Empirical Bayes Protein identifier

eagle-i ID

Resource Type

Properties

1. Resource Description

   "EBP calculates protein expression probabilities based on peptide sequence identifications from search algorithms such as Mascot and Sequest. Protein lists can be generated by choosing proteins whose expression probabilities exceed a threshold value. Varying the probability threshold allows the sensitivity of protein identification to be balanced against the false positive error rate. The statistical model assumes that every peptide sequence that could theoretically result from enzymatic digestion of a protein in the search database has a chance of being identified in the search results, whether correctly or incorrectly. The probabilities of correct identification are combined across multiple peptide searches using a function that returns the maximum probability from consensus identifications, and penalizes non-consensual identifications. Both correct and incorrect peptide sequence identifications are assumed to occur at random in this "space" of peptides, at rates that are governed by model parameters including protein length, estimated protein abundance, the size of the search database, and the number of peptide sequence identifications in the dataset. Degenerate peptides whose sequence matches multiple proteins are treated using "Occam's Razor", a principle by which the smallest set of probable proteins is chosen that is sufficient to explain the peptide sequence identifications. For each protein in the database, a likelihood ratio is calculated for the possibility that the peptide identifications whose sequence matches the protein are all incorrect. These likelihood ratios are used to estimate the expression probabilities, from which updated parameter estimates are obtained. The procedure is iterated until the algorithm converges at the maximum likelihood estimates. Replicated datasets can be analyzed by estimating multiple sets of model parameters can be estimated simultaneously. In this way, hypotheses about protein expression can be tested using the results of replicate experiments." "EBP can be run as an alternative to ProteinProphet as part of the Sashimi Trans-Proteomic Pipeline."

2. Additional Name

   EBP

3. Used by

   Institute for Translational Medicine and Therapeutics

4. Data Input

   Peptide identification data (SBCtools pepXML)

5. Data Output

   Protein identifications with expression probabilities (SBCtools protXML)

6. Software purpose

   Mass spectrometry data analysis objective

7. Related Publication or Documentation

   EBP, a program for protein identification using multiple tandem mass spectrometry datasets

8. Related Publication or Documentation

   The Post-Synaptic Density of Human Postmortem Brain Tissues: An Experimental Study Paradigm for Neuropsychiatric Illnesses

9. Website(s)

   http://bioinf.itmat.upenn.edu/ebp/

10. Related Technique

    Protein expression profiling

11. Developed by

    Price, Thomas, Ph.D.

12. Software license

    Creative Commons

13. Algorithm used

    Bayesian Model

14. Coded in

    Perl