Digestion and depletion of abundant proteins improves proteomic coverage

Two major challenges in proteomics are the large number of proteins and their broad dynamic range within 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...

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Detalles Bibliográficos
Autores principales: Fonslow, Bryan R., Stein, Benjamin D., Webb, Kristofor J., Xu, Tao, Choi, Jeong, Park, Sung Kyu, Yates, John R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2012
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531578/
https://www.ncbi.nlm.nih.gov/pubmed/23160281
http://dx.doi.org/10.1038/nmeth.2250
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author Fonslow, Bryan R.
Stein, Benjamin D.
Webb, Kristofor J.
Xu, Tao
Choi, Jeong
Park, Sung Kyu
Yates, John R.
author_facet Fonslow, Bryan R.
Stein, Benjamin D.
Webb, Kristofor J.
Xu, Tao
Choi, Jeong
Park, Sung Kyu
Yates, John R.
author_sort Fonslow, Bryan R.
collection PubMed
description Two major challenges in proteomics are the large number of proteins and their broad dynamic range within 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 observed greater than 3-fold improvement in low abundance human protein identification and quantitation metrics. This methodology should be broadly applicable to many organisms, proteases, and proteomic pipelines.
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spelling pubmed-35315782013-07-01 Digestion and depletion of abundant proteins improves proteomic coverage Fonslow, Bryan R. Stein, Benjamin D. Webb, Kristofor J. Xu, Tao Choi, Jeong Park, Sung Kyu Yates, John R. Nat Methods Article Two major challenges in proteomics are the large number of proteins and their broad dynamic range within 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 observed greater than 3-fold improvement in low abundance human protein identification and quantitation metrics. This methodology should be broadly applicable to many organisms, proteases, and proteomic pipelines. 2012-11-18 2013-01 /pmc/articles/PMC3531578/ /pubmed/23160281 http://dx.doi.org/10.1038/nmeth.2250 Text en Users may view, print, copy, download and text and data- mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
Fonslow, Bryan R.
Stein, Benjamin D.
Webb, Kristofor J.
Xu, Tao
Choi, Jeong
Park, Sung Kyu
Yates, John R.
Digestion and depletion of abundant proteins improves proteomic coverage
title Digestion and depletion of abundant proteins improves proteomic coverage
title_full Digestion and depletion of abundant proteins improves proteomic coverage
title_fullStr Digestion and depletion of abundant proteins improves proteomic coverage
title_full_unstemmed Digestion and depletion of abundant proteins improves proteomic coverage
title_short Digestion and depletion of abundant proteins improves proteomic coverage
title_sort digestion and depletion of abundant proteins improves proteomic coverage
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531578/
https://www.ncbi.nlm.nih.gov/pubmed/23160281
http://dx.doi.org/10.1038/nmeth.2250
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