Dear OpenMS-Users,

We are proud to announce the release of OpenMS 3.5. Grab it here.

A couple of things are different this time:

  • This will be the last release for MacOS Intel. We will continue providing docker images for AMD64 processors here: https://github.com/OpenMS/OpenMS/pkgs/container/openms-tools-thirdparty. If that doesn’t work, and you desperately need continued MacOS Intel support, please reach out to us at info@openms.de
  • We now have ARM64 Linux support! Both for OpenMS and pyOpenMS. These also run on MacOS silicon.
  • We will be using Github as opposed to our traditional archive as the primary repository of installers.
  • We are now a 501c3! For any nonprofit nerds out there, we’ve put together a legal entity to ensure the long term stability of OpenMS.

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

NOTICE: 3.5.0 is going to be the last official release for MacOS on Intel processors. If you need support for OpenMS on that platform moving forward, please contact us.

General

Speed improvements:

  • Loading .gz files is about 7% faster (#8069)
  • Loading of mzML files with more than m/z+intensity (e.g. ion mobility) is 20-40% faster (#8074)
  • Loading of mzML files is 7-25% faster in general (SIMD ASCII conversion) (#8105)

Linux arm64 support:

  • OpenMS releases now include a .deb for arm64 machines

Dependencies

  • PyOpenMS now depends on Autowrap 0.24.0
  • PyOpenMS now supports Cython 3.1
  • CMake now accepts Eigen 5 in addition to Eigen 3.4+ (#8366)
  • Apache Arrow/Parquet integration for high-performance columnar data export (#8091, #8145)

PyOpenMS

  • PyOpenMS now has wheels for arm64 linux machines
  • PyOpenMS wheels are now available for Python 3.14 on all supported operating systems
  • Parquet support enabled in pyopenms wheels (#8422)
  • BREAKING: DataFrame column names standardized to lowercase snake_case for PEP 8 compliance. Affected methods: MSSpectrum.get_df(), MSChromatogram.get_df(), ConsensusMap.get_metadata_df(), FeatureMap.get_df(). Example changes: RT → rt, MZ → mz, nativeID → native_id, precursorMZ → precursor_mz. Update code that references old column names.
  • Pythonic convenience methods added:
    • __len__() for MSSpectrum, MSChromatogram, MSExperiment, AASequence (#8151, #8415, #8417)
    • __str__() and __repr__() for core classes (#8429)
    • Python accessors for drift time on MSSpectrum and OpenSwathSpectrum (#8423)
  • New Python bindings for Mobilogram and MobilityPeak1D classes (#8377)
  • DataFrame wrapper for MSSpectrum with get_df() method (#8435)
  • Enum class support in Python bindings with IntEnum (#8405)
  • Static methods to query enum names for METADATA classes (#8353)
  • Fix: PyOpenMS import no longer affects Python locale settings (#8322)
  • Improved pyOpenMS documentation for Feature, MRMFeature, FeatureMap classes (#8247)

TOPP Tools

Changes

FileFilter:

  • Filter RT by blocks of MS levels (#8239)

SageAdapter:

  • Improved parameter documentation and tolerance validation (#8259)
  • Now correctly passes threads parameter via RAYON_NUM_THREADS (#8260)

CometAdapter:

  • All enzymes now available by adding CometIDs to database (#8280)

DecoyDatabase:

  • Added repeated shuffle option for improved decoy generation (#8339)

MassTraceExtractor:

  • Support for Bruker Ion Mobility (experimental). Note: requires IM peak picked data.

FeatureFinderCentroided, FeatureFinderMetabo, FeatureFinderMultiplex:

  • FAIMS support (experimental): Automatic detection and separate processing of FAIMS compensation voltage (CV) groups. Features from different CVs representing the same analyte are merged by default.

FeatureFinderMetaboIdent, FeatureFinderIdentification:

  • FAIMS support (experimental): Automatic detection and separate processing of FAIMS compensation voltage (CV) groups. Features from different CVs representing the same analyte are merged by default.
  • Bruker TimsTOF ion mobility support (experimental): Requires concatenated IM spectra in mzML format (use msconvert with --combineIonMobilitySpectra option). IM values can be specified in the input TSV/idXML.

NucleicAcidSearchEngine:

  • Add support for global fixed modifications as a search parameter

Digestor:

  • Supports replacing ambiguous amino acids (X,B,J,Z) in the FASTA input with random unambiguous amino acids in the output (#8167)

All:

  • Show load/store progress for files in all TOPP tools (#8041)

IonMobilityBinning:

  • Detect FAIMS data automatically and split output per FAIMS compensation voltage (CV)

FLASHDeconv:

  • Major update with improved scoring, FDR estimation, and isobaric quantification support (#8257)
  • Automatic mass tolerance estimation from data
  • Per-MS-level deconvolved spectrum outputs
  • TopFD version 1.7 compatible feature and TSV export formats
  • Improved precursor mass assignment for MSn spectra

Added Tools

  • OpenNuXL - A peptide-RNA/DNA cross-linking search engine
  • PeptideDataBaseSearchFI - Experimental peptide database search engine using a fragment index (FI) and the new PeptideSearchEngineFIAlgorithm
  • FeatureFinderLFQ (experimental) - Feature detection for label-free proteomics DDA-LFQ based on the Biosaur2 algorithm with support for FAIMS and TimsTOF ion mobility
  • PeakPickerIM - Ion mobility peak picker for TimsTOF and other IM data. Supports three methods: mobilogram-based, clustering, and elution profile-based picking. Supports both in-memory and low-memory streaming modes. (#8177)
  • IsobaricWorkflow (experimental) - Simple, targeted, fast workflow for isobaric quantification (#7298)

Removed Tools

  • OpenPepXLLF - Experimental search for cross-linked peptide pairs in tandem MS spectra (showed inferior performance in benchmarks)
  • IDMassAccuracy - Calculates a distribution of the mass error from given mass spectra and IDs
  • SpecLibCreator - Creates an MSP formatted spectral library
  • SpecLibSearcher - Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library

GUI Tools

  • Fix TOPPAS crash when using TOPP tools with multiple output formats (#8120)

OpenMS Library

Added

  • PeakPickerIM (experimental): New algorithm for ion mobility peak picking with three methods (mobilogram, cluster, elution profiles). (#8177)
  • IMFormat: Added CENTROIDED and UNKNOWN format types for ion mobility data. (#8177)
  • MSSpectrum/SpectrumSettings: Added setIMFormat()/getIMFormat() API for per-spectrum ion mobility format tracking. (#8177)
  • FeatureFinderAlgorithmBiosaur2 (experimental): Feature detection algorithm for label-free proteomics DDA-LFQ based on the Biosaur2 algorithm with support for FAIMS and TimsTOF ion mobility.
  • PeptideHit: Added TargetDecoyType (TARGET, DECOY, TARGET_DECOY, UNKNOWN) and setTargetDecoyType()/getTargetDecoyType(); supports target+decoy peptide hits.
  • IDScoreSwitcherAlgorithm: Added findScoreType() method for generic score type detection. Checks if main score matches requested ScoreType (PEP, QVAL, FDR, etc.) or finds it in meta values.
  • ProteinHit: Added TargetDecoyType (TARGET, DECOY, UNKNOWN) and setTargetDecoyType()/getTargetDecoyType().
  • Both: Added isDecoy().
  • Unify isotopic distributions (coarse vs. fine) for EmpiricalFormulas with charge (#8099)
  • FragmentIndex (experimental): New fragment index for fast peptide fragment lookup supporting FI-based peptide database search.
  • PeptideSearchEngineFIAlgorithm (experimental): Library algorithm leveraging FragmentIndex for peptide database search; used by the PeptideDataBaseSearchFI TOPP tool.
  • AhoCorasick: Improved high-performance string matching algorithm with path compression (#8269, #8304)
  • HashGrid: Exposed cellIndexAtClusterCenter method (#8318)

Changes

  • Removed assignRanks and sortByRanks in PeptideIdentifications and sort and filter by score instead. Also removed updateHitRanks in IDFilter (#7991)
  • Remove rank member in PeptideHit and store ranks as meta value (for backwards compatibility). (#7997)
  • std::vector<PeptideIdentification> now is encapsulated in a class PeptideIdentificationList.
  • Zlibcompression using zlib (not Qt) and Base64 decoding for zlib-compressed data using SIMD (not Qt) (#8161)
  • Exception::InvalidSize now includes mandatory context message (#8437)
  • Matrix::operator== no longer throws assert when comparing different-sized matrices (#8305)
  • Removed boost::smart_ptr dependency, using std::shared_ptr instead (#8405)
  • C++20 modernization: std::erase_if, range-based for loops, default constructors (#8229, #8230, #8233)

New Features

  • FAIMSHelper: dataset-wide FAIMS detection; ignore DRIFTTIME_NOT_SET sentinel; improved warning
  • IMDataConverter::splitByFAIMSCV: retain MS2 without explicit FAIMS CV by assigning to prior FAIMS CV
  • Added EnzymaticDigestion.semiSpecificDigestion_()
  • ProteaseDigestion: Add support for semi-specific digestion (#8130)
  • TransformationModelLowess: Add option to automate span selection via cross-validation (#8166)
  • OpenSwath:
    • Added automated iRT calibration using input transition list (#8146)
    • Added automated RT, m/z, and IM extraction window estimation based on iRT calibration (#8188)
    • Added lowess span grid search params and updated documentation for OpenSwathWorkflow TOPP tool (#8297)
    • Added priority inclusion list for iRT sampling from PQP when using automated iRT calibration (#8373)

Fixes

  • Fix overlap test in crowded FAIMS data (#8418)
  • Fix window estimation when no MS1 maps available in OpenSwath (#8308)
  • Fix column header filenames for all maps in Decharger/MetaboliteAdductDecharger (#8265)
  • Fix ternary operator misuse in FileMerger append_method logic (#8263)
  • Fix Qt6 deprecation warnings (#8248)
  • Fix FileNotFound exception misuse for file access errors (#8274)
  • Fix peaks being skipped in OpenSwath wide boundary selection method (#8316)
  • Fix mzTab-M validation errors for missing identification and database metadata (#8363)
  • Fix negative offset handling in mzML readers (#8336)

Documentation

  • Build instructions rewritten for macOS and Linux (#8042)
  • Comprehensive documentation added to DeMeanderize tool (#8264)

Best regards,
The OpenMS-Developers