Dear OpenMS users,

we are proud to announce the release of OpenMS 2.5.0. Grab it

In the following you find all important changes to the previous version:


  • support for RNA mass spectrometry
  • TMT16plex support for IsobaricAnalyzer (see PR #4295)
  • improved MsStats/MsStatsTMT output support (see PR #4181#4207)
  • extended MaxQuant-compatible mzXML support (via FileConverter) (see PR #4432#4423)
  • QualityControl Workflow (all in the QC folder)
  • OpenMS and pyOpenMS support for oligonucleotides
  • OpenSWATH support for ion mobility extraction and scoring
  • OpenSWATH support for metabolite assay library building through SIRIUS (and metabolite extraction and scoring)
  • OpenSWATH support for PRM
  • TOPPAS improvements (see PR #4100#4121#4266#4497)
  • fixes to PeptideIndexer for X!Tandem special cutting rules and ambiguous amino acids (see PR #4356)
  • support for HDF5
  • support for hyperfine isotopic distributions (through IsoSpec)
  • JSON support (see PR #3786)
  • speed improvements (loading/storing files, handling peptide sequences)
  • support for VS2019 and GCC 9.1 (see PR #4211)
  • support for outlier removal in IDPosteriorErrorProbability
  • reduced memory footprint of FeatureFinderIdentification through batch processing

New Tools:

  • Epifany — Runs a Bayesian protein inference (UTIL)
  • FeatureFinderMetaboIdent — Detects features in MS1 data based on metabolite identifications (UTIL)
  • GNPSExport — Tool to export consensus features into MGF format (TOPP)
  • NucleicAcidSearchEngine — Annotate nucleic acid identifications to MS/MS spectra (UTIL)
  • ProteomicsLFQ — A standard proteomics LFQ pipeline (TOPP) (experimental)
  • QualityControl — Computes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get (TOPP)
  • RNAMassCalculator — Calculates masses and mass-to-charge ratios of RNA sequences (UTIL)
  • MapAlignerTreeGuided — Aligns maps through hierarchical clustering based on distances computed between shared IDs.

Changed Tools:

  • OpenPepXL and OpenPepXLLF runtime and memory efficiency improved by orders of magnitude
  • IDFilter can now filter by using all MetaValues available in the ID files
  • ImageCreator uses updated gradients and has gained RT and m/z filtering options (PR #4188)

Status changed:

  • OpenPepXL (UTIL -> TOPP)
  • OpenPepXLLF (UTIL -> TOPP)

Best regards,
The OpenMS developers