protein_digest
Read-only
In-silico proteolytic digest of a protein (ExPASy PeptideCutter / PeptideMass): peptides with coordinates, average and monoisotopic masses, m/z per charge state, and the MS mass-window filter. 49 proteases and chemicals — or an enzyme of your own written in RPG rule grammar — one or several at a time; a multi-enzyme digest runs concurrently (all at once, products re-digested until nothing changes) or sequentially (one result per enzyme).
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| mode | No | multi-enzyme only. 'concurrent' = all at once, re-digesting products until nothing changes (can cut where no single enzyme cuts the intact chain); 'sequential' = one result per enzyme, each on the intact protein. | concurrent |
| semi | No | also emit semi-enzymatic peptides (one ragged terminus). | |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| enzyme | No | protease or chemical (single-enzyme digest), or 'custom' to use `customCleave`. Values: arg-c (Arg-C proteinase), asp-n (Asp-N endopeptidase), asp-n-sg (Asp-N, sequencing grade (D and C)), bnps-skatole (BNPS-Skatole), bromelain (Bromelain), caspase-1 (Caspase 1), caspase-10 (Caspase 10), caspase-2 (Caspase 2), caspase-3 (Caspase 3), caspase-4 (Caspase 4), caspase-5 (Caspase 5), caspase-6 (Caspase 6), caspase-7 (Caspase 7), caspase-8 (Caspase 8), caspase-9 (Caspase 9), chymotrypsin-high (Chymotrypsin (high specificity)), chymotrypsin-low (Chymotrypsin (low specificity)), clostripain (Clostripain (Arg-C)), cnbr (CNBr), elastase (Elastase), enterokinase (Enterokinase), factor-xa (Factor Xa), ficin (Ficin), formic-acid (Formic acid), glu-c (Glu-C (D and E)), glutamyl-endopeptidase (Glutamyl endopeptidase), granzyme-b (Granzyme B), hydroxylamine (Hydroxylamine), iodosobenzoic-acid (Iodosobenzoic acid), lysc (Lys-C), lysn (Lys-N), lysarginase (LysargiNase), neutrophil-elastase (Neutrophil elastase), ntcb (NTCB (2-nitro-5-thiocyanobenzoic acid)), papain (Papain), pepsin-ph2.0 (Pepsin (pH > 2)), pepsin-ph1.3 (Pepsin (pH 1.3)), proalanase (ProAlanase), proline-endopeptidase (Proline endopeptidase), proteinase-k (Proteinase K), staph-peptidase-i (Staphylococcal peptidase I), tev (TEV protease (Tobacco Etch Virus)), thermolysin (Thermolysin), thrombin (Thrombin), thrombin-sg (Thrombin (sequencing grade)), trypsin (Trypsin), trypsin-low (Trypsin (low specificity)), trypsin-simple (Trypsin (simple K/R)), alp (α-lytic protease (aLP)), custom (Custom cleavage rule). | trypsin |
| charges | No | charge states to report m/z for, e.g. [1,2,3] — [M+zH]z+ from the monoisotopic mass. | |
| enzymes | No | two or more proteases for a multi-enzyme digest; overrides `enzyme`. Order matters in concurrent mode. 'custom' takes its place in the order like any other. | |
| massMax | No | keep only peptides at or below this monoisotopic mass [Da]; omit for no upper bound. | |
| massMin | No | keep only peptides at or above this monoisotopic mass [Da]; omit for no lower bound. | |
| protein | Yes | the protein sequence (unambiguous one-letter codes); wire it from translate_sequence. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| cysteine | No | cysteine alkylation applied before the digest, as ExPASy PeptideMass offers it. Mass deltas are Unimod's. | none |
| maxLength | No | drop peptides longer than this (residues). | |
| minLength | No | drop peptides shorter than this (residues). | |
| customRegex | No | the 'custom' enzyme as a regular expression instead of RPG grammar (pyteomics' `rule=`): it matches at P1 and the cut falls after the match, e.g. '[KR]' cleaves after K or R. Single-enzyme only, and mutually exclusive with `customCleave`. Advanced. | |
| customCleave | No | cleaving rules for the 'custom' enzyme, in RPG grammar: the comma is the cut, so '(,A)' cleaves before A and '(K or R,)' after K or R. Empty parentheses mean any residue. | |
| metOxidation | No | methionine oxidation. 'all' oxidises every Met (masses move, peptide list unchanged); 'both' lists each Met peptide TWICE, unmodified and oxidised, as PeptideMass does. | off |
| keilExceptions | No | apply Keil's exception rules (sites trypsin does NOT cut despite matching). Only defined for trypsin. PeptideCutter and Bioconductor cleaver apply these by default, which is why this does too; pyteomics does not, so turn it off to cross-check against pyteomics. | |
| missedCleavages | No | single enzyme: allow up to this many internal sites per peptide (pyteomics). Multi-enzyme: append runs of up to this many merged adjacent peptides (RPG). | |
| customExceptions | No | exceptions for the 'custom' enzyme; each must repeat the rule it blocks, e.g. '(K or R,)(P)' = not when P follows. |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| count | Yes | peptides returned after any mass filter | |
| sites | Yes | cleavage-site positions (0-based residue index the next peptide starts at) | |
| results | Yes | multi-enzyme only: one entry per digestion (per enzyme in sequential mode, one for the whole set in concurrent), each with its own peptides, sites and coverage | |
| coverage | Yes | fraction of the protein covered by the peptides returned | |
| peptides | Yes | peptides with start/end, sequence, missed cleavages, masses and m/z (all results pooled in multi-enzyme mode) | |
| totalPeptides | Yes | peptides the digest produced BEFORE the mass filter |