In-silico Protease Digestion & Peptide Mass Calculator
Digest a protein with trypsin, Lys-C, chymotrypsin and more, and get peptide masses.
🔒 Local processing — pasted sequences are not uploaded
Predict the peptides you'll see after digesting a protein for mass spectrometry or peptide mapping. Paste a protein sequence, choose a protease or chemical cleavage agent (trypsin, Lys-C, Arg-C, chymotrypsin, Glu-C/V8, Asp-N or CNBr), and allow up to two missed cleavages; the tool applies each enzyme's published specificity and returns a sortable peptide table with start–end positions, length, and both monoisotopic and average neutral masses. Filter by a target mass window to match observed ions, then export the peptide list as CSV.
0 residues · non amino-acid characters are ignored
Cleaves C-terminal to K or R, not before P
Peptides spanning up to this many uncut sites are also listed.
Masses are neutral (uncharged) peptide masses: the sum of residue masses plus one water. Monoisotopic masses use the most-abundant isotope of each element; average masses use average isotopic residue masses. For an observed m/z, add proton mass(es) for the charge state.
How to use the Protease Digestion tool
- 1Paste a protein sequence in one-letter amino-acid code (or load the example).
- 2Pick a protease and the number of allowed missed cleavages (0–2).
- 3Read the peptide table, filter by a mass range, sort by mass or position, and export CSV.
Frequently asked questions
- Which proteases and cleavage rules are supported?
- Trypsin (cleaves C-terminal to K or R, but not before proline), Lys-C (after K), Arg-C (after R), chymotrypsin (after F, Y or W, not before proline), Glu-C/V8 (after E), Asp-N (N-terminal to D, i.e. before each aspartate) and CNBr (after M). Each enzyme's rule is shown next to the selector.
- What do missed cleavages do?
- With 0 missed cleavages you get only fully-cut peptides. Setting 1 or 2 also lists peptides that span that many uncut internal sites — the same enumeration used by MS peptide-mapping and peptide-mass-fingerprint search engines, since real digests are rarely 100% complete.
- Are the masses monoisotopic or average?
- Both. Monoisotopic masses use the most-abundant isotope of each element (matching the peaks in a high-resolution MS spectrum); average masses use average isotopic residue masses. Each value is the neutral peptide mass — the sum of residue masses plus one water — so add proton mass(es) for the observed m/z at a given charge state.