title: EBP, a program for protein identification using multiple tandem mass spectrometry datasets.
abstract: 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.
authors.affiliation: Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
authors.forename: Thomas S
authors.initials: TS
authors.lastname: Price
authors.forename: Margaret B
authors.initials: MB
authors.lastname: Lucitt
authors.forename: Weichen
authors.initials: W
authors.lastname: Wu
authors.forename: David J
authors.initials: DJ
authors.lastname: Austin
authors.forename: Angel
authors.initials: A
authors.lastname: Pizarro
authors.forename: Anastasia K
authors.initials: AK
authors.lastname: Yocum
authors.forename: Ian A
authors.initials: IA
authors.lastname: Blair
authors.forename: Garret A
authors.initials: GA
authors.lastname: FitzGerald
authors.forename: Tilo
authors.initials: T
authors.lastname: Grosser
mesh_terms: D000465:Algorithms; D000818:Animals; D002853:Chromatography, Liquid; D004625:Embryo, Nonmammalian; D029941:Fish Proteins / Q000032:analysis*; D015233:Models, Statistical; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry; D015027:Zebrafish / Q000196:embryology / Q000378:metabolism
chemical_list: D029941:Fish Proteins