Dear OpenMS-Users,

we are proud to announce the release of OpenMS 3.0. Grab it here

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

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

Best regards, The OpenMS-Developers