Orbitrap Illustration

Instrument Control Software

You can use the instrument control software to collect high-quality mass spectrometry data on the Thermo Scientific mass spectrometers. Control of the instruments is through two application packages: Tune and Method Editor.

For questions about the software, to request features, or to report defects, please email planet.orbitrap@thermofisher.com.

Orbitrap Tribrid MS Series Instrument Control Software Version 3.1 SP1QF1


Release date: December 6, 2018
Build number: 3.1.2412.25
Instruments: Orbitrap Fusion Lumos MS, Orbitrap Fusion MS, and Orbitrap ID-X MS

Software requirements: Xcalibur 4.2 

Follow the upgrade instructions provided: Orbitrap Tribrid MS Series ICSW v. 3.1 SP1QF1 Release Notes

Download the software: Orbitrap Tribrid MS Series ICSW v. 3.1 SP1QF1 and Xcalibur 4.2 Software

Download the Update OverviewOrbitrap Tribrid MS Series ICSW v.3.1 Overview

New Features

The Orbitrap Tribrid MS Series instrument control software version 3.1 incorporates the following new and improved features:
  • Support for the Orbitrap ID-X mass spectrometer
  • (Orbitrap Fusion and Orbitrap Fusion Lumos MSs only) Support for the Advanced Peak Determination (APD) option
  • Improved Installer
  • Improved Orbitrap low mass calibrations
  • Support for the intensity threshold within inclusion/exclusion lists
  • Support for the Assisted CE collision energy mode
  • Improved sort feature—by most/least intense option
  • Support for Small molecule Library Builder (template method)
  • Support for the AcquireX™ feature through the Xcalibur data system
  • Support for FlexMix™ calibration solution
  • Support for the web-based Almanac application with Push to Service and Instrument Logbook
  • Support for an ion trap charge state filter
  • Usability enhancements:
    • Application modes: Small Molecule, Peptide, Intact Proteins
    • Template updates
    • Experiments that support polarity: For both positive and negative switching
    • Improved experience for modifying experiments
    • Minimum gas flows for the HESI source (in On mode)
    • ETD calibrations no longer requiring angiotensin
    • Improved flexibility for stepped collision energy in data-dependent scans

Known Issues

  • When using Pierce FlexMixTM Calibration solution, a software issue may prevent the proper recording of newly calibrated eFT settings in the calibration file. This occurs only under defined circumstances: when positive and negative mode calibrations are run in succession, without stopping to manually change polarity.
    • Instead, simply run positive and negative mode calibrations separately. Once calibrations in one polarity complete, you must manually change the polarity in the Tune application before beginning calibrations in the opposite polarity. More information can be found here
  • Scans might be noisy and have split peaks when eFT is on, first mass is less than 84, and Orbitrap resolution is 240 000 or greater. (Reported in Release Notes for 3.0 and 3.1)
  • When using Windows 10, the View Raw File button does not open the raw file properly, nor can you double-click the raw file to open it.
    • Instead, navigate to the raw file, right-click it, and browse to the appropriate application (FreeStyle) to open the file. Select the checkbox to always open a raw file with the selected application, which then becomes the default. (Reported in Release Notes 3.0 and 3.1)
  • An issue with method conversion from older versions of software containing stepped collision energy in data-dependent scans was identified.
    • The method converted to 3.1 software will not have correct steps and must be manually updated.   
  • An issue where FT masses were shifting during polarity switching experiments that included data-dependent FTMSn (>=2) scans was identified.
    • A software patch is available – please contact shannon.eliuk@thermofisher.com

  • Register for Orbitrap Fusion, Orbitrap Fusion Lumos, and Orbitrap ID-X MS Technical updates and to receive alerts about newly discovered defects. 

Fixed Defects

Contact Us