Dear OpenMS-Users,

We are proud to announce the release of OpenMS 3.4.1. Grab it here

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

—- OpenMS 3.4.1 (May 2025) —-

Documentation:

  • TOPPAS: tutorial update (#8025)

Fixes:

  • TOPPView: fix a few error messages boxes (in IM frames, and 2D projections) (#8047)
  • RANSAC algorithm: avoid r^2 is zero; fixes crash in OpenSwathWorkflow (#8052 )

—- OpenMS 3.4.0 (May 2025) —-

General:

  • OpenMS now expects a compiler that supports C++20
  • OpenMSInfo TOPP tool now informs about custom CXX compile flags (#7846)
  • speed improvements:
    • TOPP tool FeatureFinderCentroided TOPP tool is 28-44% faster (internally GaussTraceFitter is 4-7x faster) (#7950)
    • mzML parsing is 6% faster (#7850)

Dependencies:

  • switch to Qt 6 (>= 6.5) (#7525)

OpenSwath:

  • changes to -out_features (# 7793)
    • Deprecate .tsv feature output
    • Deprecate -out_osw, -out_tsv. -out_features is used for outputting .osw or .featureXML files and file format is autodetected.
    • Enable outputting any feature file (.osw or .featureXML) from a .tsv library
  • add warning message if irt_im_extraction_window not set and im_window is set (#7813)
  • add auto add up spectra across the peak width in retention time for ion mobility extraction (#7742)
  • add peak-picking for extracted ion mobilogram (#7759)
  • add ion mobility scoring for identifying transitions for IPF (#7760)
  • bug fix: pass im_range to scoreIdentification_ instead of computing it in the function. Addresses issue #7883. (PR #7885)

Misc:

  • pyOpenMS: improve developer experience (installation/compilation) (#7735)
  • TOPP tools and TOPPAS/ExecutePipeline return exit code 14 when external third-party tools (such as Comet or Sage) are not found (#7758)
  • ProteinInference tool: Algorithm:score_type allows switching the main score (e.g., “RAW”, “PEP”) for BasicProteinInference. (#7769)
  • README.md: Added dedicated “Building OpenMS” section with direct links to platform-specific build instructions (#7912)
  • TOPPAS: tutorial now includes Pipeline and Node updating (#8025)

Fixes:

  • fix AScore algorithm when counting phosphorylation events (#7905)
  • add option to PeakFileOption to ignore loading of chromatograms or spectra from mzML (#7901)
  • fix Doxygen Docs contain stty warning for TOPP tool output (#7865)
  • fix various issues with the Windows installer (#7995, #7996, #8001)
  • TOPPView: open theoretical spectra immediately in 1D to avoid crash when opening in 3D mode (#8019)

Library:

  • IDScoreSwitcherAlgorithm: Added switchToScoreType and switchBackScoreType methods for score switching and reversion. (#7769)
  • made FASTA file reader more robust in presence of whitespaces (#7960)
  • add 3' cyclophosphate version of RNAse 4, fix handling of cleavage gains (#7928)

Removed tools:

  • XTandemAdapter
  • MascotAdapter (note: MascotAdapterOnline still exists) (#7927)

Best regards, The OpenMS-Developers