NAME
MS2::Parser - A parser for MS2 files, commonly used in mass spectrometry based proteomics projects.
VERSION
Version 0.062'
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 an array of MS2::Scan (scan info).
$ms->parse("file.ms2");
Attributes
header
# 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
}
Peak data is represented by two distinct array references; DataMZ and DataIntensity. Both arrays are used to maintain the original peak 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:
RT: CPAN's request tracker (report bugs here)
AnnoCPAN: Annotated CPAN documentation
CPAN Ratings
Search CPAN
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.
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