When using SEQUEST, what represents a good score? When using Mascot, what is the trade-off of missed identifications to false positives? These are hard questions whose answers depend on the instrument, sample complexity, FASTA database size, and experimental design. The PeptideProphet algorithm gives the answers.
PeptideProphet™ was developed by Keller, Nesvizhskii, et al.1 at The Institute for Systems Biology as a Bayesian statistical algorithm to convert SEQUEST scores into probabilities. The creators of PeptideProphet™ have written several articles2,3 explaining the advantages of this probability scheme.
|
PeptideProphet™ Explained
When interpreting tandem mass spectrometry data, a key question is how to determine which identifications are valid. The typical method is to accept all identifications that score above a chosen threshold. However, choosing an appropriate threshold is problematic, depending on the sample, the database searched, and how the sample was run on the mass spectrometer.4
PeptideProphet™ resolves this dilemma by automatically adjusting itself to the characteristics of the data.
For a discussion of the PeptideProphet ™algorithm and its advantages, continue to the slide presentation "PeptideProphet™ Explained ".
Proteome Software's Scaffold uses an independently written subroutine that implements the same algorithm as PeptideProphet™.
|
Peptide Prophet™ Explained"
by Brian Searle
PDF Format (417KB)
Power Point format
22 slides |
|
References
- Keller, A., Nesvizhskii, A. I., Kolker, E., and Aebersold R., "Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search." Anal. Chem. 2002 Oct 15;74(20):5383-92.
PubMed
- Nesvizhskii, A. I., and Aebersold, R., "Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS." Drug Discov. Today. 2004 Feb 15;9(4):173-81.
PubMed
- Carr, S., Aebersold, R., Baldwin, M., Burlingame, A., Clauser, K., and Nesvizhskii, A., "The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data", Mol. Cell Proteomics. 2004 Jun;3(6):531-3. Epub 2004 Apr 09.
PubMed
- Qian W, Liu T, Monroe M, Strittmatter E, Jacobs J, Kangas L, Petritis K, Camp D, Smith R, "Probability-Based Evaluation of Peptide and Protein Identifications from Tandem Mass Spectrometry and SEQUEST Analysis: The Human Proteome." Journal of Proteome Research, 2005 Jan-Feb; 4(1):53-62.
PubMed
|
