ms2rescore
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TIMS²Rescore
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
andpsm_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
toTrue
, even if no IM-based feature generators were configured.