TIMS²Rescore

[RalfG]

Added

• ✨ New tims2rescore CLI entrypoint with TIMS-specific configuration defaults
• ✨ IM2Deep feature generator for ion mobility
• ✨ Support for Bruker raw (.d) and miniTDF formats
• ✨ psm_id_rt_pattern and psm_id_im_pattern: New options to allow parsing of RT/IM from PSM file spectrum identifiers.

Changed

• 👷 CI: Lint with ruff instead of flake8
• ⚡ DeepLC: By default use PSMs initially passing 1% FDR threshold for calibration instead of a fixed number
• 🔊 DeepLC: Throw warning when using deeplc_retrain with less than 500 calibration PSMs
• 🔊 Raise exception if missing precursor info (retention time or ion mobility) could not found in both PSM and spectrum files.
• ⬆️ Update (and sort) dependencies in pyproject.toml
• 📦 Dockerfile: Use Python 3.11 base image instead of Ubuntu

Fixed

• 🐛 DeepLC: Fix issue with conversion to PEPREC (fixes #108, fixes #113)
• 🐛 Fix bug in infer_spectrum_path if path in configuration is None
• 🐛 Fix bug that always set im_required to True, even if no IM-based feature generators were configured.