title: Application of capture-recapture models to estimation of protein count in MudPIT experiments.
abstract: MudPIT is an automated shotgun proteomics approach that enhances the separation of peptides for sequencing by mass spectrometry analysis.We here adapt a mathematical model from ecology, namely, the capture-recapture model with a closed population and time-varying and heterogeneous individual probabilities of capture, to model the number of peptide identifications across the various cycles of a typical MudPIT experiment. In the absence of any prior information on abundance levels, the model can be used to estimate the total number of proteins in the experimental sample. We apply the model to a recent MudPIT-based experiment to estimate the total number of rat lung endothelial cell surface proteins. The model provides some practical guidelines for planning MudPIT experiments.
authors.affiliation: Department of Molecular and Experimental Medicine, Scripps Research Institute, 10550 North Torrey Pines Road, MEM216, La Jolla, California 92037, USA.
authors.forename: James A
authors.initials: JA
authors.lastname: Koziol
authors.forename: Anne C
authors.initials: AC
authors.lastname: Feng
authors.forename: Jan E
authors.initials: JE
authors.lastname: Schnitzer
mesh_terms: D000818:Animals; D004730:Endothelium, Vascular / Q000737:chemistry; D008168:Lung / Q000098:blood supply / Q000737:chemistry / Q000166:cytology; D008565:Membrane Proteins / Q000737:chemistry*; D008962:Models, Theoretical; D040901:Proteomics / Q000379:methods*; D051381:Rats; D012680:Sensitivity and Specificity; D013997:Time Factors
chemical_list: D008565:Membrane Proteins