MS::Reader::MGF - A simple but complete MGF parser


    use MS::Reader::MGF;

    my $run = MS::Reader::MGF->new('run.mgf');

    while (my $spectrum = $run->next_spectrum) {
        my $rt = $spectrum->rt;
        # see MS::Reader::MGF::Spectrum and MS::Spectrum for all available
        # methods


    $spectrum = $run->fetch_spectrum(0);  # first spectrum


MS::Reader::MGF is a parser for the MGF format for raw mass spectrometry data. It aims to provide complete access to the data contents while not being overburdened by detailed class infrastructure. Convenience methods are provided for accessing commonly used data.


MS::Reader::MGF is a subclass of MS::Reader and inherits the methods of this parental class. Please see the documentation for that class for details of available methods not detailed below.



    my $run = MS::Reader::MGF->new( $fn,
        use_cache => 0,
        paranoid  => 0,

Takes an input filename (required) and optional argument hash and returns an MS::Reader::MGF object. This constructor is inherited directly from MS::Reader. Available options include:

  • use_cache — cache fetched records in memory for repeat access (default: FALSE)

  • paranoid — when loading index from disk, recalculates MD5 checksum each time to make sure raw file hasn't changed. This adds (typically) a few seconds to load times. By default, only file size and mtime are checked.


    while (my $s = $run->next_spectrum) {
        # do something

Returns an MS::Reader::MGF::Spectrum object representing the next spectrum in the file, or undef if the end of records has been reached. Typically used to iterate over each spectrum in the run.


    my $s = $run->fetch_spectrum($idx);

Takes a single argument (zero-based spectrum index) and returns an MS::Reader::MGF::Spectrum object representing the spectrum at that index. Throws an exception if the index is out of range.



Takes a single argument (zero-based spectrum index) and sets the spectrum record iterator to that index (for subsequent calls to next_spectrum).


    my $n = $run->n_spectra;

Returns the number of spectra present in the file.


    my $idx = $run->curr_index;

Returns the index of the current iterator


    my $idx = $run->get_index_by_id($id);

Returns the index of the spectrum with ID $id


The API is in alpha stage and is not guaranteed to be stable.

Please reports bugs or feature requests through the issue tracker at



Jeremy Volkening <>


Copyright 2015-2016 Jeremy Volkening

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <>.