js-mgf

js-mgf

This module provides simple mgf file parsing

Installation

npm install js-mgf --save

Usage

Quickstart example:

var fs = require('fs');
var mgf = require('js-mgf');

var filename = 'test.mgf';

fs.readFile(filename, 'utf8', function(err, data){
  if (err) throw err;

  spectra = mgf.parse(data);
  console.log(spectra);
});

Output:

[ { title: 'First spectrum',
    rt: 500,
    pepmass: 432,
    pepintensity: 12000,
    charge: 2,
    mz: [ 123, 549, 567, 657 ],
    intensity: [ 54, 12, 100, 34 ] },
  { title: 'Second spectrum = something cool',
    rt: 510,
    pepmass: 679.32,
    charge: -3,
    mz: [ 123.4, 549.6, 567.8, 657.1 ],
    intensity: [ 54.12, 12.89, 100.67, 34.45 ] } ]

Contents of test.mgf

BEGIN IONS
TITLE=First spectrum
RTINSECONDS=500
PEPMASS=432 12000
CHARGE=2+
123 54
549 12
567 100
657 34
END IONS

BEGIN IONS
TITLE=Second spectrum = something cool
RTINSECONDS=510
PEPMASS=679.32
CHARGE=3-
123.4 54.12
549.6 12.89
567.8 100.67
657.1 34.45
END IONS

This module only has the one parse method and takes as input the text content of an mgf file. This module will read the following information:

• TITLE as title
• RTINSECONDS as rt
• PEPMASS as pepmass and pepintensity if the second intensity value is present
• CHARGE as charge
• All the mz and intensity values into the mz and intensity arrays.

No other fields will be read from the mgf file.

Tests

You can run npm test to run the tests after installing the development dependencies.

Future functionality

No future functionality is planned.

License

This software is released under the MIT license.

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