v2.1.0

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

v2.0.0

Improvements 🚀

• MS²Rescore now runs on Windows!
• Graphical user interface (GUI) added, built with Gooey
  Install with pip install ms2rescore[gui] and run python -m ms2rescore.gui
• Install, upgrade, and run scripts added for Windows users without an existing Python installation who simply want to use the new GUI
• MS²Rescore can now output a PDF with useful plots displaying the results.

Refactoring and minor changes 🔧

• ⚠️Breaking change: MS²Rescore is now written with a lowercase S (instead of "MS²ReScore). This means that some class names and exceptions have been renamed accordingly, breaking the Python API with previous versions.
• ⚠️Breaking change: The feature_sets option now expects instead of a string with a predefined feature set, such as ms2pip_rt, a list of strings including one of the following: searchengine, rt, or ms2pip. By default, MS²Rescore uses all features: ['searchengine', 'rt', 'ms2pip'].
• MS²PIP is now imported and called through the Python API instead of the CLI

Includes PRs #34 and #37.

v2.0.0-beta.5

Improvements 🚀

• PSMs with invalid amino acids (B, J, O, U, X, and Z), which are unsupported by MS²PIP, are now removed in all pipelines (Fixes #31).

Bugfixes 🐛

• Case-insensitive matching of msms.txt column names (e.g. both Mass Deviations [Da] and Mass deviations [Da] will now both be accepted)
• Fix MGF title parsing in MaxQuant pipeline

Refactoring and minor changes 🔧

• Replaced assertions with specific exceptions
• Removed empty module runner.py
• Dropped support for Python 3.6 (did not work with subprocess capture_output)

v2.0.0-beta.4

Fixed:

• Prevent duplicate columns in pin output

v2.0.0-beta.3

New:

• X!Tandem pipeline outputs flanking amino acids to PIN file (#24, #27)

Fixed:

• Temporary fix for Tensorflow NUMEXPR_MAX_THREADS (#25, compomics/DeepLC#19)
• tandem_id column was erroneously written to X!Tandem PIN files
• Use logger instead of logging

v2.0.0-beta.2

New and fixed:

• Rescore with DeepLC retention time prediction
• New pipeline for X!Tandem search results
• Support for C-terminal modifications
• Simplified configuration (see README.md and configuration.md)
• By default, the pipeline is inferred from the identification file extension
• Major code refactoring
• Many bugfixes
• Installable from PyPI

v0.2.2

Before DeepLC integration and refactoring.