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PeptideProphetTM automatically validates peptide assignments to MS/MS spectra made by database search programs such as SEQUEST. From each dataset, it learns distributions of search scores and peptide properties among correct and incorrect peptides, and uses those distributions to compute for each result a probability that it is correct. Relevant peptide properties include the number of termini compatible with enzymatic cleavage (for unconstrained searches), the number of missed enzyme cleavages, the mass difference with respect to the precursor ion, the presence of light or heavy cysteine (for ICAT experiments), and the presence of an N-glycosylation motif (for N-glycosylation capture experiments). PeptideProphet can be used as a second step following the analysis of MS/MS spectra generated from any type of mass spectrometer, and assigned peptides using any number of database search programs.

This software was developed at the Institute for Systems Biology in Seattle and is described in Analytical Chemistry 2002, 74, 5383-5392.

Typically, PeptideProphet analysis is followed by ProteinProphet, which groups peptides by their corresponding protein(s) to compute probabilities that those proteins were present in the original sample.

PeptideProphet 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 :)