peptide

2.4.0
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allowNeutralLoss

Add neutral loss on natural amino acids

allowNeutralLoss(mf: any)
Parameters
mf (any)

generatePeptideFragments

Generate peptide fragments from a molecular formula.

generatePeptideFragments(mf: string, options: object?): Array<string>
Parameters
mf (string) The molecular formula to fragment.
options (object?) Fragmentation options.
Name Description
options.a boolean (default false) Generate a-type fragments.
options.b boolean? Generate b-type fragments. Defaults to true if no options are specified, otherwise false .
options.c boolean (default false) Generate c-type fragments.
options.x boolean (default false) Generate x-type fragments.
options.y boolean? Generate y-type fragments. Defaults to true if no options are specified, otherwise false .
options.z boolean (default false) Generate z-type fragments.
options.i boolean (default false) Generate internal fragments.
options.ya boolean (default false) Generate ya-type double fragmentation.
options.yb boolean (default false) Generate yb-type double fragmentation.
options.yc boolean (default false) Generate yc-type double fragmentation.
options.zc boolean (default false) Generate zc-type double fragmentation.
options.maxInternal number (default Infinity) Maximum number of residues for internal fragments.
options.minInternal number (default 0) Minimum number of residues for internal fragments.
Returns
Array<string>: Array of fragment molecular formulas.

digestPeptide

Digest a peptide sequence using a specified enzyme.

digestPeptide(sequence: string, options: object): Array<string>
Parameters
sequence (string) The peptide sequence to digest.
options (object = {}) Digestion options.
Name Description
options.enzyme string The enzyme to use for digestion. Required. Supported values: 'chymotrypsin', 'trypsin', 'lysc', 'glucph4', 'glucph8', 'thermolysin', 'cyanogenbromide', 'any'.
options.minMissed number (default 0) Minimum number of missed cleavages.
options.maxMissed number (default 0) Maximum number of missed cleavages.
options.minResidue number (default 0) Minimum number of residues in a fragment.
options.maxResidue number (default Infinity) Maximum number of residues in a fragment.
options.minDigestions number (default 0) Minimum number of cleavage sites to use. Generates all combinations with at least this many cleavages. Defaults to 0 .
options.maxDigestions number (default Infinity) Maximum number of cleavage sites to use. Generates all combinations with at most this many cleavages. Defaults to Infinity .
Returns
Array<string>: Array of digested peptide fragments.

createFragmentsFromCleavages

Create fragments from selected cleavage sites.

createFragmentsFromCleavages(allFragments: Array<string>, cleavageSites: Array<number>): Array<{sequence: string, nbResidue: number, from: number, to: number}>
Parameters
allFragments (Array<string>) All possible fragments if all sites were cleaved.
cleavageSites (Array<number>) Indices of cleavage sites to use.
Returns
Array<{sequence: string, nbResidue: number, from: number, to: number}>: Fragment objects.