You can find out more about ProteoWizard here:
ProteoWizard: Open Source Software for Rapid Proteomics Tools Development
Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick
Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323
We have released version 1.5.x of the library, together with the first set of command line tools. Source and binary packages are available for download from our download page or from our SourceForge project page
On all platforms: mzML (1.1 and 1.0), mzXML, MGF
On Windows, with vendor libraries: Agilent, Applied Biosystems, Bruker, Thermo, Waters
Researchers at the Center for Applied Molecular Medicine (CAMM) at the University of Southern California and the Vanderbilt University Mass Spectrometry Research Center use the ProteoWizard tools extensively in daily data analysis.
The ProteoWizard libraries are being used by the Trans-Proteomic Pipeline (TPP) and the Computational Proteomics Analysis System (CPAS) tools for mzML support.
Great! Drop Darren an email darren@proteowizard.org and he'll get you signed up to the subversion repository.
To checkout the entire proteowizard, you can issue the command
svn co https://proteowizard.svn.sourceforge.net/svnroot/proteowizard/trunk/pwiz your_local_directory
Or you can browse the repository at:
http://proteowizard.svn.sourceforge.net/viewvc/proteowizard/
We (CAMM) have begun collaboration with other proteomics software groups, including the Vanderbilt University Mass Spectrometry Research Center, University of Washington, Insilicos Software, and the Seattle Proteome Center at the Institute for Systems Biology (ISB/SPC), with the goal of providing a single standard software library for proteomic data analysis. The first immediate goal is to combine efforts to add support for all vendor-specific proprietary data formats.