TSQ Series II - TSQ Quantis Plus MS - TSQ Fortis Plus MS - TSQ Series - TSQ Altis MS - TSQ Quantis MS - TSQ Altis Plus MS - TSQ Fortis MS - TSQ Series II Mass Spectrometers Hardware Manual - TSQ Series II - TSQ Quantis Plus MS - TSQ Fortis Plus MS - TSQ Series - TSQ Altis MS - TSQ Altis MS - TSQ Quantis MS - TSQ Quantis MS - TSQ Altis Plus MS - TSQ Fortis MS
TSQ Series II Mass Spectrometers Hardware Manual
Product Tree
Spectrometry > Mass Spectrometry > LC-MS Mass Spectrometers > TSQ Series > TSQ Quantis Plus MS
Spectrometry > Mass Spectrometry > LC-MS Mass Spectrometers > TSQ Series > TSQ Fortis Plus MS
Spectrometry > Mass Spectrometry > LC-MS Mass Spectrometers > TSQ Series
Spectrometry > Mass Spectrometry > LC-MS Mass Spectrometers > TSQ Series > TSQ Altis MS
Spectrometry > Mass Spectrometry > IC-MS Mass Spectrometers > TSQ Altis MS
Spectrometry > Mass Spectrometry > LC-MS Mass Spectrometers > TSQ Series > TSQ Quantis MS
Spectrometry > Mass Spectrometry > IC-MS Mass Spectrometers > TSQ Quantis MS
Spectrometry > Mass Spectrometry > LC-MS Mass Spectrometers > TSQ Series > TSQ Altis Plus MS
Spectrometry > Mass Spectrometry > LC-MS Mass Spectrometers > TSQ Series > TSQ Fortis MS
Document Type
Operating Manual
Software version
4.0
TSQ Series II
Preface
Access Documentation
Special Notices, Symbols, and Cautions
Contact Us
Introduction
TSQ Series II models
External features
Instrument panels
LED indicators
Communications panel
Power entry module
Cooling fans
Drainage system
Basic components
Overview of an LC/MS analysis
Mass range, speed, selectivity
Compatible ion sources
Compatible FAIMs interfaces
Scan parameters in the Tune and Method Editor
Scan types
Quadrupole modes
Full scan Q1 and Q3 scan types
Selected ion monitoring scan type
Product ion scan type
Precursor scan type
Neutral loss scan type
Selected reaction monitoring scan type
Quantitation enhanced data-dependent scan type
Profile and centroid data
Ion polarity modes
Functional description of the MS components
Vacuum system and inlet gases hardware and N2 gas flow paths
Vacuum pumps
Vacuum manifold
Vacuum gauges
Inlet gas supply hardware
Sheath gas, aux gas, and sweep gas flow paths
Atmospheric pressure ionization source
API source interface
Ion sweep cone
Spray cone
Ion transfer tube
Heater block
Vent prevent ball
RF lens and exit lens
Tube lens and skimmer (TSQ Fortis Plus and TSQ Fortis)
MP00 ion optics – MP00 multipole and L0 lens
MP0 ion optics and neutral blocker
Mass analyzers and collision cell
Quadrupole rod assemblies
Quadrupoles Q1 and Q3
Q2 quadrupole
Applied RF and DC fields
Mass analysis
Collision cell and CID efficiency
Quadrupole offset voltage
Mass analyzer lenses
Ion detection system
Maintain the MS on a daily basis
Before operating the MS
Check the vacuum pressure levels
Find and fix air leaks
Check the argon and nitrogen gas supplies
After operating the MS
Flush the inlet components
Purge the oil in the forepump
Empty the solvent waste container
Place the system in Standby mode
System startup, shutdown, and reset
Place the MS in On mode for operation
Place the MS in Standby mode for short periods between use
Shut down the MS system in an emergency
Shut down the MS system completely for planned service or storage
Restart the MS system afer a complete shutdown
Reset the MS if it is not communicating with the data system
MS components On/Off status
Connect the sample flow to the API source
Connect the sample flow to the H-ESI source
Connect the sample flow to the APCI source
Calibrate the MS
Prepare the MS system for calibration
(Optional) Access system preparation instructions from calibration pane
Set up syringe pump with the calibration solution
Position the H-ESI probe or calibration probe for the calibration process
Apply the favorites settings for the calibration process
Start the flow of the calibration solution to the ion source
Check the full scan for missing or interfering peaks
Evaluate the spray stability
Run the automated System Calibration routine
Run the automated System Check routine
Tune and calibration parameters
Calibration solution peak values
Starting source conditions for various LC flow rates
Check the recommended ion source settings for the LC flow rate
Recommended H-ESI source settings for various LC flow rates
Recommended LC/APCI/MS parameters
Recommended LC/NSI/MS parameters
Optimize the compound signal
View the Performing Compound Optimization animation
Set up the MS system for compound optimization
Optimize the source parameters in the optimization pane
Acquire sample data
View an animation on how to create an SRM method
Use the Tune application to acquire sample data
Use the Xcalibur data system to acquire sample data
Use templates in the Method Editor to set up the MS experiment
Maintenance
Guidelines for performing maintenance
Maintenance schedule
Maintenance animations
Tools and supplies for routine maintenance
Maintain the API source housing
Maintain the external components of the API source interface
Remove the ion sweep cone
Remove the ion transfer tube
Clean the spray cone
Clean the ion sweep cone and the ion transfer tube
Reinstall the ion transfer tube
Reinstall the ion sweep cone
Verify the cleaning process for the external components of the API source
Maintain the internal components of the API source interface
Vent the MS and remove the API source interface
Remove the MP00 assembly, the RF lens, and the exit lens from the source interface cage
Remove the MP00 assembly, the skimmer, and the tube lens
Clean the lenses
Clean the MP00 multipole
Reinstall the components of the API source interface cage
Reinstall the API source interface cage
Maintain the forepumps
Clean the air filter
Basic tune functions
Open the Tune window
Set the instrument system controls
Set the instrument power mode
Check the instrument readback status
Set the Tune preferences
Use the mass list table in the Define Scan pane
Use the History pane
Use the Favorites pane to save the system settings
Syringe and syringe pump setup
Set up the syringe pump to infuse a sample from the syringe
Connect the syringe union to the sample transfer line
Divert/Inject valve
Divert/inject valve positions
Divert/inject valve configurations
Divert/inject valve controls
Sample introduction techniques
H-ESI or H-ESI low-flow direct infusion
High-flow infusion without an autosampler
Set up loop injections for a flow-injection analysis
Set up injections using the autosampler
Replaceable parts
Chemicals
MS calibration kit
Low flow needle and ESI probe calibration kit
Performance specification kit
TSQ source installation kit
API source interface replaceable parts
Miscellaneous replaceable parts
Legal notices
Copyright
Regulatory Compliance
TSQ Altis Plus, TSQ Quantis Plus, and TSQ Fortis Plus
TSQ Altis, TSQ Quantis, and TSQ Fortis
TSQ Endura and TSQ Quantiva
FCC Compliance Statement
Notice on the Use and Handling of Thermo Scientific Instruments
WEEE Directive 2012/19/EU
Glossary
Hardware Manual
B51006200 Revision A
March 2025