Thermo Scientific TSQ Endura User manual

TSQ Series
TSQ Endura and
TSQ Quantiva
Hardware Manual
80100-97014 Revision C February 2017

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The contents of this document are subject to change without notice. All technical information in this
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all previous information received by the purchaser.
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Release history: Rev A, Sept. 2013; Rev B, Aug. 2015; Rev C, Feb. 2017
Software version: (Thermo) Foundation 3.0 SP2 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 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.
FCC Compliance Statement
Low Voltage Directive 2006/95/EC
This device complies with Low Voltage Directive 2006/95/EC and the harmonized safety standard IEC/EN/CSA/
UL 61010, 3rd Edition.
EMC Directive 2004/108/EC
This device was tested by TÜV Rheinland of North America and complies with the following EMC standards:
47 CFR 15, Subpart B, Class A: 2012 EN 61000-3-2: 2006 + A1 + A2 EN 61000-4-5: 2006
CISPR 11: 2009 + A1 EN 61000-3-3: 2008 EN 61000-4-6: 2009
ICES-003: 2012 EN 61000-4-2: 2009 EN 61000-4-8: 2010
EN 55011: 2009 + A1 EN 61000-4-3: 2006 + A1 + A2 EN 61000-4-11: 2004
EN 61326-1: 2013 EN 61000-4-4: 2004 + A1
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.

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.

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:
• WEEE product class
• Name of the manufacturer or distributor (where you purchased the product)
• Number of product pieces, and the estimated total weight and volume
• Pick-up address and contact person (include contact information)
• Appropriate pick-up time
• Declaration of decontamination, stating that all hazardous fluids or material have been removed from the product
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IMPORTANT This recycling program is not for biological hazard products or for products that have been medically
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your local regulations.

Thermo Scientific TSQ Endura and TSQ Quantiva Hardware Manual vii
C
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii
Accessing Documentation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii
Special Notices, Symbols, and Cautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiv
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xviii
Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Mass Spectrometer Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Overview of an LC/MS Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
LC/MS Functional Block Diagram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Electronic Assemblies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Controls and Indicators. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
LEDs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Power Entry Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Communications Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Cooling Fans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Chapter 2 Scan Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13
Scan Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Full Scan Q1 and Q3 Scan Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Selected Ion Monitoring Scan Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Product Scan Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Precursor Scan Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Neutral Loss Scan Type. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Selected Reaction Monitoring Scan Type . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Scan Mass-To-Charge Ratio Ranges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Data Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Ion Polarity Modes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Chapter 3 Vacuum System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23
Vacuum System Functional Block Diagram . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Schematic of the Internal Gas Supply Lines. . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Inlet Gases Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Nitrogen Gas Valves . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Argon Gas Valves . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Vent Valve. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Contents

Contents
viii TSQ Endura and TSQ Quantiva Hardware Manual Thermo Scientific
Vacuum Manifold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Vacuum Gauges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Vacuum Pumps. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Atmospheric Pressure Ionization Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
API Source Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Chapter 4 Ion Transmission and Mass Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33
Ion Optics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
MP00 Ion Optics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
MP0 Ion Optics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Mass Analyzers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Quadrupole Rod Assemblies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Applied RF and DC Fields . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Mass Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Collision Cell and CID Efficiency . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Quadrupole Offset Voltage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Mass Analyzer Lenses. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Dual-Mode, Discrete-Dynode Ion Detection System . . . . . . . . . . . . . . . . . . . . 41
Chapter 5 Syringe Pump and Divert/Inject Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .43
Syringe Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Divert/Inject Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Configurations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Controlling the Divert/Inject Valve. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Chapter 6 System Shutdown, Startup, and Reset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .47
Shutting Down the System in an Emergency. . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Placing the Mass Spectrometer in Standby Mode . . . . . . . . . . . . . . . . . . . . . . . 48
Turning On the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Shutting Down the Mass Spectrometer Completely . . . . . . . . . . . . . . . . . . . . . 49
Starting the System After a Complete Shutdown. . . . . . . . . . . . . . . . . . . . . . . . 50
Starting the LC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Starting the Data System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Starting the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Starting the Autosampler. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Resetting the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Resetting Calibration Parameters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Restarting the Data System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
On/Off Status for MS Components Under Varying Power Conditions. . . . . . . 53
Chapter 7 Daily Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .55
Before Operating the Mass Spectrometer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Checking the System Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Checking the Vacuum Pressure Levels. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Checking the Gas Supplies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

Contents
Thermo Scientific TSQ Endura and TSQ Quantiva Hardware Manual ix
After Operating the Mass Spectrometer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Flushing the Inlet Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Purging the Oil in the Forepump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Emptying the Solvent Waste Container. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Placing the System in Standby Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Chapter 8 Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .61
Maintenance Schedule. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Guidelines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Tools and Supplies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Maintaining the API Source Housing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Maintaining the API Source Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Cleaning the Ion Sweep Cone, Spray Cone, and Ion Transfer Tube . . . . . . . 66
Removing the API Source Interface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Cleaning the RF Lens, Exit Lens, MP00 RF Lens, and Lens L0. . . . . . . . . . . 72
Reinstalling the API Source Interface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Maintaining the Forepumps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Maintaining the Air Filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Chapter 9 Diagnostics and PCB and Assembly Replacement. . . . . . . . . . . . . . . . . . . . . . . . .79
Running the System Diagnostics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Replacing Fuses, PCBs, and Power Supplies . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
Chapter 10 Replaceable Parts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .81
Chemical Kit. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
Calibration Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
MS Setup Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Performance Specification Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Single Mechanical Pump Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
Dual Mechanical Pumps Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
TSQ Source Installation Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
API Source Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Miscellaneous Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .87
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .93

Contents
xTSQ Endura and TSQ Quantiva Hardware Manual Thermo Scientific

Thermo Scientific TSQ Endura and TSQ Quantiva Hardware Manual xi
F
Figure 1. Functional block diagram of the TSQ Endura and TSQ Quantiva systems . . . . . 5
Figure 2. TSQ Endura and TSQ Quantiva front panel LEDs . . . . . . . . . . . . . . . . . . . . . . . 6
Figure 3. Power entry module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Figure 4. Communication connectors (right side of the MS) . . . . . . . . . . . . . . . . . . . . . . . 9
Figure 5. Illustration of product scan type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Figure 6. Illustration of the precursor scan type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Figure 7. Illustration of the neutral loss scan type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Figure 8. Examples of compounds with a common neutral-loss fragment . . . . . . . . . . . . . 19
Figure 9. Functional block diagram of the vacuum system . . . . . . . . . . . . . . . . . . . . . . . . 24
Figure 10. Schematic of the internal gas supplies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Figure 11. Gas inlets and vacuum (foreline) port (left side of the MS) . . . . . . . . . . . . . . . . 25
Figure 12. Placement of the turbomolecular pump next to the vacuum manifold . . . . . . . . 28
Figure 13. Ion Max NG and EASY-Max NG ion sources . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Figure 14. API source interface (TSQ Endura MS cross section) . . . . . . . . . . . . . . . . . . . . 30
Figure 15. Ion transfer tubes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Figure 16. RF and exit lenses for the mass spectrometers . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Figure 17. Schematic of the mass spectrometer ion transmission path . . . . . . . . . . . . . . . . . 33
Figure 18. MP00 RF lens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Figure 19. Lens L0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .34
Figure 20. Multipole MP0 and beam blocker . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Figure 21. TK1 (left) and TK2 (right) lenses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Figure 22. Quadrupole Q1 or Q3 (TSQ Endura MS) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Figure 23. Hyperquad Q1 or Q3 (TSQ Quantiva MS) . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Figure 24. Quadrupole Q2 (bottom) separated from the active collision cell housing
(top) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Figure 25. Polarity of the RF and DC voltages applied to the Q1 and Q3 mass analyzers . . 37
Figure 26. Magnitude of the asymmetric RF and DC voltages applied to the Q1 and
Q3 rods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Figure 27. Syringe pump setup (top view) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Figure 28. Divert/inject valve positions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Figure 29. Divert/inject valve plumbed as a loop injector and as a divert valve . . . . . . . . . . 46
Figure 30. Divert/inject valve (front view) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Figure 31. Ion sweep cone removed from the MS mount assembly . . . . . . . . . . . . . . . . . . 67
Figure 32. Ion transfer tube removal tool (TSQ Endura MS) . . . . . . . . . . . . . . . . . . . . . . . 68
Figure 33. Ion transfer tube removal tool (TSQ Quantiva MS) . . . . . . . . . . . . . . . . . . . . . 68
Figure 34. Spray cone, O-ring, ion transfer tube, and ion sweep cone (TSQ Endura MS) . . 69
Figure 35. API source interface removed from the vacuum manifold (TSQ Endura MS). . 72
Figures

Figures
xii TSQ Endura and TSQ Quantiva Hardware Manual Thermo Scientific
Figure 36. Removing the multipole MP00 and lens L0 assembly. . . . . . . . . . . . . . . . . . . . 73
Figure 37. Removing the RF lens and exit lens (TSQ Endura MS) . . . . . . . . . . . . . . . . . . 74
Figure 38. Removing the lens L0 and multipole MP00 from the MP00-L0 mount cage . . 74
Figure 39. Air filter location in the mass spectrometer with the front cover removed . . . . . 77

Thermo Scientific TSQ Endura and TSQ Quantiva Hardware Manual xiii
P
Preface
The TSQ Endura and TSQ Quantiva Hardware Manual describes the modes of operation and
hardware components for the Thermo Scientific™ TSQ Endura™ and TSQ Quantiva™
systems. It also provides the instruments’ cleaning and maintenance procedures.
This guide is intended for the following Thermo Scientific mass spectrometers (MSs):
• TSQ Endura (requires one forepump)
• TSQ Quantiva (requires two forepumps)
To suggest 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 Endura and TSQ Quantiva MSs include complete documentation. For system
requirements, refer to the release notes on the software DVD.
To view the product manuals
From the Microsoft™ Windows™ taskbar, choose Start > All Programs > Thermo
Instruments > model x.x, and then open the applicable PDF file.
Contents
•Accessing Documentation
•Special Notices, Symbols, and Cautions
•Contacting Us

Preface
xiv TSQ Endura and TSQ Quantiva Hardware Manual Thermo Scientific
To view 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).
To view user documentation from the Thermo Fisher Scientific website
1. Go to thermofisher.com.
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 Table 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 Endura and TSQ Quantiva Hardware Manual xv
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.
Heavy object: Never lift or move the instrument by yourself;
you can suffer personal injury or damage the instrument
Hot surface: Before touching the API source assembly, allow
heated components to cool.
Pinch point: Keep hands away from the specified areas.
Risk of electric shock: This instrument uses voltages that can
cause electric shock and personal injury. Before servicing the
instrument, shut it down 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.
Trip obstacle: Be aware of cords, hoses, or other objects located
on the floor.
Table 1. Notices, symbols, labels, and their meanings (Sheet 2 of 2)
Notice, symbol, or label Meaning

Preface
xvi TSQ Endura and TSQ Quantiva Hardware Manual Thermo Scientific
Read and understand the following cautions that are specific to the shutdown of the mass
spectrometry system or to the removal of parts for cleaning.
CAUTION If you must turn off the mass spectrometer in an emergency, turn off the
main power switch located on the right-side power panel. This switch turns off all
power to the mass spectrometer, including the forepump, without harming components
within the system. However, do not use this method as part of the standard shutdown
procedure. Instead, see “Shutting Down the Mass Spectrometer Completely” on page 49.
To turn off the LC, autosampler, and data system computer in an emergency, use their
respective on/off switch or button.
CAUTION To avoid an electrical shock, be sure to follow the instructions in“Shutting
Down the Mass Spectrometer Completely” on page 49.
CAUTION Do not turn the instrument on if you suspect that it has incurred any kind of
electrical damage. Instead, disconnect the power supply cord and contact Thermo Fisher
Scientific technical support for a product evaluation. Do not attempt to use the
instrument until it has been evaluated. (Electrical damage might have occurred if the
system shows visible signs of damage or has been transported under severe stress.)
CAUTION Do not disconnect the power supply cord from the mass spectrometer while
the other end is still plugged into the electrical outlet.
CAUTION Do not place any objects (for example, the syringe pump or other containers
with liquids) on top of the instrument, unless instructed to in the documentation.
Leaking liquids might contact the electronic components and cause an electrical short
circuit.
CAUTION Hot surface. Allow heated components to cool to room temperature
(approximately 20 minutes) before servicing them.

Preface
Thermo Scientific TSQ Endura and TSQ Quantiva Hardware Manual xvii
CAUTION Place the mass spectrometer in Standby (or Off) mode before you open the
atmospheric pressure ionization (API) source. The presence of atmospheric oxygen in
the API source when the mass spectrometer is on could be unsafe. (The mass spectrometer
automatically turns off when you open the API source; however, it is best to take this
added precaution.)
CAUTION Follow the instrument maintenance instructions. To avoid personal injury or
damage to the instrument, do not perform any servicing other than that contained in the
TSQ Endura and TSQ Quantiva Hardware Manual or related manuals unless you are
authorized to do so.
CAUTION Use care when changing vacuum pump oil. Treat drained vacuum pump oil
and pump oil reservoirs with care. Hazardous compounds introduced into the system
might have dissolved in the pump oil. Always use approved containers and procedures for
disposing of waste oil. Whenever a pump has been operating on a system used for the
analysis of toxic, carcinogenic, mutagenic, or corrosive/irritant chemicals, you must
decontaminate the pump and certify it as free of contamination before a Thermo Fisher
Scientific field service engineer repairs or makes adjustments or before it is sent back to the
factory for service.

Preface
xviii TSQ Endura and TSQ Quantiva Hardware Manual Thermo Scientific
Contacting Us
QR Code Email Telephone
Technical Support us.techsupport.analyze
@thermofisher.com
(U.S.) 1 [phone]
Customer Service and
Sales
us.customer-support.analyze
@thermofisher.com
(U.S.) 1 [phone]
Thermo Fisher Scientific
Global Contacts
To find global contact information or customize your request
1. Go to thermofisher.com.
2. Click Contact Us and then select the type of support you
need.
3. At the prompt, type the product name.
4. Use the phone number or complete the online form.
To find product support, knowledge bases, and resources
Go to thermofisher.com/us/en/home/technical-resources.
To find product information
Go to
thermofisher.com/us/en/home/brands/thermo-scientific.
Note To provide feedback for this document, go to surveymonkey.com/s/PQM6P62 or send an email message to
Technical Publications ([e-mail]).

Thermo Scientific TSQ Endura and TSQ Quantiva Hardware Manual 1
1
Introduction
The TSQ Endura and TSQ Quantiva mass spectrometers are members of the Thermo
Scientific family of mass spectrometers. The TSQ Endura and TSQ Quantiva systems consist
of the mass spectrometer, a syringe pump, a divert/inject valve, and the Thermo Xcalibur data
system.
Note The Glossary defines some of the terms used in this manual.
Contents
•Mass Spectrometer Models
•Overview of an LC/MS Analysis
•LC/MS Functional Block Diagram
•Electronic Assemblies
•Controls and Indicators
•Cooling Fans

1Introduction
Mass Spectrometer Models
2TSQ Endura and TSQ Quantiva Hardware Manual Thermo Scientific
Mass Spectrometer Models
For descriptions of the various hardware components, see Chapter 3, “Vacuum System,”
Chapter 4, “Ion Transmission and Mass Analysis,” and Chapter 5, “Syringe Pump and
Divert/Inject Valve.”
TSQ Endura MS
The TSQ Endura is a mass spectrometer that contains a triple-quadrupole mass analyzer and
includes an external syringe pump, a divert/inject valve, and the Thermo Scientific
EASY-Max NG™ API source. The instrument requires one forepump.
TSQ Quantiva MS
The TSQ Quantiva is a mass spectrometer that contains a triple-quadrupole mass analyzer
and includes an external syringe pump, a divert/inject valve, and the Thermo Scientific
Ion Max NG™ API source. The instrument requires two forepumps.