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@openms-jenkins-bot openms-jenkins-bot released this 18 Jul 18:26
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Release3.0.0
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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

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

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