Peptide Cutter

A library for in silico proteolytic digestion of proteins and peptides.

View on npm here.

Installation

npm install peptide-cutter --save

PLEASE NOTE

This module relies on positive lookbehind regex and thus can only be run with newer versions of JavaScript. You may need to use the --harmony argument with node in order to use this module.

Also note

v2.x.x introduces breaking changes from v1.x.x in the return format

Usage

var peptideCutter = require('peptide-cutter');

var options = {
  'enzyme': 'trypsin',
  'num_missed_cleavages': 2,
  'min_length': 2,
  'max_length': 30
};

var cutter = new peptideCutter(options);

var peptides = cutter.cleave("KARATE");

Return format:

[ { sequence: 'KAR', start: 0, end: 2, missed: 1 },
  { sequence: 'KARATE', start: 0, end: 5, missed: 2 },
  { sequence: 'AR', start: 1, end: 2, missed: 0 },
  { sequence: 'ARATE', start: 1, end: 5, missed: 1 },
  { sequence: 'ATE', start: 3, end: 5, missed: 0 } ]

• sequence is the digested fragment
• start is the 0-based index of where in the original sequence the fragment can be found
• end is the 0-based index of where in the original sequence the fragment ends (this value is inclusive)
• missed is the number of missed cleavages found in this particular fragment.

About

The regex for the cleavage sites was ~~stolen~~ borrowed from the Pyteomics package which in turn comes from the Expasy PeptideCutter.

Available enzymes

• arg-c
• asp-n
• bnps-skatole
• caspase 1-10
• chymotrypsin high specificity
• chymotrypsin low specificity
• clostripain
• cnbr
• enterokinase
• factor xa
• formic acid
• glutamyl endopeptidase
• granzyme b
• hydroxylamine
• iodosobenzoic acid
• lysc
• ntcb
• pepsin ph1.3
• pepsin ph2.0
• proline endopeptidase
• proteinase k
• staphylococcal peptidase i
• thermolysin
• thrombin
• trypsin

The available enzymes and their corresponding regex are also found in expasy_rules.json

Tests

You can run npm test to run the tests after installing the development dependencies. There are basic tests to make sure all the enzymes will cleave proteins, but I cannot guarantee their completeness.

Future functionality

There are currently no planned improvements to this module. I am open to suggestions so let me know if you think something is missing.

License

This software is released under the MIT license

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