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fix(lcms): stop plain MS jcamp from being detected as Chemstation LC/MS #322

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fix(lcms): stop plain MS jcamp from being detected as Chemstation LC/MS #322

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3ca0fba
fix(lcms): stop plain MS jcamp from being detected as Chemstation LC/MS
Aug 20, 2026
a492bed
fix(lcms): replace unsound MS-vs-Chemstation blacklist with a scoped …
Aug 21, 2026
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15 changes: 15 additions & 0 deletions src/__tests__/units/actions/lcms.test.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@ import hplcMsTicPosJcamp from "../../fixtures/lc_ms_jcamp_tic_pos";
import hplcMsTicNegJcamp from "../../fixtures/lc_ms_jcamp_tic_neg";
import hplcMsUvvisJcamp from "../../fixtures/lc_ms_jcamp_uvvis";
import lcMsMzChemstationJcamp from "../../fixtures/lc_ms_jcamp_mz_chemstation";
import msJcamp from "../../fixtures/ms_jcamp";

const hasSpectrumData = (entity: any) => {
const data = entity?.spectra?.[0]?.data?.[0];
Expand Down Expand Up @@ -170,6 +171,20 @@ describe('LCMS ExtractJcamp', () => {
const pages = extractPages(entity);
expect(new Set(pages).size).toBeGreaterThan(1);
});

it('Extract a plain MS jcamp keeps the MS layout instead of LC/MS', () => {
const entity: any = ExtractJcamp(msJcamp);
expect(entity.layout).toEqual(LIST_LAYOUT.MS);
});

it('Extract Chemstation MZ still resolves LC/MS when it also carries generic chem-spectra markers', () => {
const injected = lcMsMzChemstationJcamp.replace(
'##DATA TYPE=MASS SPECTRUM',
'##DATA TYPE=MASS SPECTRUM\n##$CSCATEGORY=SPECTRUM\n##$CSSCANAUTOTARGET=1',
);
const entity: any = ExtractJcamp(injected);
expect(entity.layout).toEqual(LIST_LAYOUT.LC_MS);
});
});

describe('LCMS grouping', () => {
Expand Down
19 changes: 14 additions & 5 deletions src/features/lc-ms/parsing/chemstation.js
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Original file line number Diff line number Diff line change
Expand Up @@ -67,10 +67,9 @@ export const isChemstationLcms = (source, jcamp) => {
const scanMode = String(info.SCAN_MODE || info.SCANMODE || '').toUpperCase();
const type = String(info.TYPE || '').toUpperCase();
const software = String(info.SOFTWARE || '').toUpperCase();
const csCategory = jcamp?.info?.$CSCATEGORY;
const categories = Array.isArray(csCategory)
? csCategory.map((c) => String(c).toUpperCase())
: [];
const categories = []
.concat(jcamp?.info?.$CSCATEGORY || [])
.map((c) => String(c).toUpperCase());

const hasPolarityCategory = categories.some(
(c) => c.includes('POSITIVE') || c.includes('NEGATIVE') || c.includes('NEUTRAL'),
Expand Down Expand Up @@ -123,7 +122,7 @@ export const isChemstationLcms = (source, jcamp) => {

if (
hasMassSpectrumRootDataType
&& (hasMassSpectrumDataType || hasScanModeHint || hasTypeHint || hasSoftwareHint)
&& (hasScanModeHint || hasTypeHint || hasSoftwareHint || hasTicOrUvvisCategory)
) {
return true;
}
Expand All @@ -134,5 +133,15 @@ export const isChemstationLcms = (source, jcamp) => {
return true;
}

// A multi-page MASS SPECTRUM root with no other chromatographic signal is ambiguous:
// both a genuine Chemstation m/z export and a plain multi-page MS NTUPLES export look
// like this. The only field that reliably tells them apart is this units triplet, which
// is unique to the plain export - so it only vetoes this weak fallback, never the
// stronger positive evidence handled above.
if (hasMassSpectrumRootDataType && hasMultipleSpectra && hasPageMetadata) {
const hasMsUnitsTriplet = /##UNITS\s*=\s*M\/Z,\s*RELATIVE ABUNDANCE,\s*SECONDS/i.test(source);
return !hasMsUnitsTriplet;
}

return false;
};