EBP, a program for protein identification using multiple tandem mass spectrometry datasets.
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.
Price
Thomas S
TS
Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
Lucitt
Margaret B
MB
Wu
Weichen
W
Austin
David J
DJ
Pizarro
Angel
A
Yocum
Anastasia K
AK
Blair
Ian A
IA
FitzGerald
Garret A
GA
Grosser
Tilo
T
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
D029941:Fish Proteins