OpenMS 2.2 is a source-only release. It introduces a considerable number of new features and bug fixes.

We recommend checking out the Release2.2.0 git tag
Alternatively, you can download the full source code at

Notable changes since version 2.1 are:


  • By default, decoy sequences are now denoted by the prefix “DECOY_”

New tools:

  • FeatureLinkerUnlabeledKD — Fast feature linking using a KD tree (TOPP)
  • SpectraSTSearchAdapter — Interface to the SEARCH Mode of the SpectraST executable (UTIL)
  • DatabaseFilter — Filters a protein database (FASTA format) based on identified proteins (UTIL)
  • TargetedFileConverter — Conversion of multiple targeted file formats (CSV, TraML, etc.)
  • RNPxlSearch — Annotate RNA to peptide crosslinks in MS/MS spectra (UTIL)

Deprecated and removed tools:

  • ITRAQAnalyzer — superseded by IsobaricAnalyzer
  • TMTAnalyzer — superseded by IsobaricAnalyzer
  • ConvertTSVToTraML – superseded by TargetedFileConverter
  • ConvertTraMLToTSV – superseded by TargetedFileConverter
  • MapAlignmentEvaluation — removed as deprecated

Major changes in functionality:

  • OpenSWATH analysis
    • Support for metabolomics workflows
    • Support for scanning SWATH (SONAR)
    • Support for SQL-based file formats
  • XTandemAdapter
    • Simplified usage
    • Improved support for PTMs and newer X! Tandem versions (“Vengeance”, “Alanine”)
  • IsobaricAnalyzer
    • Support for TMT10plex
    • Support for quantification in MS3 data
  • IDMapper
    • Allows to map unidentified tandem mass spectra to features
  • FeatureFinderIdentification
    • Advanced multi-sample support using machine learning
  • FileFilter
    • Allows users to enable zlib and lossy compression (see “-lossy_compression”)
    • Allows users to set desired mass accuracy
  • IDFilter
    • Added option to filter for valid digestion products
  • FalseDiscoveryRate
    • Allow filtering by q-value in the tool (no need for IDFilter with “score:pep” option)


  • Averagine approximation for fragment isotope distributions
  • Precursor mass correction supports correction to highest intensity peak in tolerance window
  • Functionality for resampling and adding of spectra
  • Protein-protein cross-link spectrum generator
  • Terminal modifications are now separated by “.” in text output
  • SQLite support in OpenSWATH
  • TheoreticalSpectrumGenerator speed-up and removal of RichPeak code
  • Removal of template parameters from MSExperiment (reduced compile time and binary size)
  • Allow estimation of isotope distributions with predefined numbers of sulfur atoms
  • Improved handling of bracket notation for modified residues (e.g. N[2457.877]VSVK)
  • Improved handling of terminal and residue specificity of modifications
  • Improved annotation of peptide identifications with spectrum references
  • Improved handling of unknown amino acids (“X”) in sequences

File formats:

  • Improved mzML support for SONAR data and mzML with drift time (experimental)
  • Improved support for cross-link data and unknown modifications in mzIdentML
  • mzXML writer able to write MaxQuant-compatible files
  • mzML files now routinely support substantial compression (up to 5x compression, see #2449#2458)
  • Support for Percolator result files based on X! Tandem searches


  • New R script for visualizing RT transformations (trafoXML)

Known Build Issues:

You might encounter build issues on recent compilers. We recommend using Visual Studio Version 2015 and GCC 5.0 or older.

The OpenMS Developers