add functionality to parse spectra directly from ms2spectrum objects …#253
Merged
RalfG merged 5 commits intorelease/4.2from Mar 26, 2026
Merged
add functionality to parse spectra directly from ms2spectrum objects …#253RalfG merged 5 commits intorelease/4.2from
RalfG merged 5 commits intorelease/4.2from
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…ized Integrate the MS2Spectrum processing path with the existing parallelized infrastructure instead of duplicating XGBoost and encoding logic. Extract shared per-PSM processing in _process_spectra into a helper function to support both file-based and preloaded spectrum lookups.
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This pull request introduces a new function to the core processing workflow of the
ms2pippackage, enabling direct handling of PSMs (peptide-spectrum matches) that already have attachedMS2Spectrumobjects. Additionally, it makes necessary imports and updates the package's public API to expose this new functionality.New processing function for pre-attached spectra:
process_MS2_spectrafunction tocore.py, allowing users to process PSMs with pre-attachedMS2Spectrumobjects, including spectrum extraction, prediction, and optional correlation computation. This function streamlines workflows where spectra are already parsed and available in memory, like within ms2rescore.API and import updates:
MS2Spectrumfromms2rescore_rsincore.pyto support the new processing function.process_MS2_spectrato the package's public API in__init__.py, making the new processing capability accessible to users.