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MS2-Parser-0.04
River stage zero No dependents
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/ MS2::Parser

NAME

MS2::Parser - A parser for MS2 files, commonly used in mass spectrometry based proteomics projects.

VERSION

Version 0.04'

SYNOPSIS

Quick summary of what the module does.

    use MS2::Parser;

    my $ms = MS2::Parser->new();

    $ms->parse("file.ms2");

    # accessing header information
    print $ms->header->ScanType;

DESCRIPTION

This is a Moose based parser for the MS2 file format. The MS2 file format is used to record MS/MS spectra. A full description of the MS2 file format may be found in: McDonald,W.H. et al. MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications. Rapid Commun. Mass Spectrom. 18, 2162-2168 (2004).

Methods

parse

This is the main function to call. The parse method recieves a path to the ms2 file and returns a Moose object containing two attributes; A MS2::Header (header info) and a list of MS2::Scan (scan info).

    $ms->parse("file.ms2");

Attributes

    # accessing header information
    print $ms->header->ScanType;

This is a representation of how MS2 data is organized inside the object. The MS2 object has a MS2::Header object with the following structure:

    internals: {
        AcquisitionMethod   "Data-Dependent",
        Comments            "RawXtract modified by Tao Xu, 2007",
        CreationDate        "4/13/2009 6:45:15 PM",
        DataType            "Centroid",
        Extractor           "RAWXtract",
        ExtractorOptions    "MS2",
        ExtractorVersion    "1.9.9.2",
        FirstScan           1,
        InstrumentType      "ITMS",
        IsolationWindow     undef,
        LastScan            33000,
        ScanType            "MS2"
    }

scan

    # accessing header information
    print $ms->scan->[0]->Mass;

    # copiyng the arraylist reference to an array.
    my @array = $ms->scanlist;

The MS2 object has a MS2::Scan object list with the following structure:

        internals: {
            ActivationType     "CID",
            Charge             7,
            DataIntensity      [
                [0] 15.6,
                [1] 27.8,
                [2] 12.6,
                [3] 16.2,
                [4] 28.7,
                [5] 15.6
            ],
            DataMZ             [
                [0] 308.8282,
                [1] 362.2597,
                [2] 390.5037,
                [3] 547.0424,
                [4] 563.5495,
                [5] 661.8907
            ],
            FirstScan          000006,
            InstrumentType     "ITMS",
            IonInjectionTime   25.000,
            Mass               2833.0688,
            PrecursorFile      "Pfu_Orbit_041209_05.ms1",
            PrecursorInt       214647.2,
            PrecursorMZ        405.58749,
            PrecursorScan      1,
            RetTime            0.03,
            SecondScan         000006
        }

The Data attribute is represented by two distinct array references; DataMZ and DataIntensity. Both arrays are used to maintain the data order.

AUTHOR

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

BUGS

Please report any bugs or feature requests to bug-ms2-parser at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=MS2-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 MS2::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 the the Artistic License (2.0). You may obtain a copy of the full license at:

http://www.perlfoundation.org/artistic_license_2_0

Any use, modification, and distribution of the Standard or Modified Versions is governed by this Artistic License. By using, modifying or distributing the Package, you accept this license. Do not use, modify, or distribute the Package, if you do not accept this license.

If your Modified Version has been derived from a Modified Version made by someone other than you, you are nevertheless required to ensure that your Modified Version complies with the requirements of this license.

This license does not grant you the right to use any trademark, service mark, tradename, or logo of the Copyright Holder.

This license includes the non-exclusive, worldwide, free-of-charge patent license to make, have made, use, offer to sell, sell, import and otherwise transfer the Package with respect to any patent claims licensable by the Copyright Holder that are necessarily infringed by the Package. If you institute patent litigation (including a cross-claim or counterclaim) against any party alleging that the Package constitutes direct or contributory patent infringement, then this Artistic License to you shall terminate on the date that such litigation is filed.

Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT HOLDER AND CONTRIBUTORS "AS IS' AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES. THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT PERMITTED BY YOUR LOCAL LAW. UNLESS REQUIRED BY LAW, NO COPYRIGHT HOLDER OR CONTRIBUTOR WILL BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THE PACKAGE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.