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Fractionation profiling: a fast and versatile approach for mapping vesicle proteomes and protein–protein interactions

We developed “fractionation profiling,” a method for rapid proteomic analysis of membrane vesicles and protein particles. The approach combines quantitative proteomics with subcellular fractionation to generate signature protein abundance distribution profiles. Functionally associated groups of prot...

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Autores principales: Borner, Georg H. H., Hein, Marco Y., Hirst, Jennifer, Edgar, James R., Mann, Matthias, Robinson, Margaret S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The American Society for Cell Biology 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4196868/
https://www.ncbi.nlm.nih.gov/pubmed/25165137
http://dx.doi.org/10.1091/mbc.E14-07-1198
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author Borner, Georg H. H.
Hein, Marco Y.
Hirst, Jennifer
Edgar, James R.
Mann, Matthias
Robinson, Margaret S.
author_facet Borner, Georg H. H.
Hein, Marco Y.
Hirst, Jennifer
Edgar, James R.
Mann, Matthias
Robinson, Margaret S.
author_sort Borner, Georg H. H.
collection PubMed
description We developed “fractionation profiling,” a method for rapid proteomic analysis of membrane vesicles and protein particles. The approach combines quantitative proteomics with subcellular fractionation to generate signature protein abundance distribution profiles. Functionally associated groups of proteins are revealed through cluster analysis. To validate the method, we first profiled >3500 proteins from HeLa cells and identified known clathrin-coated vesicle proteins with >90% accuracy. We then profiled >2400 proteins from Drosophila S2 cells, and we report the first comprehensive insect clathrin-coated vesicle proteome. Of importance, the cluster analysis extends to all profiled proteins and thus identifies a diverse range of known and novel cytosolic and membrane-associated protein complexes. We show that it also allows the detailed compositional characterization of complexes, including the delineation of subcomplexes and subunit stoichiometry. Our predictions are presented in an interactive database. Fractionation profiling is a universal method for defining the clathrin-coated vesicle proteome and may be adapted for the analysis of other types of vesicles and particles. In addition, it provides a versatile tool for the rapid generation of large-scale protein interaction maps.
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spelling pubmed-41968682014-12-30 Fractionation profiling: a fast and versatile approach for mapping vesicle proteomes and protein–protein interactions Borner, Georg H. H. Hein, Marco Y. Hirst, Jennifer Edgar, James R. Mann, Matthias Robinson, Margaret S. Mol Biol Cell Articles We developed “fractionation profiling,” a method for rapid proteomic analysis of membrane vesicles and protein particles. The approach combines quantitative proteomics with subcellular fractionation to generate signature protein abundance distribution profiles. Functionally associated groups of proteins are revealed through cluster analysis. To validate the method, we first profiled >3500 proteins from HeLa cells and identified known clathrin-coated vesicle proteins with >90% accuracy. We then profiled >2400 proteins from Drosophila S2 cells, and we report the first comprehensive insect clathrin-coated vesicle proteome. Of importance, the cluster analysis extends to all profiled proteins and thus identifies a diverse range of known and novel cytosolic and membrane-associated protein complexes. We show that it also allows the detailed compositional characterization of complexes, including the delineation of subcomplexes and subunit stoichiometry. Our predictions are presented in an interactive database. Fractionation profiling is a universal method for defining the clathrin-coated vesicle proteome and may be adapted for the analysis of other types of vesicles and particles. In addition, it provides a versatile tool for the rapid generation of large-scale protein interaction maps. The American Society for Cell Biology 2014-10-15 /pmc/articles/PMC4196868/ /pubmed/25165137 http://dx.doi.org/10.1091/mbc.E14-07-1198 Text en © 2014 Borner et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0). “ASCB®,” “The American Society for Cell Biology®,” and “Molecular Biology of the Cell®” are registered trademarks of The American Society of Cell Biology.
spellingShingle Articles
Borner, Georg H. H.
Hein, Marco Y.
Hirst, Jennifer
Edgar, James R.
Mann, Matthias
Robinson, Margaret S.
Fractionation profiling: a fast and versatile approach for mapping vesicle proteomes and protein–protein interactions
title Fractionation profiling: a fast and versatile approach for mapping vesicle proteomes and protein–protein interactions
title_full Fractionation profiling: a fast and versatile approach for mapping vesicle proteomes and protein–protein interactions
title_fullStr Fractionation profiling: a fast and versatile approach for mapping vesicle proteomes and protein–protein interactions
title_full_unstemmed Fractionation profiling: a fast and versatile approach for mapping vesicle proteomes and protein–protein interactions
title_short Fractionation profiling: a fast and versatile approach for mapping vesicle proteomes and protein–protein interactions
title_sort fractionation profiling: a fast and versatile approach for mapping vesicle proteomes and protein–protein interactions
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4196868/
https://www.ncbi.nlm.nih.gov/pubmed/25165137
http://dx.doi.org/10.1091/mbc.E14-07-1198
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