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 Fusion MS Series Instrument Control Software Version 3.0 SP1

Release date: October 10, 2017
Build number: 3.0.2041
Instruments: Orbitrap Fusion Lumos MS and Orbitrap Fusion MS

Software requirements: Xcalibur 4.1 with Foundation 3.1 SP4 (note Foundation installs automatically with Xcalibur 4.1)

Follow the upgrade instructions provided: Orbitrap Fusion Series Instrument Control Software vs. 3.0 SP1 Release Notes

Download the software: Orbitrap Fusion MS Series ICSW version 3.0 SP1 and Xcalibur 4.1 SP1

Download the Update Overview: Orbitrap Fusion MS Series Instrument Control Software v.3.0 SP1 Overview

New Features

  • (Orbitrap Fusion Lumos only) Support for new 1M (1 million resolution) option (licensed feature)
  • (Orbitrap Fusion Lumos only) Support for new Ultraviolet Photodissociation (UVPD) option
    • Note: UVPD requires the use of the Thermo Scientific FreeStyle™ 1.3 application for viewing data.
  • (Orbitrap Fusion Lumos only) Support for new Advanced Peak Determination (APD) option (licensed feature)
  • Enabled 7500 resolution option for 30 Hz Orbitrap ddMS2 analysis (under specified conditions)
  • Isolation offset parameters expanded to support using mass to define the offset, in addition to the previously enabled m/z. Added the option for recording either the offset mass or the original mass in the raw data file.
  • Expanded experiment tree flexibility to provide SPS MS3 and standard outcomes in the same experiment
  • Support for defining specific number of scans per outcome
  • Support for relative intensity filter for MSn scans
  • Support for target-specific RF Lens (%) setting for tMSn and tSIM scans
  • Support for defining CID activation time
  • Support added or moved to Tune Diagnostics for these features:
    • Low mass calibration
    • Threshold modification for excluding isotopes (default 40%), located in Diagnostics > Tools > Method > Set
    • Dynamic Exclusion Isotope Threshold
    • Ion trap resolution calibration
  • Usability enhancements in the instrument control software provided through a variety of features:
    • Support for auto-configure for peripheral devices (syringe, divert valve, UVPD)
    • System state restored to Standby when source is changed
    • “Pause acquisition” in Tune application
    • Prime syringe pump from Tune window
    • Ability to import a method directly from a raw data file into Method Editor
    • Tables that support chemical formulas and peptide sequences
    • Templates that support global parameters/multiple experiments
    • Templates that link to additional information at PlanetOrbitrap.com
    • ToolTip information and setting recommendation improvements
    • Factory template updates
    • Revised Help and manuals
    • Method Editor improved to alert you when opening a method from a different version of the software
    • New method-specific scan header contents—Excludes information that is irrelevant to that method. Includes modifications for mass offset and for SPS ions. The scan header also now contains information about absolute collision energy applied when using normalized collision energy.

Known Issues

  • When an experiment has both an SPS MS3 outcome and a standard data-dependent outcome at the same level, scans might not execute properly. To avoid this known defect, set the Scan Priority of the SPS scan to 2. (Reported in Release Notes for 3.0 and 3.0 SP1)
  • 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 3.0 SP1)
  • Occasionally 1M diagnostics will fail to pass. If “Calibrate Orbitrap, 1M” fails, reset to defaults by running Diagnostics | System | Orbitrap | Utilities | Set Default OT Transfer Voltages and then run “Calibrate Orbitrap, 1M” again.(Reported in Release Notes for 3.0 and 3.0 SP1)
  • 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 3.0 SP1)
  • New Issue (Reported Dec 08, 2017): In 3.0 software, normalized HCD collision energy is now reported in the raw file as absolute collision energy. If your software analysis platform is making use of this information (ie. library searching in Compound Discoverer and TraceFinder), this may negatively affect your results. In prior software versions, only normalized HCD collision energy is reported. In 3.1 (not released at this time), both will be reported as is done on Exactive series MS systems. A software patch is available – please contact shannon.eliuk@thermofisher.com
  • Register for Orbitrap Fusion or Orbitrap Fusion Lumos MS Technical updates to receive alerts about newly discovered defects. 

Fixed Defects

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