We are proud to announce the next OpenMS release (version 2.1) with many internal changes, additions, and bug fixes.

Binary packages are available for Windows (64-bit) and Mac OS X dmg (64-bit).

Download: OpenMS binary release 2.1.0

The online documentation contains the installation instructions.

Notable changes since version 2.0.1 are:

New tools:

  • ExternalCalibration — Applies an external mass recalibration (TOPP)
  • OpenSwathFileSplitter — Splits SWATH files into n files, each containing one window (TOPP)
  • MultiplexResolver — Completes peptide multiplets and resolves conflicts within them (UTIL)
  • TICCalculator — Calculates the TIC from a mass spectrometric raw file (useful for benchmarking) (UTIL)

Deprecated and removed tools:

  • PILISIdentification — performs a peptide/protein identification with the PILIS engine (TOPP)
  • PILISModelCV — Perform a cross-validation of the PILIS model parameters (TOPP)
  • PILISModelTrainer — Train the PILIS model with a given set of spectra and identifications (TOPP)
  • PILISSpectraGenerator — Generate spectra, given a list of peptides and a PILIS model (TOPP)

Major changes in functionality:

  • Update notification: starting with OpenMS 2.1 all TOPP tools will check for updated versions of the tools
    online and will print an information message if a newer version is available. This version check occurs only
    once per day and tool. Information on which tools are executed will be collected anonymously to identify which
    tools are no longer used and to optimally distribute development resources. If the feature causes problems or
    concerns, it can be disabled through a command line switch or environment variable (see the documentation).
  • InternalCalibration:
    • supports calibration using a table of lock masses and peptide ids.
    • global or RT-chunked calibration
    • linear & quadratic models (with intensity weighting)
    • outlier removal via RANSAC
    • reoccurring calibrations can be quickly applied to other files using the novel ExternalCalibration tool
  • OpenSwathWorkflow
    • support for metabolites / small molecules
  • MapAlignerIdentification
    • support for “lowess” transformation model
  • AccurateMassSearch:
    • support for multiple databases
  • FeatureFinderMetabo
    • isotope spacing model for carbon-rich molecules (e.g. lipids)
    • PeakPickerHiRes and MassTraceExtractor:
    • support for FWHM annotation

File formats:

  • Improved mzIdentML support (experimental)
  • Improved pepXML support
  • Improved support for indexed mzML files
  • Improved TraML support


  • By default, decoy sequences are now denoted by a prefix ‘DECOY_’.

Third-party software:

  • update for X!Tandem VENGEANCE (2015.12.15)
  • update for MS-GF+ Release v2016.10.14, released October 14, 2016
  • update for pwiz 3.0.9935