Basic tune functions - TSQ Quantis Plus MS - TSQ Fortis Plus MS - TSQ Series - TSQ Altis MS - TSQ Quantis MS - TSQ Altis Plus MS - TSQ Fortis MS - Basic tune functions - 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
Mass Spectrometry > LC-MS Mass Spectrometers > TSQ Series > TSQ Quantis Plus MS
Mass Spectrometry > LC-MS Mass Spectrometers > TSQ Series > TSQ Fortis Plus MS
Mass Spectrometry > LC-MS Mass Spectrometers > TSQ Series
Mass Spectrometry > IC-MS Mass Spectrometers > TSQ Altis MS
Mass Spectrometry > LC-MS Mass Spectrometers > TSQ Series > TSQ Altis MS
Mass Spectrometry > IC-MS Mass Spectrometers > TSQ Quantis MS
Mass Spectrometry > LC-MS Mass Spectrometers > TSQ Series > TSQ Quantis MS
Mass Spectrometry > LC-MS Mass Spectrometers > TSQ Series > TSQ Altis Plus MS
Mass Spectrometry > LC-MS Mass Spectrometers > TSQ Series > TSQ Fortis MS
Document Type
Operating Manual
  • TSQ Series II Mass Spectrometers
  • 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

This appendix describes basic Tune functions that are referenced throughout this guide. For additional information about the Tune window, refer to the Tune Help.

  • 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
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