release/3.5.0

Dear OpenMS-Users,

we are proud to announce the release of OpenMS 3.5.0. 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 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 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 file...

release/3.4.1

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:

---

Minor updates to the Dockerfile.

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 )

---

Best regards,
The OpenMS-Developers

release/3.4.0

Dear OpenMS-Users,

we are proud to announce the release of OpenMS 3.4. Grab it here

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

---

General:

• OpenMS now expects a compiler that supports C++20
• OpenMSInfo now informs about custom CXX compile flags (#7846)
• speed improvements:
  • TOPP tool FeatureFinderCentroided 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)

Fixes:

• 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)

Library:

• IDScoreSwitcherAlgorithm: Added switchToScoreType and switchBackScoreType methods for score switching and reversion. (#7769)

• Made FASTA file reader more robust in presence of whitespaces

• removed tools:

  • XTandemAdapter
  • MascotAdapter (note: MascotAdapterOnline still exists)

---

Best regards,
The OpenMS-Developers

release/3.3.0

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

release/3.2.0

Dear OpenMS-Users,

we are proud to announce the release of OpenMS 3.2.
The source code and precompiled installers (Windows, Linux, MacOSX) are available at the bottom of this page or here.

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

---

What's new:

• Changes breaking backwards compatibility:
  • Rename of parameters for TOPP tool FeatureFinderCentroided (debug -> advanced), and PeakPickerWavelet/TOFCalibration (optimization -> optimization:type) (#7154)
  • Rename of parameters for TOPP tool IDFilter (score:pep -> score:psm; score:prot -> score:protein; score:protgroup -> score:proteingroup) with 'nan' as new default (#7541)
  • 3.2.0 KNIME package requires KNIME 5.3 or later
• Support for SubsetNeighborSearch (SNS) via DecoyDatabase (#7565)

Library:

• Extend FileHandler to support load and store operations for our major datastructures (spectra, features, identifications, etc.). Replaced file type specific code with the more generic FileHandler calls to decouple the IO code from other parts of the library.
• SiriusAdapter reworked to SiriusExport: Instead of running SIRIUS directly, this reworked tool takes multiple mzML and feautureXML (optional) files exporting a single SIRIUS .ms input file as well as an input table with compound info from features for the new AssayGeneratorMetaboSirius tool. (#7234)
• Splitting AssayGeneratorMetabo into two tools: In line with the changes to SiriusExport this tool has been split into two separate workflows. AssayGeneratorMetabo generates an assay library from mzML and feautreXML files using an heuristic approach picking the highest intensity MS2 peaks (like before). AssayGeneratorMetaboSirius takes an existing SIRIUS project directory as input to generate an assay library based on fragmentation trees. (#7234)
• better documentation for all SpectraFilter... tools (#7183)
• TOPPView:
  • offer Ion mobility view from 2D spectra view (#7423)
  • view ion mobility frames, irrespective of its MS level (formerly only MS1 was supported) (#7427)
• OpenSwath: Add output on peak shape metrics to .osw file (#7222)

New Tools:

• IonMobilityBinning - Merges spectra with similar IM values and creates N output mzML's by discretizing the IM range (#7459)
• AssayGeneratorMetaboSirius -- Assay library generation from a SIRIUS project directory (Metabolomics)
• SiriusExport -- Metabolite identification using single and tandem mass spectrometry

Fixes:

• FileConverter: more robust (#7176)
• MSFragger: allow relative path to database (#7155)
• MSGFPlusAdapter: allow concurrent creation of indexed database (#7272)
• CometAdapter: work around bug in Comet 2024.01 rev. 0 to avoid empty results (#7540)
• ParamEditor: fixed error for the subsection parameter (ParamNode) to go through store function (#7180)
• TOPPView:
  • fix crash when viewing certain Chromatograms (#7220)
  • in 2D view, show correct adjacent layers in context menu, if user clicked to the right of the last MS1 scan (now shows the 4 rightmost MS1 scans, used to show the 4 leftmost scans) (#7423)
  • fix glitches in 1D view and layer names (#7549)
  • Show prefix ions (e.g. b1) when generating theoretical spectra (#7567)
• TOPPAS: open files in TOPPView (#7213)
• pyOpenMS: Log warnings in pure Python code with warnings.warn instead of print (#7418)
• more robust parsing of mzIdentML (#7153)
• OpenSwath: Fix bug in diaPASEF window determination (#7546)

Misc:

• FileInfo: Report ion mobility ranges (if any) (#7459)
• OpenMSInfo reports the ILP solver (CoinOr or glpk) (#7156)
• add citation information for OpenMS 3.0 (Nat. Methods) (#7383)
• Add export for Common Workflow Language (CWL) (#6156)
• Add tool description lib (TDL) dependency (#6156)

Changed/new parameters: see CHANGELOG_PARAMS for details

Note: The goal of our library is to provide useful, reusable code in a way that’s easy to understand and use.
To make OpenMS simpler, more focused and more accessible we gradually remove potentially outdated tools and algorithms.
If you, as a user, are negatively affected by this step please contact us. We listen to our users and will try to find
an alternative solution or reverse a particular decision for removal.

Cleanup/Removal:

• removed tools:

  • SpectraFilterMarkerMower -- Applies thresholdfilter to peak spectra (#7183)
  • FeatureFinderIsotopeWavelet -- Detects two-dimensional features in LC-MS data
  • PeakPickerWavelet -- Finds mass spectrometric peaks in profile mass spectra
  • PrecursorMassCorrector -- Corrects the precursor entries of MS/MS spectra, by using MS1 information
  • TOFCalibration -- Applies time of flight calibration
  • ERPairFinder -- Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans
  • RNPxlSearch -- Annotate RNA/DNA-peptide cross-links in MS/MS spectra
  • SpectraFilterSqrtMower -- Applies thresholdfilter to peak spectra
  • FeatureFinderMRM -- Detects two-dimensional features in LC-MS data
  • MapAlignerSpectrum -- Corrects retention time distortions between maps by spectrum alignment
  • ProteinResolver -- protein inference
  • SiriusAdapter -- Tool for metabolite identification using single and tandem mass spectrometry
  • SpectraFilterBernNorm -- Applies thresholdfilter to peak spectra
  • SpectraFilterScaler -- Applies thresholdfilter to peak spectra

• removed library code:

  • HiddenMarkovModel
  • PeakPickerMaxima
  • DeNovo related, old marker code

• removed tutorials:

  • Tutorial_PeakPickerCWT
  • Tutorial_TOFCalibration

• removed tests:

  • TOFCalibration_test
  • ContinuousWaveletTransformNumIntegration_test
  • ContinuousWaveletTransform_test
  • FeatureFinderAlgorithmIsotopeWavelet_test
  • IsotopeWaveletTransform_test
  • IsotopeWavelet_test
  • OptimizePeakDeconvolution_test
  • OptimizePick_test
  • PeakPickerCWT_test
  • PeakShape_test

• Deprecated (and likely removed in the next release)

  • XTandemAdapter

---

Best regards,
The OpenMS-Developers

OpenMS 3.1.0

Dear OpenMS-Users,

We are excited to share an experimental update with our community, mainly targeted at platforms that depend on Conda packages.
Please note that this is a partial and unannounced release, focused on delivering novel features and major changes that we're actively testing and refining.
While these features are still in an experimental phase, we encourage adventurous users and platform integrators to explore and provide feedback.

The source code and precompiled installers (Windows, Linux, MacOSX) are available at the bottom of this page or here.

Note: the Windows installer has been updated (Nov 16th 2023) to re-establish functionality of the OpenMS GUI tools (like TOPPView, TOPPAS etc) - which were misconfigured in the first release.

Important Notes:

• Features are experimental and may undergo changes or be removed in future releases based on user feedback and stability.
• We welcome your feedback and suggestions to help us improve and refine these experimental features.
• For stability and production use, we recommend sticking with the latest stable release.

Please use this opportunity to test and provide feedback on these new features, as your input will play a vital role in shaping their development.

Thank you for being a part of our community and for helping us make OpenMS even better!

What's new:

• Major change: removed the distinction between TOPP tool and util and the TOPP and UTIL build targets were merged to a single TOPP target. All utils are considered tools now and categorized as "Utilities".
• Added SageAdapter. Support for standard identification tasks with sage (https://github.com/lazear/sage) (experimental).
• Require some advanced instruction sets for x64 CPUs: SSE3 (g++/clang) or AVX (MSVC); and NEON for ARM64 CPUs (#6978)
  and report them via the OpenMSInfo tool (#7022)
• Base64 encoding/decoding using the SIMDe library (#6978)
• Filter features in ProteomicsLFQ according to feature p-value (additional parameters feature_with(out)_id_min_score, MBR is automatically active if targeted_only = false)

Fixes:

• Fix a crash when loading mzML data with multiple threads which contains non-MS spectra, e.g. 'electromagnetic radiation spectrum' (#7011)
• InternalCalibration: improve visualization of calibration plots (#7064)
• Restore TOPPAS tutorial (#7076)
• various low impact UBSan fixes
• make mzData more robust against wrong 'length' attributes for binary data (#7113)

Misc:

• Report reading/writing throughput (MiB/sec) when loading/storing mzML (#7035)
• Add ability to create decoy features in FeatureFinderIdentification
• Restore developer quick guide in Doxygen docu - see https://openms.de/current_doxygen/html/index.html (#7109)
• Updated the changelog helper to set LD_LIBRARY_PATH automatically and other fixes
• Added "area" column to EICextractor output

Cleanup of old/unused tools and code:

• Removed old tools and associated code in the library for InclusionExclusionListCreator, SvmTheoreticalSpectrumGenerator, PrecursorIonSelector, and MSSimulator
  Note: general SVC and SVR is still supported with the SimpleSVM class.
• Removed old RT and PT predict code and tools RTModel, RTPredict, PTModel, PTPredict, RTEvaluation and associated library code (SVMWrapper and LibSVMEncoder).
• Removed PepNovoAdapter
• Removed CompNovoAdapter and library code
• Removed simplistic evaluation tools FFEval, LabeledEval, TransformationEvaluation
• Removed EnzymaticDigestionLogModel
• Removed FidoAdapter (same functionality now in our own inference engines)

Full Changelog: Release3.0.0...Release3.1.0

OpenMS 3.0.0

Dear OpenMS-Users,

we are proud to announce the release of OpenMS 3.0.0 (June 2023).

The source code and precompiled installers (Windows, Linux, MacOSX) are available at the bottom of this page or here.

For detailed installation instructions and more options, please visit https://openms.readthedocs.io/en/release3.0.0/openms-applications-and-tools/installation.html.

This is a full release, i.e. a major version increase from 2.0 to 3.0. Highlights of these changes are listed at the end of this page.

Note: The Windows-Installer has been updated on Nov 16th 2023 to allow installation on systems with a lot of other software preinstalled (potentially leading to errors during installation of OpenMS).

Important changes to the previous version 2.8 from Feb 2022:

---

New Tools:

• FLASHDeconv -- Ultra-fast high-quality deconvolution enables online processing of top-down MS data (TOPP)
• FLASHDeconvWizard -- A GUI assistant for FLASHDeconv execution.

New Features:

e.g.

• TMT18plex support (#6390)
• ProteinQuantifier supports iBAQ (#6107)
• OpenSwath: Add support for diaPASEF data with overlapping m/z and IM windows, and add new outputs on ion mobility features (delta_im), IM calibration (#5911, #6234, #6268)
• OpenSwathDecoyGenerator speed improvement and remove duplicates (#6054)
• NucleicAcidSearchEngine (NASE): user defined ribonucleotides with phosphorothioate linkages (#6337), JSON based ribonucleotides and updated to latest Modomics database (#6482)
• TargetedSpectraExtractor: more features (#6106)
• TOPPView: TheoreticalSpectrumGenerationDialog now supports generation of isotope patterns for metabolites (#6023); faster loading of external drag'n'drop data (#6837)
• colored commandline/console on all platforms (#6275)
• support for 'no cleavage' for XTandemAdapter and CometAdapter (#6133).
• Percolator pin file reader (#6824)
• JSON export for OMS files(SQLite) (#6114)
• ParamEditor with more convenient StringList editing (#5135)
• load parameter values from a JSON formatted .json file. (Accessible via -ini. This will be
  helpful for Common Workflow Language users and others)
• FileFilter can remove convex hulls of features and consensusFeatures to reduce file size (#6140)
• Faster compile time (#6618)
• Improving code quality by fixing lots of linting warnings and leaks (e.g. #6839, #6831, #6829)

Documentation

• website redesign (visit openms.org)
• OpenMS user documentation is moved to openms.readthedocs.io/en/latest.
• OpenMS API reference and advanced developer documentation remains inside OpenMS doxygen
  documentation (https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/release/)
• pyopenms: pyopenms-extra is renamed to pyopenms-docs.

Bug fixes

e.g.

• GaussFilter when using ppm as width (#6830)
• NASE a-B ion masses (#6718), ID-Mapper for TMT data (#6758)
• FeatureFinderMetaboliteIdentification speed improvements (#6619)
• IDRipper speed improvements (#6584)
• Honor MissedCleavages in SimpleSearchEngine (#6889)
• TOPPView: fixed lots of display glitches, e.g. axis labels, goto dialog and easier re-use of components, etc (#6673, #6616, #6592, #6703, #6793)
• mzTab fixes for empty IDs (#6445)
• Fix GNPS error for empty scans in Bruker files (#6898)
• PrecursorPurity: handle unknown charge (#6283)
• OpenSwath: Fix duplicated transition error when multiple genes map to a single peptide (#5653)
• Fixed race condition when logging messages.

Removed tools:

• InspectAdapter
• OMSSAAdapter
• MyriMatchAdapter
• CruxAdapter

Supported compilers (when building from source):

• g++ (7.0 or later, tested up to v13.0)
• clang (?, tested up to v16)
• Visual Studio (2019(v16.8.4) or later)

Full changelog: OpenMS 2.8 → 3.0

---

OpenMS 2.0 → 3.0 highlights

• FLASHDeconv and FLASHDeconvWizard: Harness ultra-fast high-quality deconvolution of top-down MS data. These tools enable rapid and accurate deconvolution, ensuring efficient and precise data analysis.

• NucleicAcidSearchEngine: Enter the world of RNA analysis with NucleicAcidSearchEngine, a tool that annotates nucleic acid identifications to MS/MS spectra.

• OpenPepXL, OpenPepXLLF and related tools: Perform comprehensive protein-protein cross-link analysis covering a wide range of chemical cross-linkers.

• Epifany: Take your protein inference to new heights with Epifany, a Bayesian protein inference tool that offers accurate and reliable results for complex proteomics analyses.

• FeatureFinderMetaboIdent: Detect features in MS1 data based on metabolite identifications with FeatureFinderMetaboIdent. This tool enhances metabolomics analyses by accurately identifying features for further investigation. Check out our Umetaflow workflow or the pyopenms documentation for details.

• GNPSExport: Export consensus features into MGF format with GNPSExport. This tool simplifies data sharing and collaboration, streamlining your data analysis workflow.

• ProteomicsLFQ: Explore a standard proteomics LFQ pipeline in a single tool: ProteomicsLFQ. A tool designed for reliable quantification of proteins.

• QualityControl: Compute various QC metrics from input files with QualityControl, providing essential quality assessments for your data. This versatile tool offers a comprehensive view of data quality.

• Optimized RT alignment with MapAlignerTreeGuided, a new tool that aligns maps through hierarchical clustering based on shared IDs.

• MetaProSIP, the tool for protein-SIP experiments gained support for Deuterium and heavy Oxygen labeling.

General Enhancements: Streamlining your developer experience
The OpenMS 3.0 codebase has been updated to C++17. Additionally, the configuration storage path on Linux has changed to ~/.config/, making it easier to manage user-specific configurations.

Library and Performance Improvements: Enhancing Data Analysis
The OpenMS library has undergone significant updates, resulting in improved mass calculations, peak integration, and isotope distributions. The library now supports more precise peak integration methods, ensuring the accuracy and reliability of your data analysis.

User Interface and Usability: Enhancing Your Workflow
Several GUI tools have received notable improvements in OpenMS 3.0. TOPPView, TOPPAS, and ParamEditor have been enhanced for better usability and additional data visualization capabilities.

Module Removals and Deprecated Tools: Streamlined and Focused
OpenMS 3.0 removes several deprecated modules and tools. This focused approach ensures a more efficient and effective user experience.

For an exhaustive list of changes between OpenMS 2.0 - OpenMS 3.0 please refer to the changelogs.

Best regards,
The OpenMS-Developers

OpenMS 2.8.0

Dear OpenMS-Users,

we are proud to announce the release of OpenMS 2.8.0. Grab it
here

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

---

• source + conda release only. This means installers, workflows and GUI are untested.
• Restructuring of Imported CMake targets and pyOpenMS CMake
• Reduce exposition of third-party libraries to interface
• greatly improved pyOpenMS documentation and extra functions (in the pyopenms-extra submodule)
• Fixes IDMapper for isobaric labelling experiments (will lead to much more identifications)
• Deisotoping algorithm using KL
• PeptideIndexer supports ambiguous AA's in Peptide sequence (as reported by recent Mascot versions) (#5776)
• SeqAn external library removed from source tree (not needed anymore)
• Resolve compatibility issues between IDRipper and IDMerger (#4957)
• Basic MzTabM support for AccurateMassSearch
• Changed default parameter keep_unidentified_masses to "true" (AccurateMassSearch/AccurateMassSearchEngine)

---

Best regards,
The OpenMS-Developers

What's Changed

• Added wrap-doc methods #8 by @rahul799 in #5459

• Code Arrangement Changes #8 by @Arraxx in #5476

• code arrangement changes -10 by @Arraxx in #5492

• [Update] Allow more isotope errors in Comet by @jpfeuffer in #5502

• [FIX] Better error message for nr runs in PLFQ IDs by @jpfeuffer in #5503

• [FIX] Add origin for simulated IDs by @jpfeuffer in #5504

• [Feature] picked protein fdr by @jpfeuffer in #5488

• [Fix] picked protein fdr by @jpfeuffer in #5509

• Update Plot2DCanvas.cpp by @timosachsenberg in #5480

• code arrangement changes -14 by @Arraxx in #5510

• Code Arrangement changes-15 by @Arraxx in #5519

• adding-wrap-doc-method-17 by @rahul799 in #5520

• fix bug if experimental design is not given by @timosachsenberg in #5522

• fix bug in Epifany introduced by new ParamValue class by @timosachsenberg in #5527

• adding-wrap-doc-method-19 by @rahul799 in #5532

• [fix] add qc-cv legacy CVs by @poshul in #5529

• adding-wrap-doc-method-20 by @rahul799 in #5537

• PLFQ Write chromatograms for debugging by @jpfeuffer in #5536

• [Feature] Try to add descriptions to Param class repr in pyopenms by @jpfeuffer in #5544

• [Fix] Remaining memory leaks in tests by @dvdvgt in #5494

• [cython] link to openmp by @jpfeuffer in #5498

• [FIX] AMS mztab by @oliveralka in #5549

• [FIX] PyOpenMS macOS 11.5.1 (10.16) by @oliveralka in #5477

• [fix] aaseq python ext. by @jpfeuffer in #5555

• overwrite design file names with input file names (as we know those e… by @timosachsenberg in #5557

• adding-wrap-doc-method-22 by @rahul799 in #5560

• Do not overwrite OPENMS_DATA_PATH in PyOpenMS if it is already set by @radusuciu in #5562

• [FIX] Consider fixed mods for terms, reading pepXML by @jpfeuffer in #5548

• [FIX] Forgot C-term fixed mod lookup in pepXML by @jpfeuffer in #5564

• [CMAKE] option to enable LTO by @timosachsenberg in #5559

• [FEATURE] Export isotope errors when reading pepXML by @jpfeuffer in #5565

• Added Unimod Modifications to parameters of MSFraggerAdapter by @tillenglert in #5512

• [refactor] moved percolator in file functionality into library by @timosachsenberg in #5570

• [FIX] AssayGeneratorMetabo Test (wo SIRIUS) by @oliveralka in #5551

• [Internal] Add ParamCTDFile to write Param to CTD File with only standard dependecies by @rubengruenberg in #5475

• [Fix] missing cstddef for ptrdiff_t by @jpfeuffer in #5576

• [ADD] IDMerger annotate_file_origin default true by @oliveralka in #5578

• [Feature] basicproteininference on cxml by @jpfeuffer in #5561

• [Pyopenms] Update help in init.py by @jpfeuffer in #5583

• make reindexing the default by @timosachsenberg in #5581

• [GH Actions] remove cmake_find_debug by @jpfeuffer in #5586

• [FIX] add missing include by @hroest in #5588

• [Feature] make modifications better for pyopenms by @jpfeuffer in #5584

• fixed unused variable warnings by @timosachsenberg in #5597

• Feature/im calibration bugfix by @hroest in #5595

• Spectra are not stored if only meta data is read. by @timosachsenberg in #5600

• Fix/comparator utils by @JangJang3 in #5601

• [pyopenms] fix wrapping of idXML store by @timosachsenberg in #5605

• Feature/header cleanup inc by @hroest in #5608

• [pyopenms] use np.empty instead of np.zeros by @jpfeuffer in #5607

• Fix doxygen warnings by @cbielow in #5609

• Feature/header cleanup inc by @hroest in #5610

• prep for quick MS1 peak accession for pyOpenMS / numpy by @timosachsenberg in #5606

• [FEATURE] speed improvement in OpenSwathAssayGenerator and OpenSwathDecoyGenerator by @hroest in #5611

• [DOC] improved IM set/get documentation by @cbielow in #5614

• Reduce OpenMS exposure to third-party headers by @hroest in #5603

• [ADD] Spectrum Plotting and Spectrum Mirror Plotting Functions by @matteopilz in #5615

• Fix msfragger file origin by @jpfeuffer in #5620

• [FIX] use static inline for namespace by @hroest in #5627

• [FEATURE] New Deisotoping Algorithm by @emilpaulitz in #5306

• [FIX] MetaboliteSpectralMatcher by @jpfeuffer in #5630

• fix ODR by @timosachsenberg in #5632

• [pyopenms] Fix pyopenms int size (on windows) by @timosachsenberg in #5634

• Fix tool scan in TOPPView by @timosachsenberg in #5640

• add pandas df conversion by @axelwalter in #5622

• Isotopic distribution approximation by @emilpaulitz in #5633

• Perf mini by @cbielow in #5644

• Feature/separate interfaces by @hroest in #5626

• [PYOPENMS] wrap check_spectrum_type parameter for pphires by @hroest in #5647

• Swath by @vmusch in #5635

• the amount of SN warnings in FFMid are just too much for jupyter note… by @timosachsenberg in #5648

• only detect features on MS1 (don't mix levels) by @timosachsenberg in #5651

• [fix] Elution peak detection: rare segfault if no features were detected (e.g., in blanks) by @timosachsenberg in #5652

• Emf test and ffmid move by @timosachsenberg in #5654

• Update PercolatorInfile.cpp by @timosachsenberg in #5624

• Feature/pep evidences df by @axelwalter in #5656

• [FIX] Decoding ontology in PeptideIdentification df conversion by @axelwalter in #5659

• [FIX] add parameter to disable output of warnings in GaussFilter by @timosachsenberg in #5661

• [gitpod] add python3-pip to use run-clang-tidy by @timosachsenberg in #5664

• add backlink to MS run in FFmetaboIdent by @timosachsenberg in #5662

• ffid annotate spectra file path already in algorithm by @timosachsenberg in #5663

• fix TOPPView checkbox state export by @timosachsenberg in #5667

• apply clang-tidy modernize by @timosachsenberg in #5670

• Fix race condition in TOPPView b...

OpenMS 2.7.0

Dear OpenMS-Users,

we are proud to announce the release of OpenMS 2.7.0. Grab it
here

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

---

General:

• OpenMS now expects a compiler that supports C17
• Config storage path on linux changed to ~/.config/
• Some documentation improvements to pyOpenMS https://pyopenms.readthedocs.io/en/latest/

Adapters/Third-party support:

• Added support for SIRIUS 4.9.0
• Added basic Triqler export
• Improved NOVOR support
• Improved MSFragger support
• Removed Inspect support
• Easier 15N-labeling support for XTandemAdapter by shipping the required AA mass modification file (#5026)

What's new:

• Add some support for integrating spectral information when conducting DDA metabolomics experiments
• SimpleSearchEngine and algorithm: Additional spectrum features for percolator added
• FeatureFinderMetaboIdent: Targeted feature extraction is now also available from pyOpenMS
• AssayGeneratorMetabo: Added SIRIUS 4.9.0 support, allowing internal decoy generation and added internal feature linking support
• QCCalculator: export in mzQC file format is now available

New Tools:

• OpenMSDatabasesInfo -- Prints the content of OpenMS' enzyme and modification databases to TSV (UTIL)
• TriqlerConverter -- Converter to input for Triqler (UTIL)

Removed Tools:

• FeatureFinderSuperHirn -- Finds mass spectrometric features in mass spectra (TOPP)
• InspectAdapter -- Annotates MS/MS spectra using Inspect (TOPP)

Further fixes:

• Support for GLPK 5.x (#5127)
• IPF (identification of peptidoforms): add a check for terminal residue modification when generating theoretical peptidoforms
• Reduced build times on Windows
• Reduced AddressSanitizer warnings

File formats:

• Exporter for MSP files
• Improved support for reading NIST MSP files

Dependencies:

• Promoted SeqAn v1 to C17. Moved Seqan from contrib to main source tree (as it is not officially maintained anymore).

Library:

• Removed Elements.xml and Residues.xml. Hard-coded elements and residues for better performance/startup times.
• Moved algorithm of FeatureFinderMetaboIdent into library
• Added support for isotopic labelling experiments (MDV)
• Removed SuperHirn library

GUI tools:

• TOPPView: Various bug fixes
• TOPPView: Dynamic detection of tools in TOPPView upon startup
• TOPPView: Improved DIA data browsing
• TOPPAS: add a recent files submenu
• ParamEditor: with more convenient StringList editing
• SwathWizard: Allow opening in TOPPView

---

Best regards,
The OpenMS-Developers

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