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FAQ

What is ProteoWizard?

You can find out more about ProteoWizard here:

How do I cite ProteoWizard?

If you use or incorporate the ProteoWizard tools or libraries, please cite our Bioinformatics Application Note [abstract] [pdf] :

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

What is the current status of ProteoWizard?

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

What formats does ProteoWizard support?

On all platforms: mzML (1.1 and 1.0), mzXML, MGF

On Windows, with vendor libraries: Agilent, Applied Biosystems, Bruker, Thermo, Waters

Who is using ProteoWizard?

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.

I want to contribute!

Great! Drop Darren an email darren@proteowizard.org and he'll get you signed up to the subversion repository.

Where is your 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/

What's next on the development roadmap?

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.