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ProteinProphet^TM

ProteinProphet^TM 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:

• Peptides corresponding to 'single-hit' proteins (those to which no other peptides correspond) are less likely to be correct that those corresponding to 'multi-hit' proteins. ProteinProphet learns from each dataset by how much peptide probabilities should be adjusted to reflect this protein grouping information.
  
• Many peptides are present in more than a single database protein entry. ProteinProphet apportions such peptides among all corresponding proteins in such a way as to derive the simplest list of proteins that explain the observed peptids.
  

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:

• mzXML Converters and Parsers, Summary HTML creator, Interact, XPRESS quantitation, and ASAPRatio quantitation available at http://sf.net/projects/sashimi/.
  
• PeptideProphet available at http://sf.net/projects/peptideprophet/.
  
  
  

Why open source?

• Open source software gives you a flexibility that cannot be equaled by any proprietary source software. It can be easily tailored to address your particular needs.
  
• Open source software gives you full insight on how your data is being handled.
  
• Open source software is probably the most democratic way to establish a widely accepted standard in data analysis.
  

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 :)