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Refactor parsing of precursor data from spectrum files #162

Merged
merged 4 commits into from
Dec 5, 2024
Merged

Refactor parsing of precursor data from spectrum files #162

merged 4 commits into from
Dec 5, 2024

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RalfG
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@RalfG RalfG commented Jul 31, 2024 •
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Added

  • 🚸 If observed m/z values are available in the PSM list, always check if PSMs match with spectra

Changed

  • 🚸 Do not continue if precursor info (m/z, RT, or IM) is missing for some PSMs, but not for all. This should not occur, unless something went wrong. Previously such PSMs were simply selectively removed from the dataset.
  • 🔊 Clearer logging while parsing precursor info from spectrum files: Always raise error if a PSM cannot be found in the spectrum files and provide example PSM IDs from both PSM and spectrum file.
  • ♻️ General refactoring of parse_spectra module

@RalfG
Refactor parsing of spectrum data:
0c93509 
- Clearer logging when parsing precursor info from spectrum files
- Always check if PSMs match with spectra based on observed precursor m/z (if available in PSM list)
- Always raise error if not all PSMs can be found in spectrum file(s), before MS²PIP
- Provide example PSM IDs from both PSM and spectrum file when matching fails.
- Move all code to parse_spectra
@RalfG RalfG added this to the v3.2.0 milestone Jul 31, 2024
@RalfG RalfG requested review from paretje and ArthurDeclercq July 31, 2024 15:01
@RalfG RalfG mentioned this pull request Aug 2, 2024
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paretje
paretje reviewed Dec 4, 2024
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ms2rescore/feature_generators/maxquant.py Outdated Show resolved Hide resolved
ms2rescore/parse_spectra.py Outdated Show resolved Hide resolved
@RalfG RalfG merged commit 581da04 into main Dec 5, 2024
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@RalfG RalfG deleted the refactor-parse-spectra branch December 5, 2024 11:19
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@paretje paretje paretje left review comments

@ArthurDeclercq ArthurDeclercq Awaiting requested review from ArthurDeclercq

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@RalfG @paretje