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Bioinformatics Advance Access originally published online on July 7, 2008
Bioinformatics 2008 24(21):2534-2536; doi:10.1093/bioinformatics/btn323
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

ProteoWizard: open source software for rapid proteomics tools development

Darren Kessner 1,*, Matt Chambers 2, Robert Burke 1, David Agus 1 and Parag Mallick 1,3,*

1Spielberg Family Center for Applied Proteomics, Cedars-Sinai Medical Center, 2Department of Biochemistry, Vanderbilt University, Nashville, TN and 3 Department of Chemistry & Biochemistry, University of California, Los Angeles, CA, USA

*To whom correspondence should be addressed.


  Abstract

Summary: The ProteoWizard software project provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard proteomics and LCMS dataset computations. The library contains readers and writers of the mzML data format, which has been written using modern C++ techniques and design principles and supports a variety of platforms with native compilers. The software has been specifically released under the Apache v2 license to ensure it can be used in both academic and commercial projects. In addition to the library, we also introduce a rapidly growing set of companion tools whose implementation helps to illustrate the simplicity of developing applications on top of the ProteoWizard library.

Availability: Cross-platform software that compiles using native compilers (i.e. GCC on Linux, MSVC on Windows and XCode on OSX) is available for download free of charge, at http://proteowizard.sourceforge.net. This website also provides code examples, and documentation. It is our hope the ProteoWizard project will become a standard platform for proteomics development; consequently, code use, contribution and further development are strongly encouraged.

Contact: darren{at}proteowizard.org; parag{at}ucla.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: John Quackenbush

Received on April 18, 2008; revised on May 21, 2008; accepted on June 18, 2008

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