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New software lets researchers filter enormous proteomic data sets

Oct. 11, 2012, 10:07 AM

An upcoming issue of the journal Nature Biotechnology announces the release of ProteoWizard Toolkit 3.0, a free set of cross-platform (PC, Mac, Linux) software libraries and applications designed to facilitate proteomics research.

The article is now available on the journal’s website.

Listed first among the paper’s several authors is Vanderbilt’s Matthew Chambers, a bioinformatics systems engineer who has contributed work on ProteoWizard since early in the project.

Scientists use ProteoWizard to access, filter and analyze huge proteomic data sets generated by different mass spectrometers.

Machines from different companies generate mass spectrometry data in divergent formats. ProteoWizard fills a crucial role in letting users manipulate data files regardless of which company’s mass spectrometer produced the data. According to Chambers, it is the most comprehensive input-output toolkit in proteomics.

“I started very early in the project because I was excited about this idea of a unified interface to access any kind of file,” Chambers said.

For the past three years Chambers has been the primary developer of the ProteoWizard library, the core of the toolkit.

For more information see the ProteoWizard website at

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