a Perl parser for MzML data.
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
lib/MzML
t
Changes
MANIFEST
Makefile.PL
README
README.pod
ignore.txt

README.pod

NAME

MzML::Parser - A Perl parser for the mzML data format.

SYNOPSIS

Quick summary of what the module does.

Perhaps a little code snippet.

my $p = MzML::Parser->new();
my $res = $p->parse("miape_sample.mzML");
...

DESCRIPTION

From 2005-2008 there has existed two separate XML formats for encoding raw spectrometer output: mzData developed by the PSI and mzXML developed at the Seattle Proteome Center at the Institute for Systems Biology. It was recognized that the existence of two separate formats for essentially the same thing generated confusion and required extra programming effort. Therefore the PSI, with full participation by ISB, has developed a new format by taking the best aspects of each of the precursor formats to form a single one. It is intended to replace the previous two formats. This new format was originally given a working name of dataXML. The final name is mzML. The first specification was published in June 2008. This format was officially released at the 2008 American Society for Mass Spectrometry Meeting, and is since then relatively stable with very few updates. On 1 June 2009, mzML 1.1.0 was released.

The parser will transform the mzML file into a completely structured set of objects, according to the 1.1.0 specification published in http://www.peptideatlas.org/tmp/mzML1.1.0.html.

Object Structure

In order to acces the information organized deeply into the nested structure, i suggest to you to use the module Data::Printer. The future versions of this module will have accessors methods to more specifically access some of the information inside the object.

THis is an example of how the object is organized:

MzML::Registry  {
    Parents       Moose::Object
    public methods (11) : cvlist, dataProcessingList, fileDescription, instrumentConfigurationList, meta, mzML, referenceableParamGroupList, run, sampleList, scanSettingsList, softwareList
    private methods (0)
    internals: {
        cvlist                        MzML::CvList,
        dataProcessingList            MzML::DataProcessingList,
        fileDescription               MzML::FileDescription,
        instrumentConfigurationList   MzML::InstrumentConfigurationList,
        mzML                          MzML::MzML,
        referenceableParamGroupList   MzML::ReferenceableParamGroupList,
        run                           MzML::Run,
        sampleList                    MzML::SampleList,
        scanSettingsList              MzML::ScanSettingsList,
        softwareList                  MzML::SoftwareList
    }
}

AUTHOR

Felipe da Veiga Leprevost, <leprevost at cpan.org>

BUGS

Please report any bugs or feature requests to bug-mzml-parser at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=MzML-Parser. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.

SUPPORT

You can find documentation for this module with the perldoc command.

perldoc MzML::Parser

You can also look for information at:

ACKNOWLEDGEMENTS

LICENSE AND COPYRIGHT

Copyright 2014 Felipe da Veiga Leprevost.

This program is free software; you can redistribute it and/or modify it under the terms of either: the GNU General Public License as published by the Free Software Foundation; or the Artistic License.

See http://dev.perl.org/licenses/ for more information.