NAME

MS::Reader::MzIdentML::Peptide - mzIdentML peptide object

SYNOPSIS

    my $pep = $search->fetch_peptide_by_id('PEP_1');

    say $pep->id;
    say $pep->seq;
    for (@{ $pep->mods }) {
        say $_->{monoisotopicMassDelta};
    }

DESCRIPTION

The MS::Reader::MzIdentML::Peptide class represents a <Peptide> element in the search results. This is a specific peptide isoform with known sequence and modifications, and can be referenced elsewhere in the results.

METHODS

id

    my $id = $pep->id;

Returns the peptide ID, which is a unique identifier within the results file

seq

    my $seq = $pep->seq;

Returns the peptide sequence as a one-letter IUPAC string

mods

    my $mods = $pep->mods;

Returns a reference to an array of modifications, each of which is a nested hash structure. The details of this structure are currently undocumented and need to be deduced using Data::Dumper to be utilized. At some point a Modification class will be implemented to make utilization of this data easier.

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.

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/>.