OpenMS 2.6.0

Dear OpenMS-Users,

we are proud to announce the release of OpenMS 2.6.0. Grab it here: https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/2.6.0

Our bioconda packages are available here https://anaconda.org/search?q=OpenMS

KNIME plugins are available soon via the KNIME update mechanism.

And our pyOpenMS 2.6.0 packages will be available soon here https://pypi.org/project/pyopenms/

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


We now create nightly pyopenms wheels (https://pypi.org/project/pyopenms-nightly/) and conda packages (https://anaconda.org/OpenMS/)

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

Various:

  • 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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Bleeding edge, unsupported, nightly builds (i.e. developer snapshots) of OpenMS are available from our: unstable nightly build archive. Use at your own risk.

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More information

For additional information about OpenMS command line tools please visit the Getting Started page.