Ms2rescore

Early development release of v3

Early development release of v3

Bugfixes 🪲
- GUI: Fixed parsing of new-style MaxQuant modification names (76, backport of 75)

Improvements 🚀
- Additional PEAKS search engine features

Bugfixes 🪲
- Changed peptideshaker name in the
- Fix the mgf title field extraction to be compatible with PEAKS XPro output (fixes 44)
- Removed `shell=True` option from Percolator command (fixes 55)
- MS²Rescore now returns an error if an error occured while running Percolator (added `check=True` to `subprocess.run`)
- Deprecation warning "passing set as indexer" fix
- Python 3.9 compatibility for GUI

Refactoring and minor changes 🔧
- Ignore Deprecation-/Future-/UserWarnings in GUI mode (fixes https://github.com/compomics/ms2rescore/issues/61)
- Cleanup imports and remove importlib_resources backport (Python 3.6 compatibility not needed anymore)
- Set Gooey target to allow gui startup from `ms2rescore-gui` entrypoint and add `ms2rescore-gui` entrypoint (GUI can now be started from the terminal with both `python -m ms2rescore.gui` and `ms2rescore-gui`).
- Relax scikit-learn dependency to <2 (v1.0.0 now released)
- Fix UserWarning in `percolator.py` (unused groups in regex for Pandas `str.match()`)

Improvements 🚀
- Refactored parsing of MaxQuant Modified sequence to allow for new long form modification labels (e.g. `PEPM(Oxidation (M)K` instead of `PEPM(ox)K`) (PR 47, fixes 41)
- Added regex pattern option to the config to allow more flexible PSM ID matching with the MGF TITLE field (PR 42)
- Added `MGF TITLE pattern`, `num CPU`, and `feature set` options to the GUI (PR 43)

Bugfixes 🪲
- Spaces and hyphens are now supported for input file names (Changed Percolator subprocess command) (PR 43)
- Set default value of `mgf_title_pattern` to `None` to be compatible with PEAKS pipeline (PR 46)

Refactoring and minor changes 🔧
- Removed print statement from id_file_parser module (PR 42)
- Replaced deprecated pandas functions (PR 46)

Improvements 🚀

- Added support for PEAKS mzid identification files!
- Retention time predictor calibrates now for each raw file independently resulting in more accurate calibrations.


Bugfixes 🪲

- MaxQuant pipeline: Carbamidomethyl is not listed as default fixed modification anymore, as this could not be overridden. Searches without carbamidomethyl as fixed modification are now supported. However, carbamidomethyl now always needs to be specified explicitly if applicable!
- When parsing MGF files, all lines ending on `0.0` (including lines ending on `10.0`) were removed, instead of only 0 intensity peaks. This is now fixed.


Refactoring and minor changes 🔧

- PIN pipeline: Allow mass shift modification labels with + sign (e.g. `R.IM[+15.99492]MAR.D`).
- PEAKS and MaxQuant pipelines: Precursor charge from ID file now overwrites `CHARGE` in MGF file. (Identification and instrument precursor charges do not always match; identification charge should be prioritized).
- Plotting module can only be run when Percolator is run as part of MS²Rescore.
- If no decoy PSMs are present, MS²Rescore raises an error and stops.
- Removed obsolete `mgf` option from `maxquant_to_rescore` configuration.

PR 35