MS2::Parser - A parser for MS2 files, commonly used in mass spectrometry based proteomics projects.
Version 0.061'
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;
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).
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");
# 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" }
# 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.
Felipe da Veiga Leprevost, <leprevost at cpan.org>
<leprevost at cpan.org>
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.
bug-ms2-parser at rt.cpan.org
You can find documentation for this module with the perldoc command.
perldoc MS2::Parser
You can also look for information at:
RT: CPAN's request tracker (report bugs here)
http://rt.cpan.org/NoAuth/Bugs.html?Dist=MS2-Parser
AnnoCPAN: Annotated CPAN documentation
http://annocpan.org/dist/MS2-Parser
CPAN Ratings
http://cpanratings.perl.org/d/MS2-Parser
Search CPAN
http://search.cpan.org/dist/MS2-Parser/
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
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To install MS2::Parser, copy and paste the appropriate command in to your terminal.
cpanm
cpanm MS2::Parser
CPAN shell
perl -MCPAN -e shell install MS2::Parser
For more information on module installation, please visit the detailed CPAN module installation guide.