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Originally published In Press as doi:10.1074/mcp.T600049-MCP200 on December 12, 2006.
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Molecular & Cellular Proteomics 6:527-536, 2007.
© 2007 by The American Society for Biochemistry and Molecular Biology, Inc.

Technology

EBP, a Program for Protein Identification Using Multiple Tandem Mass Spectrometry Datasets*,S

Thomas S. Price{ddagger}, Margaret B. Lucitt{ddagger}, Weichen Wu{ddagger}, David J. Austin{ddagger}, Angel Pizarro{ddagger}, Anastasia K. Yocum§, Ian A. Blair§,¶, Garret A. FitzGerald{ddagger},|| and Tilo Grosser{ddagger},**

From the {ddagger} Institute for Translational Medicine and Therapeutics and § Center for Cancer Pharmacology, University of Pennsylvania, Philadelphia, Pennsylvania 19104

MS/MS combined with database search methods can identify the proteins present in complex mixtures. High throughput methods that infer probable peptide sequences from enzymatically digested protein samples create a challenge in how best to aggregate the evidence for candidate proteins. Typically the results of multiple technical and/or biological replicate experiments must be combined to maximize sensitivity. We present a statistical method for estimating probabilities of protein expression that integrates peptide sequence identifications from multiple search algorithms and replicate experimental runs. The method was applied to create a repository of 797 non-homologous zebrafish (Danio rerio) proteins, at an empirically validated false identification rate under 1%, as a resource for the development of targeted quantitative proteomics assays. We have implemented this statistical method as an analytic module that can be integrated with an existing suite of open-source proteomics software.

** To whom correspondence should be addressed: The Inst. for Translational Medicine and Therapeutics, University of Pennsylvania, 809 BRB II/III, 421 Curie Blvd., Philadelphia, PA 19104. Tel.: 215-573-7600; Fax: 215-573-9004; E-mail: tilo{at}spirit.gcrc.upenn.edu


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Home page
 Mol. Cell. ProteomicsHome page
M. B. Lucitt, T. S. Price, A. Pizarro, W. Wu, A. K. Yocum, C. Seiler, M. A. Pack, I. A. Blair, G. A. FitzGerald, and T. Grosser
Analysis of the Zebrafish Proteome during Embryonic Development
Mol. Cell. Proteomics, May 1, 2008; 7(5): 981 - 994.
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