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Parse ion mobility from idXML to PSM object #109

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Merged
RalfG merged 4 commits into from
Jan 20, 2025
Merged

Parse ion mobility from idXML to PSM object #109

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f40e952
parse ion mobility (IM) from idxml to PSM obj
jonasscheid Jan 17, 2025
1e53b84
Merge branch 'main' into parse-im-idxml
jonasscheid Jan 17, 2025
17f0486
Update psm_utils/io/idxml.py
jonasscheid Jan 17, 2025
e89ea96
Merge branch 'main' into parse-im-idxml
jonasscheid Jan 17, 2025
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2 changes: 1 addition & 1 deletion psm_utils/io/idxml.py
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Original file line number Diff line number Diff line change
Expand Up @@ -194,8 +194,8 @@
score=peptide_hit.getScore(),
precursor_mz=peptide_id.getMZ(),
retention_time=peptide_id.getRT(),
# NOTE: ion mobility will be supported by OpenMS in the future
ion_mobility=float(peptide_id.getMetaValue("IM")) if peptide_id.getMetaValue("IM") is not None else None
protein_list=[

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psm_utils/io/idxml.py:198:13: SyntaxError: Expected ',', found name
accession.decode() for accession in peptide_hit.extractProteinAccessionsSet()
],
rank=peptide_hit.getRank() + 1, # 0-based to 1-based
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