Dear OpenMS-Users,

we are proud to announce the release of OpenMS 3.3. Grab it here

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

What’s new:

  • Changes breaking backward compatibility:
    • the QualityControl TOPP tool has some renamed parameters and supports output directories (#7497)
  • Low-level peak extraction helper for MSExperiments (#7628)
  • pyOpenMS: use Numpy2 (#7539)
  • Docker files are now part of the main OpenMS repo (#7303)
  • Added new functionality to SageAdapter + compatibility with new Sage versions (#7577)

Misc:

  • FileInfo:
    • support MzTab files (#7568)
  • TOPPAS
    • supports writing results to output directories (for TOPP tools that have such parameters) (#7497)
    • TOPPAS tutorial enhanced (#7497)
  • FeatureFinderMetabo
    • added report_smoothed_intensities parameter (#7594)
  • Write out percolator features in search engine adapters (by default, no PSMFeatureExtractor is needed)
  • Add isobaric correction defaults for tmt6plex and 11plex (#7601)
  • Decoy phosho added to unimod.xml (#7612)
  • Add additional convenience functions for MSExperiment (#7630)
  • Improve file list comparison (#7645)
  • pyOpenMS: Add more convenient constructor for AASequence (#7650)
  • Add annotate_features param in Deisotoper.cpp (#7643)
  • internal enhancements (#7652)

Fixes:

  • OpenMS does not compile when using GLPK (instead of COINOR) (#7626)
  • fix MassCalculator error (‘residue type has no name’) (#7698)
  • pyOpenMS
    • get_feature_df() in MRMTransitionGroupCP, output is now as expected (#7646)
  • Fix scan number extraction for merged spectra (#7599)
  • Cmake fix (#7625)
    • use Boost config instead of find module (new policy of CMake)
    • escape quotes in whitespace strings
    • remove invalid PRE_BUILD option (in combination with OUTPUT)
    • update diff regex and actual results (which seem to have changed with recent Sage versions…)
  • MzTab: preallocate enough memory instead of allocating in the loops (#7624)
    • add check that otherwise will result in out of memory error
    • reduce memory fragmentation on huge files
  • KNIME Plugin: Fix categories (#7622)

Best regards, The OpenMS-Developers