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lazearlazear
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fix: prioritization between isolation window m/z and selected ion m/z (#210)
1 parent 252cf61 commit db2e8cc

1 file changed

Lines changed: 102 additions & 2 deletions

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‎crates/sage-cloudpath/src/mzml.rs‎

Lines changed: 102 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -242,8 +242,9 @@ impl MzMLReader {
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precursor.charge = Some(extract_value!(ev));
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}
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SELECTED_ION_MZ => {
245-
if precursor.mz == 0.0 {
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precursor.mz = extract_value!(ev)
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let val = extract_value!(ev);
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if val != 0.0 {
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precursor.mz = val;
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}
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}
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SELECTED_ION_INT => {
@@ -606,4 +607,103 @@ mod test {
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assert_eq!(s.intensity.len(), s.mz.len());
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Ok(())
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}
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#[tokio::test]
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async fn parse_spectrum_issue_210() -> Result<(), MzMLError> {
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// Handle cases where both isolation window target m/z is set and different than selected ion m/z
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let s = r#"
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<spectrum id="spectrum=8678309" index="8678309" defaultArrayLength="102" dataProcessingRef="dp_sp_1">
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<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" />
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<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2" />
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<precursorList count="1">
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<precursor>
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<isolationWindow>
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<cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="457.75" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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<cvParam cvRef="MS" accession="MS:1000828" name="isolation window lower offset" value="1.5" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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<cvParam cvRef="MS" accession="MS:1000829" name="isolation window upper offset" value="0.75" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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</isolationWindow>
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<selectedIonList count="1">
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<selectedIon>
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<cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="457.723968505859" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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<cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2" />
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</selectedIon>
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</selectedIonList>
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</precursor>
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</precursorList>
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</spectrum>
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"#;
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let mut spectra = MzMLReader::with_file_id(0).parse(s.as_bytes()).await?;
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assert_eq!(spectra.len(), 1);
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let s = spectra.pop().unwrap();
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assert!((s.precursors[0].mz - 457.723968) < 0.0001);
640+
assert_eq!(
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s.precursors[0].isolation_window,
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Some(Tolerance::Da(-1.5, 0.75))
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);
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// Check different ordering of fields in mzML
646+
let s = r#"
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<spectrum id="spectrum=8678309" index="8678309" defaultArrayLength="102" dataProcessingRef="dp_sp_1">
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<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" />
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<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2" />
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<precursorList count="1">
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<precursor>
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<selectedIonList count="1">
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<selectedIon>
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<cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="457.723968505859" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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<cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2" />
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</selectedIon>
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</selectedIonList>
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<isolationWindow>
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<cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="457.75" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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<cvParam cvRef="MS" accession="MS:1000828" name="isolation window lower offset" value="1.5" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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<cvParam cvRef="MS" accession="MS:1000829" name="isolation window upper offset" value="0.75" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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</isolationWindow>
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</precursor>
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</precursorList>
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</spectrum>
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"#;
667+
let mut spectra = MzMLReader::with_file_id(0).parse(s.as_bytes()).await?;
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669+
assert_eq!(spectra.len(), 1);
670+
let s = spectra.pop().unwrap();
671+
assert!((s.precursors[0].mz - 457.723968) < 0.0001);
672+
assert_eq!(
673+
s.precursors[0].isolation_window,
674+
Some(Tolerance::Da(-1.5, 0.75))
675+
);
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677+
// Check fallback keeping iso window m/z of fields in mzML
678+
let s = r#"
679+
<spectrum id="spectrum=8678309" index="8678309" defaultArrayLength="102" dataProcessingRef="dp_sp_1">
680+
<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" />
681+
<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2" />
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<precursorList count="1">
683+
<precursor>
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<isolationWindow>
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<cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="457.75" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
686+
<cvParam cvRef="MS" accession="MS:1000828" name="isolation window lower offset" value="1.5" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
687+
<cvParam cvRef="MS" accession="MS:1000829" name="isolation window upper offset" value="0.75" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
688+
</isolationWindow>
689+
<selectedIonList count="1">
690+
<selectedIon>
691+
<cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2" />
692+
</selectedIon>
693+
</selectedIonList>
694+
</precursor>
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</precursorList>
696+
</spectrum>
697+
"#;
698+
let mut spectra = MzMLReader::with_file_id(0).parse(s.as_bytes()).await?;
699+
700+
assert_eq!(spectra.len(), 1);
701+
let s = spectra.pop().unwrap();
702+
assert!((s.precursors[0].mz - 457.75) < 0.0001);
703+
assert_eq!(
704+
s.precursors[0].isolation_window,
705+
Some(Tolerance::Da(-1.5, 0.75))
706+
);
707+
Ok(())
708+
}
609709
}

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