v1.4.0

Added

• ✨ Support for Thermo raw (requiring dotnet runtime) and gzipped spectrum files, through mobiusklein/mzdata (#226, by @paretje)
• ✨ New Python API usage mode correlate-single to correlate to a single ObservedSpectrum object with predictions (#232)
• ✨ Added support for Python 3.12 and 3.13, Numpy v2, and newer Pandas and XGBoost versions (#228)
• ✅ CI: Add integration test for predict-single (#228)

Changed

• ⚠️ Ion mobility is now returned instead of collisional cross section when IM2Deep is used through the add_ion_mobility option (#236, by rodvrees)
• 🏗️ Model files are now downloaded from Zenodo instead of Genesis (#225, by paretje, fixes #229)
• 📝 Docs: Updated README to include correlate-single; moved webserver API docs from old Wiki (#239)

Removed

• 🐍 Removed support for Python 3.8 (EOL) and for musllinux distributions (#228, #237)
• 🗑️ Removed old conversion scripts, mostly implemented in psm_utils (#239)
• 🗑️ Removed old train script, to be replaced with page in docs (#239)

v4.0.0

Fully refactored and drastically more user-friendly version of MS²PIP:

• More modular Python API
• One consolidated command-line interface with subcommands
• Support for all file formats readable by psm_utils
• Support for MGF, mzML, and Bruker raw spectrum files
• Support for ProForma 2.0 peptide notation (no modification configuration required anymore)
• Support for multiple peptides/PSMs per spectrum
• Detailed documentation on ms2pip.readthedocs.io
• ...

v4.0.0-dev14

Full Changelog: v4.0.0-dev13...v4.0.0-dev14

v4.0.0-dev13

Full Changelog: v4.0.0-dev12...v4.0.0-dev13

v4.0.0-dev12

Full Changelog: v4.0.0-dev11...v4.0.0-dev12

v4.0.0-dev11

Full Changelog: v4.0.0-dev10...v4.0.0-dev11

v4.0.0-dev10

Full Changelog: v4.0.0-dev9...v4.0.0-dev10

v4.0.0-dev9

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v4.0.0-dev8

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v4.0.0-dev7

Full Changelog: v4.0.0-dev6...v4.0.0-dev7