OpenMS 2.6.0

Dear OpenMS-Users,

we are proud to announce the release of OpenMS 2.6.0. Grab it here:

Our bioconda packages are available here

KNIME plugins are available soon via the KNIME update mechanism.

And our pyOpenMS 2.6.0 packages will be available soon here

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

We now create nightly pyopenms wheels ( and conda packages (

Adapters/Third-party support:

  • LuciphorAdapter now stores which modifications were used for localization (#4771) and localization scores are reported in mzTab #4772
  • Added Percolator3.0 support, fixed ConsensusID reading from wrong (Percolator-overwritten) meta data (#4829), and adapted the Regex parsing of XTandem Percolator output files #4849
  • Added options introduced in new MSGF versions #4713
  • Updated IsoSpec fine structure isotopic calculator sources to v 2.1.0 #4733
  • Updated other third-party tools

What's new:

  • Introduced a Wizard for Swath data (#4647 #4706 #4758 #4769 #4773 #4837), which also reports summary statistics about Swath TargetedExperiments #4788 #4790
  • UTIL StaticModification: Applies a set of modifications to all PeptideIDs in an idXML file (UTIL)
  • TOPP DatabaseSuitability: Computes a suitability score for a database which was used for a peptide identification search. Also reports the quality of LC-MS spectra. #4791 #4781 #4814
  • Added support for QC of labeled experiments (iTRAQ/TMT)
  • Added automated QC computations for MRM (#4637)
  • Adapted consensusXML and mzTab to support protein groups (#4630)
  • Consensus/IDMerger: Introduced use of merge idx to ensure keeping track of primaryRuns
  • Epifany: Added calculation of protein group FDR, ID filtering for protein group scores (#4802) and support for inference on not just individual samples but also consensusXML files
  • FeatureFinderCentroided/FeatureFinderAlgorithmPicked: Improved runtime performance #4652 #4701
  • FeatureFinderIdentification: Improved SLIM-labeling experiment support
  • FileConverter: Improved runtime performance when producing mzML output #4750
  • FeatureLinkerQT: Introduced Fibonacci heaps for large runtime optimization (#4721) and fixed related preconditions/segfaults #4756 #4760 #4778
  • IDFilter: added support for consensusXMLs #4798 #4799
  • MapAlignerIdentification: New option to use an "identity" transformation when data is too sparse to determine alignment model #4628
  • MzTabExporter: changed to only export one main score, and to derive nativeIDs from data (#4767). Now ensures that all output rows contain the same number of columns #4801
  • MzTabExporter on LFQ consensusXMLs produces 100% PRIDE validated mzTabs now
  • ProteomicsLFQ: Added spectral counting as quantification method (#4726). Introduced performance improvements for AASequence and string parsing, especially for modified sequences. Various further improvements (e.g. #4669)
  • SimpleSearchEngine (multithreaded), TheoreticalSpectrumGenerator, MSSpectrum: Runtime optimization #4709
  • Further introduction of more file streaming to address possible memory consumption issues #4682 #4694

Further fixes:

  • We now limit double precision to 17 digits during file writes #4636
  • Ensure that CometAdapter always writes indexed mzML fixes for CometAdapter (#4653), fixed the writing of terminal modifications with specific origin in Comet (#4742), the writing of protein terminal mods in Comet and MSGF adapter #4710, and the Comet pepXML modification parsing #4755
  • Removed secondary search engine settings duplication in mzTab MTD section. #4720
  • Improved XTandem output protein parsing #4789 to fix Issue #4770
  • Increased (partial) support for parsing mzid with nonstandard, non-CV-term scores, fixes #4859
  • Fixes to NucleicAcidSearchEngine mzTab output #4692
  • ConsensusID now passes spectrum reference meta values along #4703
  • Fix to LFQ requantification #4633
  • Improved MapAlignerTreeGuided memory usage (#4704) and fixed segfault when featureXML contains no IDs #4665
  • TOPPAS fixes #4780


  • OMMSAAdapter now writes out native ids and spectrum references #4852
  • FileInfo: Report more charge distribution and MS2 activation-method information for Raw files #4836
  • Added sum formula output in RNAMassCalculator #4677
  • Added automatic OpenMS tool reporting of peak memory usage #4712
  • Some extra tools documentation outputs #4822 #4823
  • Extended mapping of filetypes and mimetypes for knime output formats documentation #4839
  • RTEvaluation: fixed output formats #4533
  • Some further clarifications, standardization/consolidation of outputs formats/consistency
  • Continued fixes/improvement of documentation
  • Removed deprecated version of PeakPickerHiRes (LowMemPeakPickerHiResRandomAccess and LowMemPeakPickerHiRes). Their functionality can be accessed through options of PeakPickerHiRes

Best regards, The OpenMS-Developers


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