . . . 35
Resetting the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Pumping the MS Down . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Resetting Calibration Parameters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Starting the LC, Gases, and Autosampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Chapter 11 MS Components On/Off Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .41
Chapter 12 Maintaining the MS on a Daily Basis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .43
Before Operating the Mass Spectrometer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Finding and Fixing Air Leaks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Checking the Vacuum Pressure Levels. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Checking the Argon and Nitrogen Gas Supplies . . . . . . . . . . . . . . . . . . . . . . 46
After Operating the Mass Spectrometer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Flushing the Inlet Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Purging the Oil in the Forepump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Emptying the Solvent Waste Container. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Placing the System in Standby Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Chapter 13 Recommended Inlet and Flow Rates. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .49
Guidelines for LC/H-ESI/MS Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

Contents
Thermo Scientific TSQ Altis, Quantis, and Fortis Hardware Manual ix
Guidelines for LC/APCI/MS Parameters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Guidelines for LC/NSI/MS Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Chapter 14 Connecting the Sample Flow to the Source. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .51
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Connecting the Sample Flow to the H-ESI Source . . . . . . . . . . . . . . . . . . . . . . 51
Connecting the Sample Flow to the APCI Source . . . . . . . . . . . . . . . . . . . . . . . 52
Chapter 15 Calibrating the MS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .55
Preparing the Syringe Pump for Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Preparing the MS for Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Determining the Initial API Source Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Evaluating the Spray Stability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Calibration Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Calibrating and Tuning the MS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Check Mass Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Mass Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
EM Gain Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Tune and Mass Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Calibration Solution Peak Values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Chapter 16 Optimizing the Compound Signal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .67
Performing Compound Optimization Animation . . . . . . . . . . . . . . . . . . . . . . . 67
Setting Up for Compound Optimization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Optimizing Parameters in the Optimization Pane . . . . . . . . . . . . . . . . . . . . . . . 68
Chapter 17 Scan Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .71
Quadrupole Capacities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Summary of Scan Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Full Scan Q1 and Q3 Scan Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Selected Ion Monitoring Scan Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Product Scan Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Precursor Scan Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Neutral Loss Scan Type. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Selected Reaction Monitoring Scan Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Chapter 18 Data Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .79
Profile and Centroid Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Ion Polarity Modes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
Chapter 19 Acquiring Sample Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .81
Creating an SRM Method Animation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
Using Tune to Acquire Sample Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82

Contents
xTSQ Altis, Quantis, and Fortis Hardware Manual Thermo Scientific
Using the Xcalibur Data System to Acquire Sample Data . . . . . . . . . . . . . . . . . 84
Selecting the External Start Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
Acquiring Data Files with the Xcalibur Data System . . . . . . . . . . . . . . . . . . . 85
Using Templates in Thermo Xcalibur Instrument Setup . . . . . . . . . . . . . . . . . . 86
Chapter 20 Maintenance Schedule and Supplies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .87
MS Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Maintenance Schedule. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Guidelines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Tools and Supplies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Chapter 21 Maintaining the API Source and Replacing the H-ESI Needle . . . . . . . . . . . . . .93
Cleaning the API Source Housing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Replacing the H-ESI Needle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Chapter 22 Maintaining the RF Lens, Exit Lens, MP00 RF Lens, and Lens L0 . . . . . . . . . . . . .95
Removing the API Source Interface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Removing the RF Lens, Exit Lens, MP00 RF Lens, and Lens L0
(Altis/Quantis) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Removing the Exit Lens, MP00, and Lens L0 (Fortis). . . . . . . . . . . . . . . . . . . . 99
Cleaning the RF Lens, Exit Lens, MP00, and Lens L0. . . . . . . . . . . . . . . . . . . 100
Reinstalling the API Source Interface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Chapter 23 Maintaining the API Source Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .103
Performing Source Maintenance Animation . . . . . . . . . . . . . . . . . . . . . . . . . . 103
Removing the Ion Sweep Cone and the Ion Transfer Tube . . . . . . . . . . . . . . . 104
Cleaning the Spray Cone and O-ring . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
Cleaning the Ion Transfer Tube . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
Cleaning the Ion Sweep Cone . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
Chapter 24 Maintaining the Forepumps and the Air Filter. . . . . . . . . . . . . . . . . . . . . . . . . . . .111
Maintaining the Forepumps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Maintaining the Air Filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Appendix A Using Basic Tune Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .113
Performing Compound Optimization Animation . . . . . . . . . . . . . . . . . . . . . . 113
Opening the Tune Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
Setting the Instrument System Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Setting the Instrument Power Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
Checking the Instrument Readback Status . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
Setting the Tune Preferences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118