Releases · CompOmics/ms2rescore

21 Jul 18:54

RalfG

v3.1.0

✨ New tims2rescore CLI entrypoint with TIMS-specific configuration defaults
✨ IM2Deep feature generator for ion mobility
✨ Support for Bruker raw (.d) and miniTDF formats (was also back-ported to v3.0.3)
✨ psm_id_rt_pattern and psm_id_im_pattern: New options to allow parsing of RT/IM from PSM file spectrum identifiers.
✨ max_psm_rank_input and max_psm_rank_output: New options to control rescoring and reporting of multiple PSMs per spectrum (default 5 and 1)
✨ Also store peptide-level q-value and PEPs in the output PSM list, under the metadata field.
✨ profile option to write a cProfile report of the rescoring process (for debugging)
✨ Option to pass train_fdr to Mokapot (test_fdr was already supported as kwarg)
⚡ Faster spectrum file reading with timsrust and mzdata Rust libraries
📝 Add TIMS²Rescore docs and citation on README; more detailed docs on formula modifications

👷 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
🔧 Config: Change write_report default value from true to false

🐛 Report: Fix calculation of number of retained peptides in identification overlap chart
🐛 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.

Full Changelog: v3.0.3...v3.1.0

Assets 3