mgf-parser

Parse an MGF file into a JSON.

Installation

$ npm i mgf-parser

Usage

import { readFileSync } from 'node:fs';
import { join } from 'node:path';

import { parse } from 'mgf-parser';

const rawData = readFileSync(join(import.meta.dirname, './data.mgf'), 'utf8');

const result = parse(rawData, { uniqueX: true, maxY: 100 });

// result[0].kind -> 'IONS'
// result[0].meta -> { TITLE: 'Spectrum 1', PEPMASS: '983.6', ... }
// result[0].data -> { x: [846.6, 846.8, ...], y: [25.08, 15.12, ...] }

parse(rawData[, options])

Parses the text input rawData and returns one entry per BEGIN / END block:

Property	Type	Description
kind	string	Record type, i.e. what follows BEGIN — usually IONS.
meta	Record<string, string>	Parameters of the entry, on top of the global parameters.
data	DataXY	The mass spectrum, as x (m/z) and y (intensity) arrays.

Options:

Option	Type	Default	Description
recordTypes	string	''	Regular expression the record type must match. By default all entries are returned.
sortX	boolean	false	Sort the spectrum by increasing m/z.
uniqueX	boolean	false	Merge repeating m/z values, summing their intensities. Implies sortX.
normedY	boolean	false	Normalize the spectrum so that the sum of the intensities is 1.
maxY	number	undefined	Rescale the spectrum so that the largest intensity equals maxY. Conflicts with normedY.

Supported syntax

The parser follows the Mascot generic format:

• Parameters declared before the first BEGIN are global: they are copied into the meta of every entry, where a parameter of the entry overrides them.
• Lines starting with #, ;, ! or / are comments, and blank lines are ignored.
• A peak line holds an m/z and an intensity, optionally followed by the fragment charge, which is ignored. Values may be separated by , \t, , or ;.

An unparsable line, or fragment ions found outside of a BEGIN / END block, throws an error mentioning the line number.

API Documentation

License

MIT