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Digestion and depletion of abundant proteins improves proteomic coverage

Academic Article
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Overview

related to degree

  • Stein, Benjamin, Ph.D. in Chemistry, Scripps Research 2008 - 2015

authors

  • Fonslow, B. R.
  • Stein, Benjamin
  • Webb, K. J.
  • Xu, T.
  • Choi, J.
  • Park, S. K.
  • Yates III, John

publication date

  • January 2013

journal

  • Nature Methods  Journal

abstract

  • Two major challenges in proteomics are the large number of proteins and their broad dynamic range in the cell. We exploited the abundance-dependent Michaelis-Menten kinetics of trypsin digestion to selectively digest and deplete abundant proteins with a method we call DigDeAPr. We validated the depletion mechanism with known yeast protein abundances, and we observed greater than threefold improvement in low-abundance human-protein identification and quantitation metrics. This methodology should be broadly applicable to many organisms, proteases and proteomic pipelines.

subject areas

  • Humans
  • Mass Spectrometry
  • Peptide Fragments
  • Proteins
  • Proteome
  • Proteomics
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Identity

PubMed Central ID

  • PMC3531578

International Standard Serial Number (ISSN)

  • 1548-7091

Digital Object Identifier (DOI)

  • 10.1038/nmeth.2250

PubMed ID

  • 23160281
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Additional Document Info

start page

  • 54

end page

  • 56

volume

  • 10

issue

  • 1

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