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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 3.x of the library, together with a set of command line tools. Binary packages are only available for download from our download page, but source code is available both there and at our GitHub project

What formats does ProteoWizard support?

On all platforms: mzML (1.1 and 1.0), mzXML, mz5, MGF, MS1/MS2, mzIdentML, and traML

On Windows, with vendor libraries: Agilent, Bruker, Sciex, Shimadzu, Thermo, and UIMF.

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! We are happy to review Pull Requests to our GitHub repository.

Where is your source code repository?

In 2018, we migrated from SourceForge to GitHub (and from SVN to Git).

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