What this tool is
ProteinCut takes a protein sequence, cleaves it in silico with the enzyme (or reagent) you choose, and computes the theoretical mass of every resulting peptide - the standard reference calculation for peptide mass fingerprinting (PMF). It is a faithful local re-implementation of ExPASy PeptideMass (web.expasy.org/peptide_mass/): the 25-enzyme/reagent cleavage table (trypsin and its variants, Lys-C/Lys-N, Arg-C, Asp-N, Glu-C, CNBr, chymotrypsin, pepsin, proteinase K, thermolysin, formic-acid hydrolysis, ...), 0-5 missed cleavages, cysteine alkylation (iodoacetic acid / iodoacetamide / 4-vinyl pyridine / acrylamide), methionine oxidation, seven ion forms ([M+H]+ ... [M+5H]5+, up to 5+ charge), monoisotopic vs average masses, mass-range filters and mass/position sorting.
Everything is computed in your own browser: residue masses, atomic weights and the cleavage table ship with the page - there is no backend and nothing is uploaded. Input and options are kept in local storage. The mass data come from the same NIST dataset and calculation core as MassCalc / PepFragCalc on this site: monoisotopic = sum of the most abundant isotopes, average = sum of the standard atomic weights, intact neutral mass = N-term H + Σ residues + C-term OH. The isoelectric point uses the Bjellqvist method (the same pKa set as ExPASy Compute pI/Mw), i.e. the pH at which the net charge is zero.
Features
- ExPASy-identical cleavage rules25 enzymes/reagents, each rule checked line by line against ExPASy PeptideMass Table 1 - including the three trypsin specificity variants, Trypsin/CNBr (C-terminal Met to homoserine lactone), Glu-C in phosphate vs bicarbonate buffer, and microwave-assisted formic acid hydrolysis. No simplified subset.
- Cysteine and methionine modificationsCysteines: reduced / iodoacetic acid (carboxymethyl) / iodoacetamide (carbamidomethyl) / 4-vinyl pyridine (pyridylethyl), optionally plus acrylamide adducts; methionine oxidation as a separate toggle. Modifications are applied globally per your options and flagged in the results.
- Seven ion forms × two mass types[M+H]+, [M], [M-H]-, [M+2H]2+, [M+3H]3+, [M+4H]4+ and [M+5H]5+ (up to 5+ charge) - pick one to display; switch between monoisotopic (high-resolution searches) and average (low-resolution) masses without recomputing.
- Missed cleavages, filters and sorting0-5 missed cleavages (with multi-miss combinations), the same minimum/maximum mass presets as ExPASy, and sorting by peptide mass (descending) or by position in the protein.
- Protein summary: mass and pIThe top card reports the intact protein's theoretical mass (both monoisotopic and average) and isoelectric point (Bjellqvist); a > header line in the input becomes the protein name.
- Local and trilingualPure front-end, zero dependencies, nothing uploaded; light/dark theme and Simplified / Traditional Chinese / English interfaces; results copy out as TSV for Excel in one click.
How to use it
- Paste the protein sequence into the box (or load the human serum albumin example); a line starting with > is used as the name and the letters of every other line are joined.
- Pick the enzyme/reagent and missed-cleavage count; set cysteine treatment, methionine oxidation, ion form and monoisotopic/average mass when needed.
- The output has two parts: the protein summary (length / mass / pI) and the peptide table (position, missed cleavages, sequence, mass, modification tags); peptides containing B/Z/X are listed separately without masses.
- Narrow the table with the minimum/maximum mass presets and sorting, then hit "Copy results (TSV)" to take it into Excel or your proteomics software.
FAQ
- How does this differ from ExPASy PeptideMass?
- The calculation is the same: same cleavage table, same cysteine/methionine options, same ion forms and monoisotopic/average masses. The differences are that it is fully local - there is no UniProt lookup (ExPASy also accepts Swiss-Prot/TrEMBL AC/IDs; paste the sequence here instead) - and there is no ExPASy-style annotation of database PTMs/conflicts/splice variants. Your sequence never leaves the browser, so unpublished proteins are safe.
- Monoisotopic or average mass - which one do I use?
- High-resolution instruments (TOF, Orbitrap, FT-ICR) usually match monoisotopic m/z; on low-resolution instruments (ion traps, quadrupoles) peptides rich in heavy isotopes appear closer to the average mass. This tool uses the same NIST atomic weights as MassCalc/PepFragCalc: monoisotopic = most abundant isotopes, average = standard atomic weights.
- What is the CNBr homoserine lactone?
- When cyanogen bromide cleaves the C-terminal side of Met, the C-terminal Met is converted into homoserine lactone (HSL): compared with the regular "N-term H + residues + C-term OH" peptide, it is lighter by one CH4S (≈ −48.003 Da monoisotopic). This tool applies that conversion automatically to C-terminal Met residues cut by CNBr and Trypsin/CNBr, and tags them in the modifications column.
- What about B, Z, X and J?
- As in ExPASy: B = Asx (D/N), Z = Glx (E/Q) and X = any amino acid are ambiguous, so peptides containing them get no mass and are listed in a separate section; J is treated as Ile or Leu (same mass, C6H11NO, mono 113.0841 Da) and takes part in digestion and mass calculation normally.
- Are sequences uploaded? How large can proteins be?
- No - the page is fully static with no backend; everything is computed locally and the input only goes to browser local storage. Typical proteins (≲ 1000 residues) finish in milliseconds; for much larger ones, keep in mind that raising the missed-cleavage count grows the number of peptides combinatorially, so step up from 0 to 1 and beyond gradually.
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