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Techniques & Tools Technology, Proteomics, Mass Spectrometry

Our Open Source Future: Software

Title Image of Article Our Open Source Future: Software

Proteomics – the overarching study of protein populations – has been transformed by modern mass spectrometry’s ability to provide accurate and high-resolution analysis of intact proteins and the peptides derived from them.

But something else that advanced mass spectrometry does very well is to produce vast amounts of data. And large datasets are difficult and time consuming to analyze, especially when working in a cross-platform environment with proprietary, closed formats. Consequently, research teams are spending more and more of their time developing custom data analysis software.

Now, perhaps, there is a magic wand to deal with the problem. ProteoWizard is a free central resource where proteomics software developers can share high-quality source code and benefit from the work done by others; a proteomics toolkit, if you will.

Initiated in 2007 by researchers at the Mallick Lab at the Spielberg Family Center for Applied Proteomics, Stanford University, ProteoWizard is reaching critical mass with active contributions from the MacCoss group at University of Washington and the Tabb group at Vanderbilt University.

Parag Mallick, professor at Stanford, web designer and president of the ProteoWizard Software Foundation, believes open source offers the ultimate in collaboration. “By openly distributing ProteoWizard we are able to collaborate with labs all over the world to create an ecosystem that spurs innovation in proteomics and helps democratize the field,” he says.

Three key principles underpin ProteoWizard’s potential for widespread success. The first is robustness; ProteoWizard software is of commercial quality or better. This is ensured by strict adherence to current software design principles, giving users confidence in the stability of products and support for them. 

Second, ProteoWizard is cross-platform in nature, compatible with Windows, Linux and Macintosh systems.

Third, and most importantly, its core is fully open source, and its development is open to, indeed dependent upon, widespread collaboration. Mallick welcomes newcomers with open arms: “We’ve been fortunate to have dozens of researchers contribute to ProteoWizard and are actively encouraging new developers to join the effort”.

For more information about contributing to ProteoWizard or to download the toolkits available, visit proteowizard.


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About the Author
Rich Whitworth

Rich Whitworth completed his studies in medical biochemistry at the University of Leicester, UK, in 1998. To cut a long story short, he escaped to Tokyo to spend five years working for the largest English language publisher in Japan. "Carving out a career in the megalopolis that is Tokyo changed my outlook forever. When seeing life through such a kaleidoscopic lens, it's hard not to get truly caught up in the moment." On returning to the UK, after a few false starts with grey, corporate publishers, Rich was snapped up by Texere Publishing, where he spearheaded the editorial development of The Analytical Scientist. "I feel honored to be part of the close-knit team that forged The Analytical Scientist – we've created a very fresh and forward-thinking publication." Rich is now also Content Director of Texere Publishing, the company behind The Analytical Scientist.

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