FAQ

What is ProteoWizard?

ProteoWizard is a set of tools and libraries to facilitate proteomics data analysis and to facilitate developing applications for proteomics data analysis.

How do I cite ProteoWizard?

If you use or incorporate the ProteoWizard tools or libraries, please cite our Nature Biotechnology Commentary

A cross-platform toolkit for mass spectrometry and proteomics. Chambers, M.C., MacLean, B., Burke, R., Amode, D., Ruderman, D.L., Neumann, S., Gatto, L., Fischer, B., Pratt, B., Egertson, J., Hoff, K., Kessner, D., Tasman, N., Shulman, N., Frewen, B., Baker, T.A., Brusniak, M.-Y., Paulse, C., Creasy, D., Flashner, L., Kani, K., Moulding, C., Seymour, S.L., Nuwaysir, L.M., Lefebvre, B., Kuhlmann, F., Roark, J., Rainer, P., Detlev, S., Hemenway, T., Huhmer, A., Langridge, J., Connolly, B., Chadick, T., Holly, K., Eckels, J., Deutsch, E.W., Moritz, R.L., Katz, J.E., Agus, D.B., MacCoss, M., Tabb, D.L. & Mallick, P. Nature Biotechnology 30, 918-920 (2012). [article]

and/or 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 2.1.x of the library, together with a 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: Thermo, Agilent, Bruker, Thermo, Waters and AB Sciex.

Who is using ProteoWizard?

Hundreds of labs around the world are using different ProteoWizard tools. The central developers are at the Center for Applied Molecular Medicine (CAMM) at the University of Southern California, the Canary Center for Early Detection at Stanford University, the Vanderbilt University Mass Spectrometry Research Center and at the MacCoss lab at the University of Washington, Seattle. Each of these groups use ProteoWizard extensively in daily data analysis.

The ProteoWizard libraries are also 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 Matt an email: 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://svn.code.sf.net/p/proteowizard/code/trunk/pwiz your_local_directory Or you can browse the repository at: https://sourceforge.net/p/proteowizard/code/

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. Our immediate priorities are putting together a simple GUI, supporting mzIdentML, and extending ProteoWizard to other languages by adding SWIG support.

Get ProteoWizard at SourceForge.net. Fast, secure and Free Open Source software downloads