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ProteinProphetTM automatically validates protein identifications made on the basis of peptides assigned to MS/MS spectra by database search programs such as SEQUEST. Importantly, it addresses two critical issues:

Results of ProteinProphet analysis are presented as HTML in a concise and flexible manner that allows filtering, sorting, and easy access to the database search results.

This software was developed at the Institute for Systems Biology in Seattle and is described in Analytical Chemistry 2003, 75, 4646-4658.

Typically, ProteinProphet analysis follows PeptideProphet, which computes probabilities that peptides assigned to MS/MS spectra are correct, and in the case of quantitaiton experiments, XPRESS and/or ASAPRatio.

ProteinProphet is one component of the open source LC/MS/MS analysis pipeline developed at the ISB

Other components include:

Why open source?

How can I help?

There are many ways you can help us and you don't need to be a mass spectrometrist or a programmer in order to do it. The easiest way to help us is to provide us with feedback on our tools! Let us know if something doesn't work, if a change to a particular tool would make it more useful, if there's a useful tool or feature that's missing, etc. If you think you are qualified to help us in more specific ways, write to us! We'd love to add your name to the developers' section :)