From f40e952156cdd4313973b2f4f2762748700223fd Mon Sep 17 00:00:00 2001 From: jonasscheid Date: Fri, 17 Jan 2025 15:06:45 +0000 Subject: [PATCH 1/2] parse ion mobility (IM) from idxml to PSM obj --- psm_utils/io/idxml.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/psm_utils/io/idxml.py b/psm_utils/io/idxml.py index 9a43293..f535d61 100644 --- a/psm_utils/io/idxml.py +++ b/psm_utils/io/idxml.py @@ -187,7 +187,7 @@ def _parse_psm( 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=[ accession.decode() for accession in peptide_hit.extractProteinAccessionsSet() ], From 17f0486336d2f458d3fd3754aefd448ae41b492b Mon Sep 17 00:00:00 2001 From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Date: Fri, 17 Jan 2025 19:30:58 +0100 Subject: [PATCH 2/2] Update psm_utils/io/idxml.py Co-authored-by: Kevin Velghe --- psm_utils/io/idxml.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/psm_utils/io/idxml.py b/psm_utils/io/idxml.py index 2bd2e14..c993d85 100644 --- a/psm_utils/io/idxml.py +++ b/psm_utils/io/idxml.py @@ -194,7 +194,7 @@ def _parse_psm( score=peptide_hit.getScore(), precursor_mz=peptide_id.getMZ(), retention_time=peptide_id.getRT(), - ion_mobility=float(peptide_id.getMetaValue("IM")) if peptide_id.getMetaValue("IM") is not None else None + ion_mobility=float(im) if (im := peptide_id.getMetaValue("IM")) is not None else None, protein_list=[ accession.decode() for accession in peptide_hit.extractProteinAccessionsSet() ],