Peptide mass match

Sequence Pyr-Ala-Lys-Ser-Gln-Gly-Gly-Ser-Asn-OH

One-letter or hyphenated three-letter code, up to 200 residues; written the same way as in the peptide calculator.

N-terminus Free amine (H-)Acetyl (Ac-) C-terminus Free acid (-OH)Amide (-NH2) Disulfide bonds

Observed values

One per line (a second column, such as intensity, is ignored), or separated by commas. Up to 200.

The values are m/z of ionsDeconvoluted masses Tolerance Unit Dappm Match

Try: Substance P electrospray spectrum · Thymosin β4, deconvoluted masses (illustrative values)

What each value is checked against

Species and ions considered

Group	What
The peptide	Protonated ions [M+zH]z+ at every charge state up to about one charge per 400 Da; sodium and potassium adducts up to 3+; isotope peaks up to M+3.
Chemical variants	One or two oxidations (Met, Trp); one or two deamidations (Asn, Gln); the free acid of an amidated peptide; reduced disulfides; loss of water; pyroglutamate from an N-terminal glutamine.
Synthesis by-products	Deletion of any one residue in the sequence; Pbf, tert-butyl, Boc or trityl protecting groups left on residues that carry them; an Fmoc group left on a free N-terminus.
Dimers	Non-covalent dimers, and disulfide-linked dimers when the sequence has a free cysteine, at the charge states that tell them apart from the monomer.

Tolerance

With the tolerance left on auto, each value is matched to within six units of its last decimal place: ±0.6 Da for 1420, ±0.06 for 1419.7, ±0.006 for 1419.70, but never tighter than 10 ppm. That suits values copied from certificates, which are often rounded. For your own high-resolution data, give the instrument's accuracy in ppm instead.

Some explanations cannot be told apart by mass alone. Deamidation (+0.984 Da) and the first isotope peak (+1.003 Da) differ by 0.019 Da, which only a high-resolution measurement separates. Leucine and isoleucine have identical masses, and so do a peptide and its D-epimer. Where more than one explanation fits, the alternatives are listed under the best one.

Deconvoluted masses from a certificate are often average masses, not monoisotopic, and for large peptides often the most abundant isotope peak. Choose "deconvoluted masses" and both are considered. How the masses and ions are calculated is set out in the mass spectrometry article, and where synthesis by-products come from in How synthetic peptides are made.

A match shows that a value is consistent with the sequence, not that the material is that peptide: identity, purity and content are separate questions, as the certificate of analysis guide explains.

Sources & Further Reading

1. Meija J, Coplen TB, Berglund M, Brand WA, De Bièvre P, Gröning M, et al. Isotopic compositions of the elements 2013 (IUPAC Technical Report). Pure and Applied Chemistry 2016;88(3):293–306. doi:10.1515/pac-2015-0503
2. Roepstorff P, Fohlman J. Letter to the editors: proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomedical Mass Spectrometry 1984;11(11):601. doi:10.1002/bms.1200111109
3. Biemann K. Contributions of mass spectrometry to peptide and protein structure. Biomedical and Environmental Mass Spectrometry 1988;16(1–12):99–111. doi:10.1002/bms.1200160119

Cosmic Peptides. (2026, October 25). Peptide mass match. Cosmic Peptides Research Library. Retrieved October 26, 2026, from https://cosmicpeptides.com/research/tools/mass-match

@misc{cosmicpeptides_research_tools_mass_match,
  author       = {{Cosmic Peptides}},
  title        = {Peptide mass match},
  howpublished = {Cosmic Peptides Research Library},
  year         = {2026},
  month        = oct,
  url          = {https://cosmicpeptides.com/research/tools/mass-match},
  urldate      = {2026-10-26},
  note         = {Last reviewed 2026-10-25}
}

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