What it does
Mass spectrometry identifies proteins from the masses of their pieces. This calculator does the sums you need around that, for any protein sequence:
- In-silico digest: cuts the protein the way an enzyme would, and lists every peptide with its position, missed cleavages, monoisotopic mass and m/z at charge 1+ and 2+.
- Peptide mass fingerprint: paste the m/z values you measured (for example from MALDI-TOF) and see which peaks match a peptide within your tolerance in ppm, and how much of the protein those peptides cover.
- Fragment ions: the b, y and a ions of any peptide at charge 1+ to 3+, with water and ammonia losses if you want them, as a table and a stick picture. Use it to read an MS/MS spectrum by hand.
Options
- Enzyme: trypsin (cuts after K and R, but not before P), trypsin ignoring the P rule, Lys-C, Arg-C, Glu-C, Asp-N, chymotrypsin (after F, Y and W) and cyanogen bromide (after M).
- Missed cleavages: real digests often skip a site. Allowing 1 or 2 adds the longer peptides that join neighbours.
- Shortest and longest peptide: very short peptides are rarely seen and match too easily, so the default starts at 4 residues.
- Carbamidomethyl cysteines: tick this if you reduced and alkylated with iodoacetamide (adds C2H3NO, 57.0215, to every Cys). Oxidised methionines adds an oxygen to every Met.
- Tolerance and charges for matching: 10 ppm suits a modern instrument; older MALDI work often used 50 to 100 ppm.
Worked example
Press Use the example. It loads a made-up protein of 136 amino acids and 13 made-up measured peaks. With trypsin, one missed cleavage and peptides of 4 to 40 residues, there are 27 peptides, 14 of them with no missed cleavage. The site in …GHK-PTC… is not cut, because trypsin does not cut before proline.
The peptide DFSLQGECK (positions 16 to 24) has a monoisotopic mass of 1082.4703, so [M+H]⁺ is 1083.4775 and [M+2H]²⁺ is 542.2424. The measured peak 1083.4749 matches it with an error of −2.4 ppm. In total, 10 of the 13 peaks match at 10 ppm, one of them a peptide with a missed cleavage (DEYGKNHQVTSLPMCFR). The matched peptides cover 71.3 % of the sequence. The three peaks with no match stand for noise or modified peptides.
DFSLQGECK is also shown under Fragment ions: b2 is 263.1026 and y1 (the C-terminal K) is 147.1128.
FAQ
Monoisotopic or average? Use monoisotopic masses for anything measured with isotope peaks resolved, which is most modern instruments. The average mass is in the CSV for very large peptides.
Why doesn’t my peak match? Check the modifications (alkylation, oxidation), the charge, the enzyme’s missed cleavages, and the tolerance. Phosphorylation, glycosylation and other modifications are not included.
Is my data uploaded? No. Everything runs in your browser and works offline.
Where the numbers come from
- Residue and modification masses worked out by fibub from chemical formulas with exact isotope masses (general chemistry facts); proton mass from CODATA. Cleavage rules are the common textbook descriptions of each enzyme.
- Checked against pyteomics on the example and four random proteins: the trypsin, chymotrypsin and Asp-N peptide lists, all 369 monoisotopic masses (to 1 part in a billion), average masses, and the a, b and y ions.
- The example protein and measured peaks are made up for this tool; the protein is not a real one.
Standard scientific values, such as constants, atomic weights and melting points, are facts found in every textbook; we name where ours were checked. If you are an author or publisher and want a value, a credit or a table changed or removed, tell us and we will act quickly.
Last updated 2026-11-09.