About the ProteoWizard Software Foundation and Project
ProteoWizard 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 chemistry and LCMS dataset computations.
The primary goal of ProteoWizard is to eliminate the existing barriers to proteomic software development so that researchers can focus on the development of new analytic approaches, rather than having to dedicate significant resources to mundane (if important) tasks, like reading data files.
The first challenge of writing analysis tools is reading the myriad of data formats prevalent throughout the proteomics field. In addition to the open mzML, mzXML, and mzData formats, each vendor typically encodes their data in a vendor-specific, proprietary, closed format. The third challenge is the lack of a single, standard cross-platform library that performs common calculations, such as protein digestion, mass computation, peak integration, charge state detection and isotope deconvolution. Consequently, these calculations have been repeatedly implemented in the course of developing more sophisticated tools.
As the proteomics field continues to grow, an increasing number of research groups are writing custom software for data analysis. Our goal is for ProteoWizard to become a repository where proteomics software developers can share their work, and benefit from the work of others. We welcome contributions of existing code, or new projects that will benefit the proteomics community.
The key tenets of ProteoWizard are:
- Robustness: ProteoWizard is meant to be a production quality, commercial grade set of tools and libraries. Code is well designed and architected using modern software design principles. Consequently, users can trust its stability and treat it as an ongoing, supported resource.
- Permissively Licensed, Open Source: ProteoWizard's core is fully open source, licensed under the Apache License. This license is non-viral and allows use by both academic and commercial entities. Insilicos and LabKey Software have been invaluable partners in the development of ProteoWizard. We encourage other commercial and academic groups to contribute to building this general resource for our whole field.
- Cross Platform: The ProteoWizard Core builds natively on Windows, Linux and Macintosh and thus can support application development readily on a variety of platforms.
The ProteoWizard software project was initiated in 2007, by the Mallick lab, at the Spielberg Family Center for Applied Proteomics. We are extremely grateful to Dr. David Agus for his initial and ongoing support for this initiative. Since 2007, numerous other groups have been actively contributing code, and expertise to the project. Notably, the MacCoss group at University of Washington and the Tabb group at Vanderbilt Unversity. In 2010, The ProteoWizard Project was spun out from the Center for Applied Molecular Medicine, at the University of Southern California, into a California, Non-Profit Corporation - the ProteoWizard Software Foundation. We are greatly appreciative to the USC Stevens Institute for helping with the creation of the ProteoWizard Software Foundation.