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

PMID: 17164401 (view PubMed database entry)
DOI: 10.1074/mcp.t600049-mcp200 (read at publisher's website )

Thomas S Price, Margaret B Lucitt, Weichen Wu, David J Austin, Angel Pizarro, Anastasia K Yocum, Ian A Blair, Garret A FitzGerald, Tilo Grosser,

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.

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2007, 6(3):527-536]

Cited: 33 times

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