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Application of capture-recapture models to estimation of protein count in MudPIT experiments

Academic Article
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Overview

authors

  • Koziol, James
  • Feng, A. C.
  • Schnitzer, J. E.

publication date

  • May 2006

journal

  • Analytical Chemistry  Journal

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.

subject areas

  • Animals
  • Endothelium, Vascular
  • Lung
  • Membrane Proteins
  • Models, Theoretical
  • Proteomics
  • Rats
  • Sensitivity and Specificity
  • Time Factors
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Identity

International Standard Serial Number (ISSN)

  • 0003-2700

Digital Object Identifier (DOI)

  • 10.1021/ac051248f

PubMed ID

  • 16643015
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Additional Document Info

start page

  • 3203

end page

  • 3207

volume

  • 78

issue

  • 9

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