NAME

PepXML::Parser - A Perl parser for the pepXML file format.

VERSION

Version 0.01

SYNOPSIS

Quick summary of what the module does.

my $parser = PepXML::Parser->new();

my $pepxml = $parser->parse("sample.pepxml");

my %msms = $pepxml->get_msms_pipeline_analysis();

my @proteins = $pepxml->get_proteins();

my @peptides = $pepxml->get_unique_peptides();

...

DESCRIPTION

pepXML is an open data format developed at the SPC/Institute for Systems biology for the storage, exchange, and processing of peptide sequence assignments of MS/MS scans. pepXML is intended to provide a common data output format for many different MS/MS search engines and subsequent peptide-level analyses. Several search engines already have native support for outputting pepXML and converters are available to transform output files to pepXML.

Data Structure & Access

Once the file is parsed, a deeply nested data strcuture is organized in memory, with all the information stored inside the the top level class called PepXML::PepXMLFile. Use the public methods described bellow in order to acces the data.

PepXML::PepXMLFile  {
    Parents       Moose::Object
    public methods (17) : get_enzymes, get_hits, get_modifications, get_msms_pipeline_analysis, get_parameters, get_peptides, get_proteins, 
    get_run_summary, get_search_summary, get_unique_peptides, get_unique_proteins, meta, msms_pipeline_analysis, msms_run_summary, 
    sample_enzyme, search_hit, search_summary
    private methods (0)
    internals: {
        msms_pipeline_analysis   PepXML::MsmsPipelineAnalysis,
        msms_run_summary         PepXML::RunSummary,
        sample_enzyme            [
            [0] PepXML::Enzyme
        ],
        search_hit               [
            [0]  PepXML::SearchHit,
            [1]  PepXML::SearchHit,
            [2]  PepXML::SearchHit,
            [3]  PepXML::SearchHit,
            [4]  PepXML::SearchHit,
            [5]  PepXML::SearchHit,
            ...
        ],
        search_summary           PepXML::SearchSummary
    }

Public Methods

get_msms_pipeline_analysis

Return type: hash.

my %msms = $pepxml->get_msms_pipeline_analysis();

Data access:

{
date                   "2015-04-09T18:54:11",
summary_xml            "/Adult_Adrenalgland_Gel_Elite_49_f01.pep.xml",
xmlns                  "http://regis-web.systemsbiology.net/pepXML",
xmlns_schemaLocation   "http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v117.xsd",
xmlns_xsi              "http://www.w3.org/2001/XMLSchema-instance"
}

get_enzymes

Return tupe: array of PepXML::Enzyme objects.

my @enzymes = $pepxml->get_enzymes();

Data access:

[0] PepXML::Enzyme  {
    Parents       Moose::Object
    public methods (5) : cut, meta, name, no_cut, sense
    private methods (0)
    internals: {
        cut      "KR",
        name     "Trypsin",
        no_cut   "P",
        sense    "C"
    }
}

get_run_summary()

Return type: PepXML::RunSummary Object.

my $summary = $pepxml->get_run_summary();

Data access:

PepXML::RunSummary  {
    Parents       Moose::Object
    public methods (6) : base_name, meta, msManufacturer, msModel, raw_data, raw_data_type
    private methods (0)
    internals: {
        base_name        "Sample",
        msManufacturer   "Thermo Scientific",
        msModel          "LTQ Orbitrap Elite",
        raw_data         ".mzXML",
        raw_data_type    "raw"
    }
}

get_search_summary()

Return Type: PepXML::SearchSummary Object.

PepXML::SearchSummary is a complex object, some internal methods are accessors to other objects, like the aminoacid_modification for example.

my $search_summary = $pepxml->get_search_summary();

Data access:

PepXML::SearchSummary  {
    Parents       Moose::Object
    public methods (11) : aminoacid_modification, base_name, enzymatic_search_constraint, fragment_mass_type, meta, parameter, precursor_mass_type, search_database, search_engine, search_engine_version, search_id
    private methods (0)
    internals: {
        aminoacid_modification        [
            [0] PepXML::AAModification,
            [1] PepXML::AAModification
        ],
        base_name                     "/Adult_Adrenalgland_Gel_Elite_49_f01",
        enzymatic_search_constraint   PepXML::EnzSearchConstraint,
        fragment_mass_type            "monoisotopic",
        parameter                     [
            [0]  PepXML::Parameter,
            [1]  PepXML::Parameter,
            [2]  PepXML::Parameter,
            [3]  PepXML::Parameter,
            [4]  PepXML::Parameter,
            [5]  PepXML::Parameter,
            ...
        ],
        precursor_mass_type           "monoisotopic",
        search_database               PepXML::SearchDatabase,
        search_engine                 "Comet",
        search_engine_version         "2015.01 rev. 1",
        search_id                     1
    }
}

get_modifications()

Return Type: array of PepXML::AAModification objects.

my @mods = $pepxml->get_modifications();

Data access:

[0] PepXML::AAModification  {
    Parents       Moose::Object
    public methods (6) : aminoacid, mass, massdiff, meta, symbol, variable
    private methods (0)
    internals: {
        aminoacid   "M",
        mass        147.035385,
        massdiff    15.994900,
        symbol      "*",
        variable    "Y"
    }
},
[1] PepXML::AAModification  {
    Parents       Moose::Object
    public methods (6) : aminoacid, mass, massdiff, meta, symbol, variable
    private methods (0)
    internals: {
        aminoacid   "C",
        mass        160.030649,
        massdiff    57.021464,
        symbol      "",
        variable    "N"
    }
}

get_parameters()

Return Type: array of PepXML::Parameter objects.

my @params = $pepxml->get_parameters();

Data access:

[0] PepXML::Parameter  {
    Parents       Moose::Object
    public methods (3) : meta, name, value
    private methods (0)
    internals: {
        name    "# comet_version ",
        value   2015.01
    }
},
[1] PepXML::Parameter  {
    Parents       Moose::Object
    public methods (3) : meta, name, value
    private methods (0)
    internals: {
        name    "activation_method",
        value   "ALL"
    }
},
...

get_db_info()

Return type: PepXML::SearchDatabase object.

my $db = $pepxml->get_db_info;

Data access:

PepXML::SearchDatabase  {
    Parents       Moose::Object
    public methods (3) : local_path, meta, type
    private methods (0)
    internals: {
        local_path   "Ens78plusREV_plusPeps.fa",
        type         "AA"
    }
}

get_hits()

Return type: array of PepXML::SearchHit objects.

my @hits = $pepxml->get_hits();

Data access:

[0] PepXML::SearchHit  {
    Parents       Moose::Object
    public methods (22) : assumed_charge, calc_neutral_pep_mass, end_scan, hit_rank, index, massdiff, meta, num_matched_ions, num_matched_peptides, num_missed_cleavages, num_tol_term, num_tot_proteins, peptide, peptide_next_aa, peptide_prev_aa, precursor_neutral_mass, protein, retention_time_sec, search_score, spectrum, start_scan, tot_num_ions
    private methods (0)
    internals: {
        assumed_charge           3,
        calc_neutral_pep_mass    1118.485333,
        end_scan                 517,
        hit_rank                 5,
        index                    9,
        massdiff                 0.005685,
        num_matched_ions         12,
        num_matched_peptides     3916,
        num_missed_cleavages     0,
        num_tol_term             2,
        num_tot_proteins         2,
        peptide                  "DSGHPGHAEGR",
        peptide_next_aa          "E",
        peptide_prev_aa          "R",
        precursor_neutral_mass   1118.491019,
        protein                  "ENSP00000374387",
        retention_time_sec       572.8,
        search_score             {
            deltacn       0.009,
            deltacnstar   0.000,
            expect        2.14E+01,
            sprank        46,
            spscore       172.1,
            xcorr         0.961
        },
        spectrum                 "Adult_Adrenalgland_Gel_Elite_49_f01.00517.00517.3",
        start_scan               517,
        tot_num_ions             40
    }
}

get_proteins()

Return type: array

my @proteins = $pepxml->get_proteins();

get_unique_proteins()

Return type: array

my @proteins = $pepxml->get_unique_proteins();

get_peptides()

Return type: array

my @peptides = $pepxml->get_peptides();

get_unique_peptides()

Return type: array

my @peptides = $pepxml->get_unique_peptides();

AUTHOR

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

BUGS

Please report any bugs or feature requests to bug-pepxml-parser at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=PepXML-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 PepXML::Parser

You can also look for information at:

RT: CPAN's request tracker (report bugs here)

http://rt.cpan.org/NoAuth/Bugs.html?Dist=PepXML-Parser
AnnoCPAN: Annotated CPAN documentation

http://annocpan.org/dist/PepXML-Parser
CPAN Ratings

http://cpanratings.perl.org/d/PepXML-Parser
Search CPAN

http://search.cpan.org/dist/PepXML-Parser/

ACKNOWLEDGEMENTS

LICENSE AND COPYRIGHT

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.

To install PepXML::Parser, copy and paste the appropriate command in to your terminal.

cpanm

cpanm PepXML::Parser

CPAN shell

perl -MCPAN -e shell
install PepXML::Parser

For more information on module installation, please visit the detailed CPAN module installation guide.

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NAME

VERSION

SYNOPSIS

DESCRIPTION

Data Structure & Access

Public Methods

get_msms_pipeline_analysis

get_enzymes

get_run_summary()

get_search_summary()

get_modifications()

get_parameters()

get_db_info()

get_hits()

get_proteins()

get_unique_proteins()

get_peptides()

get_unique_peptides()

AUTHOR

BUGS

SUPPORT

ACKNOWLEDGEMENTS

LICENSE AND COPYRIGHT

Module Install Instructions