lcms-peptide-qc

Deterministic positive-mode LC-MS calculations for research peptide workflows.

What it does

• calculates protonated m/z from a neutral monoisotopic mass and integer charge;
• inverts observed m/z to neutral mass;
• reports signed and absolute mass error in ppm;
• generates a charge-state table;
• processes a small, explicit CSV fixture format for repeated observations.

Use peptide-qc first when the neutral mass comes from a standard sequence, then pass its mass.monoisotopicDa result into this package. Keeping the two steps separate makes the mass source inspectable.

Install and use

npm install lcms-peptide-qc
npx lcms-peptide-qc analyze \
  --mass-da 1000 \
  --charge 2 \
  --observed-mz 501.007376466621 \
  --json

For a charge-state table:

npx lcms-peptide-qc charge-states --mass-da 1000 --max-charge 5 --json

For repeated synthetic observations, the CSV header must be exactly id,neutralMassDa,charge,observedMz:

npx lcms-peptide-qc csv --file examples/observations.csv --json

Scientific assumptions and limits

The model is positive mode and uses the proton mass 1.007276466621 Da. It assumes the supplied neutral mass is the correct monoisotopic neutral mass and does not infer isotope envelopes, adducts, fragmentation, retention time, charge from a spectrum, or instrument calibration. An m/z match is not an identity confirmation. It does not read mzML and does not replace a validated LC-MS method or analyst review.

This is research-use-only and educational software. Do not interpret a ppm value as a certificate of purity or identity. The package is maintained by Péptido México, a commercial supplier of research materials; that relationship is disclosed in CITATION.cff.

Development

npm test
npm run pack:check

Fixtures are synthetic and contain no customer data, private batch records or real analytical files.

The latest suite release is archived on Zenodo with reproducible citation metadata.

Citation

See CITATION.cff and cite the exact release when possible.