NAME

MS::Reader::MGF::Spectrum - An MGF spectrum object

SYNOPSIS

    use MS::Reader::MGF;
    use MS::CV qw/:MS/;

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

    while (my $spectrum = $run->next_spectrum) {
        
        # $spectrum inherits from MS::Spectrum, so you can do:
        my $id  = $spectrum->id;
        my $rt  = $spectrum->rt;
        my $mz  = $spectrum->mz;
        my $int = $spectrum->int;
        my $lvl = $spectrum->ms_level;

        # in addition,

        # print the underlying data structure
        print $spectrum->dump;

    }

DESCRIPTION

MS::Reader::MGF::Spectrum objects represent spectra parsed from an MGF file. The class is an implementation of MS::Spectrum and so implements the standard data accessors associated with that class, as well as a few extra, as documented below. The underlying hash is a nested data structure containing all information present in the original MGF record. This information can be accessed directly (see below for details of the data structure) when class methods do not exist for doing so.

METHODS

id

    my $id = $spectrum->id;

Returns the ID of the spectrum

mz

    my $mz = $spectrum->mz;
    for (@$mz) { # do something }

Returns an array reference to the m/z data array

int

    my $int = $spectrum->int;
    for (@$int) { # do something }

Returns an array reference to the peak intensity data array

rt

    my $rt = $spectrum->rt;

Returns the retention time of the spectra, in SECONDS

ms_level

    my $l = $spectrum->ms_level;

For MS::Reader::MGF::Spectrum objects, always returns -1, as the MS level is not known from the file.

dump

    my $dump = $spectrum->dump;

Returns a textual representation (via Data::Dumper) of the data structure. This can facilitate access to data parsed from the MGF record but not accessible via an accessor method.

CAVEATS AND BUGS

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

Please reports bugs or feature requests through the issue tracker at https://github.com/jvolkening/p5-MS/issues.

SEE ALSO

• MS::Spectrum

AUTHOR

Jeremy Volkening <jdv@base2bio.com>

COPYRIGHT AND LICENSE

Copyright 2015-2019 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 <http://www.gnu.org/licenses/>.

cpanm MS

perl -MCPAN -e shell
install MS