Acquire sample data - 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 - Acquire sample data - 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

To manually acquire sample data, use either the Tune application, the Xcalibur data system, or an equivalent data acquisition software.

NOTE

Before you begin, ensure that all mass spectrometer calibrations are up to date.

See the following topics:

  • 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
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