Finnigan version 0.02 ===================== This module is part of the Unfinnigan project aimed at decoding the proprietary data files used to acquire data from Thermo mass spectrometers. These are are known as "raw" files and they were intended to be read with proprietary software (Xcalibur) running on the Windows operating system. This module allows complete access to scan data without the need to install any vendor software. It can decode several recent file formats (versions 57, 62 and 63) and it comes with a suite of command-line tools that can be used to examine various elements of the data. One of the tools, uf-mzxml, replaces ReAdW in the task of converting the Finnigan data to mzXML. The module and the tools have been tested in an ongoing SILAC proteomics project, where users are writing their own data analysis scripts. For more details, go to http://code.google.com/p/unfinnigan/ PLATFORM Thermo software runs only on Intel platforms and therefore every word in their files uses little-endian encoding. The (un)Finnigan modules have also been tested only on Intel platforms. The decoder is built around Perl's unpack() function and there is a chance that some of the templates may be incorrectly interpreted on a big-endian platform. The tests should reveal that -- please let me know if anything breaks. INSTALLATION To install this module type the following: perl Makefile.PL make make test make install To install in user-space (without requiring root permissions), run Makefile.PL like this: perl Makefile.PL PREFIX=/ Everything will work if your environment includes your home directory in these variables: PERL5LIB=...:/lib/perl5/site_perl PATH=/bin:... MANPATH=/man:... DEPENDENCIES This module requires these other modules: Data::Hexdumper DateTime::Format::WindowsFileTime Devel::Size (only in uf-mzxml, not essential) Encode File::Temp (only in uf-mzxml) Getopt::Declare Getopt::Long MIME::Base64 (in uf-mzxml and mzxml-unpack) Module::Find (not essential) Storable (only in uf-mzxml) XML::Generator (only in uf-mzxml) Tie::IxHash (only in uf-mzxml) The non-essential dependencies can be removed by commenting out the corresponding lines in the code. If you are not going to use uf-mzxml, further dependencies can be removed by commenting them out in Makefile.PL COPYRIGHT AND LICENCE Put the correct copyright and licence information here. Copyright (C) 2010 by Gene Selkov This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.10.0 or, at your option, any later version of Perl 5 you may have available.