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Digestion and depletion of abundant proteins improves proteomic coverage.

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.

SUBMITTER: Fonslow BR 

PROVIDER: S-EPMC3531578 | biostudies-literature | 2013 Jan

REPOSITORIES: biostudies-literature

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Digestion and depletion of abundant proteins improves proteomic coverage.

Fonslow Bryan R BR   Stein Benjamin D BD   Webb Kristofor J KJ   Xu Tao T   Choi Jeong J   Park Sung Kyu SK   Yates John R JR  

Nature methods 20121118 1

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  ...[more]