Extend support for timsTOF instruments - Githubissues

compomics / ms2rescore

Modular and user-friendly platform for AI-assisted rescoring of peptide identifications

https://ms2rescore.readthedocs.io

Apache License 2.0

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Extend support for timsTOF instruments #122

Closed RalfG closed 3 months ago

RalfG commented 4 months ago

Added

New feature generator: IM2Deep modification-aware CCS prediction

Changed

Improved parsing from RT and IM from spectrum file if needed (moved out of feature generators)
Pass PSMList directly to DeepLC instead of using PEPREC DataFrame.
Use indexed mzML and MGF implementations from Pyteomics for faster parsing of RT and IM
Log warning if not sufficient PSMs were found for DeepLC retraining
Improve procedure for getting calibration PSMs (currently for DeepLC and IM2Deep)

Fixed

Also try parsing IM from mzML from precursorList > precursor > selectedIonList > selectedIon > inverse reduced ion mobility (previously only scanList > scan > reverse ion mobility)