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@RalfG RalfG released this 21 Jul 18:54
· 55 commits to main since this release
v3.1.0
7ccb280
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Learn about vigilant mode.

Added

  • ✨ 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

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

Fixed

  • 🐛 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

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