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

Contents
Thermo Scientific TSQ Altis, Quantis, and Fortis Hardware Manual xi
Using the Mass List Table in the Define Scan Pane. . . . . . . . . . . . . . . . . . . . . 119
Adding a Row to the Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
Deleting a Row from the Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
Deleting Multiple Rows from the Table . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
Adding or Removing Scan Parameters from the Table. . . . . . . . . . . . . . . . . 120
Importing a Mass List from a File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
Exporting a Mass List to a File. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Using the History Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Using the Favorites Pane to Save System Settings . . . . . . . . . . . . . . . . . . . . . . 121
Appendix B Setting Up the Syringe with the Syringe Pump . . . . . . . . . . . . . . . . . . . . . . . . . . .125
Connecting the Syringe Union to the Syringe . . . . . . . . . . . . . . . . . . . . . . . . . 125
Setting Up the Syringe Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
Appendix C Divert/Inject Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .129
About the Divert/Inject Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
Divert/Inject Valve Configurations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
Loop Injection. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
Divert Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
Divert/Inject Valve Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
Appendix D Setting Up Sample Introduction Techniques. . . . . . . . . . . . . . . . . . . . . . . . . . . . .133
Setting Up H-ESI or Low Flow H-ESI Direct Infusion. . . . . . . . . . . . . . . . . . 133
Setting Up H-ESI Direct Infusion. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
Setting Up Low Flow H-ESI Direct Infusion . . . . . . . . . . . . . . . . . . . . . . . 135
Setting Up High-Flow Infusion Without an Autosampler. . . . . . . . . . . . . . . . 137
Setting Up Loop Injections for Flow-Injection Analysis. . . . . . . . . . . . . . . . . . 138
Setting Up Injections Using the Autosampler . . . . . . . . . . . . . . . . . . . . . . . . . 139
Appendix E Replaceable Parts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .141
Chemical Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
Calibration Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
MS Setup Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
Performance Specification Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
Single Mechanical Pump Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
Dual Mechanical Pumps Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
TSQ Source Installation Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
API Source Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
Miscellaneous Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .147
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .155

Contents
xii TSQ Altis, Quantis, and Fortis Hardware Manual Thermo Scientific

Thermo Scientific TSQ Altis, Quantis, and Fortis Hardware Manual xiii
F
Figure 1. Block diagram of MS hardware components . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Figure 2. Ion optics and mass analyzer assemblies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Figure 3. Placement of the turbomolecular pump next to the vacuum manifold . . . . . . . . 10
Figure 4. Functional block diagram of the Altis vacuum system . . . . . . . . . . . . . . . . . . . . 12
Figure 5. Gas inlets and vacuum (foreline) port (left side of the MS) . . . . . . . . . . . . . . . . 16
Figure 6. API source interface for the TSQ Altis MS (cross section) . . . . . . . . . . . . . . . . . 18
Figure 7. Altis ion transfer tube . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Figure 8. Quantis ion transfer tube . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Figure 9. Fortis ion transfer tube . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Figure 10. Altis RF Lens and exit lens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Figure 11. Quantis RF lens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Figure 12. Fortis exit lens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Figure 13. MP00 lens (left) and lens L0 (right) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Figure 14. MP0 multipole with neutral beam blocker (1) . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Figure 15. EL11 (left) and EL12 (right) lenses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Figure 16. LEDs on the instrument front panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Figure 17. Power entry module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Figure 18. Communication connectors (right side of the MS) . . . . . . . . . . . . . . . . . . . . . . 28
Figure 19. Main power switch on the power module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Figure 20. Electronic service switch and main power switch . . . . . . . . . . . . . . . . . . . . . . . 34
Figure 21. Reset button (1) on the communication panel . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Figure 22. Electronic service switch and main power switch . . . . . . . . . . . . . . . . . . . . . . . 37
Figure 23. Connection to the H-ESI or the low-flow H-ESI source. . . . . . . . . . . . . . . . . . 52
Figure 24. Connection to the APCI spray insert . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Figure 25. Syringe pump settings box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Figure 26. Define Scan parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Figure 27. Plot Chromatogram dialog box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Figure 28. Calibration pane options. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Figure 29. Report Generation Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Figure 30. Error range for the EMRS calibrants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Figure 31. Ion signal intensity as a function of the lens L0 offset voltage . . . . . . . . . . . . . . 63
Figure 32. Mass spectrum of EMRS in positive ion mode . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Figure 33. Mass spectrum of EMRS in negative ion mode . . . . . . . . . . . . . . . . . . . . . . . . . 65
Figure 34. Optimizing the source parameters in the Optimization pane . . . . . . . . . . . . . . 69
Figure 35. Example optimization of the RF lens (SRIG RF) tuning for m/z 997.55 . . . . . . 70
Figure 36. Examples of the optimization results tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Figure 37. Illustration of product scan type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Figures

Figures
xiv TSQ Altis, Quantis, and Fortis Hardware Manual Thermo Scientific
Figure 38. Illustration of the precursor scan type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Figure 39. Illustration of the neutral loss scan type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Figure 40. Examples of compounds with a common fragment . . . . . . . . . . . . . . . . . . . . . . 77
Figure 41. Examples of Profile (left) and Centroid (right) Data . . . . . . . . . . . . . . . . . . . . . 79
Figure 42. Data Acquisition pane in the Tune window . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Figure 43. Run Sequence dialog box (partial) showing the selected start instrument . . . . . 84
Figure 44. Change Instrument in Use dialog box. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Figure 45. Templates in Method Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Figure 46. API source interface removed from the vacuum manifold. . . . . . . . . . . . . . . . . 96
Figure 47. Removing the multipole MP00 and lens L0 assembly (TSQ Altis MS). . . . . . . 97
Figure 48. Removing the RF lens and exit lens (TSQ Quantis MS). . . . . . . . . . . . . . . . . . 98
Figure 49. Removing the lens L0 and multipole MP00 from the MP00-L0 mount cage . . 98
Figure 50. Removing the multipole MP00 and lens L0 assembly (TSQ Fortis) . . . . . . . . . 99
Figure 51. Removing the exit lens (TSQ Fortis) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
Figure 52. Removing the lens L0 and multipole MP00 from the MP00-L0 mount cage . 100
Figure 53. Ion sweep cone removed from the MS mount assembly . . . . . . . . . . . . . . . . . 104
Figure 54. Ion transfer tube removal tool (TSQ Altis MS) . . . . . . . . . . . . . . . . . . . . . . . . 105
Figure 55. Ion transfer tube removal tool (TSQ Quantis MS) . . . . . . . . . . . . . . . . . . . . . 106
Figure 56. Ion transfer tube removal tool (TSQ Fortis MS) . . . . . . . . . . . . . . . . . . . . . . . 106
Figure 57. Spray cone, O-ring, ion transfer tube, and ion sweep cone (TSQ Quantis and
TSQ Fortis) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
Figure 58. Air filter location in the MS with the front cover removed . . . . . . . . . . . . . . . 112
Figure 59. Tune window showing the Define Scan pane . . . . . . . . . . . . . . . . . . . . . . . . . 114
Figure 60. Tune Preferences dialog box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
Figure 61. Q3 Resolution selected and added to the SRM Table . . . . . . . . . . . . . . . . . . . 120
Figure 62. Favorites pane. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
Figure 63. State name box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
Figure 64. PEEK tubing connection to syringe union . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
Figure 65. Syringe pump with syringe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
Figure 66. Divert/inject valve positions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
Figure 67. Divert/Inject valve plumbed as a divert valve . . . . . . . . . . . . . . . . . . . . . . . . . . 131
Figure 68. Divert/inject valve (front view) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
Figure 69. H-ESI direct infusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
Figure 70. Low-flow H-ESI direct infusion set up . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
Figure 71. HPLC infusion Tee valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
Figure 72. Injector valve set up . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
Figure 73. Divert/Inject valve plumbed as a divert valve . . . . . . . . . . . . . . . . . . . . . . . . . 140

Thermo Scientific TSQ Altis, Quantis, and Fortis Hardware Manual xv
P
Preface
The TSQ Altis, Quantis, and Fortis Hardware Manual describes how to set up and calibrate the
Thermo Scientific™ TSQ Altis™, TSQ Quantis™, and TSQ Fortis™ triple quadrupole mass
spectrometry systems. It also describes the modes of operation, hardware components, and
how to maintain the instrument.
• Suggesting Changes to the Documentation or to the Help
• Accessing Documentation
• Special Notices, Symbols, and Cautions
•ContactingUs
Suggesting Changes to the Documentation or to the Help
Complete a brief survey about this document by clicking the button below.
Thank you in advance for your help.
Accessing Documentation
The TSQ Altis, TSQ Quantis, and TSQ Fortis MSs include complete documentation. For
system requirements, refer to the release notes on the software DVD.
Viewing the Product Manuals
• (Windows 7) From the Microsoft™ Windows™ taskbar, choose Start > All Programs >
Thermo Instruments > model x.x, and then open the applicable PDF file.
• (Windows 10) From the Windows taskbar, choose Start > All Apps > Thermo
Instruments > model x.x, and then open the applicable PDF file.

Preface
xvi TSQ Altis, Quantis, and Fortis Hardware Manual Thermo Scientific
Viewing the Help
Do the following as applicable:
• Thermo Tune application: Click the Options icon, , and choose Tu n e H e l p .
• Thermo Xcalibur™ Method Editor: Choose an option from the Help menu (or press
the F1 key).
Viewing User Documentation from the Thermo Fisher Scientific Website
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2. Point to Services & Support and click Manuals on the left.
3. In the Refine Your Search box, search by the product name.
4. From the results list, click the title to open the document in your web browser, save it, or
print it.
To return to the document list, click the browser Back button.
Special Notices, Symbols, and Cautions
Make sure you understand the special notices, symbols, and caution labels in this guide. Most
of the special notices and cautions appear in boxes; those pertaining to safety also have
corresponding symbols. Some symbols are also marked on the instrument itself and can
appear in color or in black and white. For complete definitions, see Ta ble 1.
Table 1. Notices, symbols, labels, and their meanings (Sheet 1 of 2)
Notice, symbol, or label Meaning
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
product.
Note Highlights information of general interest.
Tip Highlights helpful information that can make a task easier.

Preface
Thermo Scientific TSQ Altis, Quantis, and Fortis Hardware Manual xvii
Caution: Read the cautionary information associated with this
task.
Chemical hazard: Observe safe laboratory practices and
procedures when handling chemicals. Only work with volatile
chemicals under a fume or exhaust hood. Wear gloves and other
protective equipment, as appropriate, when handling toxic,
carcinogenic, mutagenic, corrosive, or irritant chemicals. Use
approved containers and proper procedures to dispose of waste
oil and when handling wetted parts of the instrument.
Hot surface: Before touching the API source assembly, allow
heated components to cool.
Risk of electric shock: This instrument uses voltages that can
cause electric shock and/or personal injury. Before servicing,
shut down the instrument and disconnect it from line power.
While operating the instrument, keep covers on.
Risk of eye injury: Eye injury can occur from splattered
chemicals, airborne particles, or sharp objects. Wear safety
glasses when handling chemicals or servicing the instrument.
Sharp object: Avoid handling the tip of the syringe needle.
Table 1. Notices, symbols, labels, and their meanings (Sheet 2 of 2)
Notice, symbol, or label Meaning

Preface
xviii TSQ Altis, Quantis, and Fortis Hardware Manual Thermo Scientific
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Thermo Scientific TSQ Altis, Quantis, and Fortis Hardware Manual 1
1
Introduction
The TSQ Altis, TSQ Quantis, and TSQ Fortis MSs are triple quadrupole atmospheric
pressure ionization (API) mass spectrometers.
• Mass Spectrometry Models
• MS Mass-To-Charge Ratio Ranges
Mass Spectrometry Models
The MS models are the TSQ Altis, TSQ Quantis, and TSQ Fortis.
TSQ Altis MS
The TSQ Altis MS can address your most stringent analytical challenges for targeted
quantitation workflows. The improved Active Ion Management (AIM™) technology,
segmented quadrupoles, novel electron multipliers, and enhanced ion transmission tubes,
help you to achieve unprecedented experimental sensitivity for all molecular species in
complex matrices without sacrificing robustness.
Note The Glossary defines some of the terms used in this manual.

1Introduction
Mass Spectrometry Models
2TSQ Altis, Quantis, and Fortis Hardware Manual Thermo Scientific
TSQ Quantis MS
The TSQ Quantis MS can easily answer critical analytical challenges during targeted
quantitation workflows. With its segmented quadrupoles, faster rod drives, and improved
electron multipliers, the TSQ Quantis MS delivers unprecedented robustness with best-class
sensitivity for everyday use and for every user.
TSQ Fortis MS
The reliable instrument design, intuitive software, and comprehensive workflow solutions of
the TSQ Fortis MS ensures superior productivity in the quantitation of hundreds of
compounds of all types—in any matrix, by any user.