Proteogenomics and systems biology: quest for the ultimate missing parts

Expert Review of Proteomics
Jean Armengaud

Abstract

This review describes how intimately proteogenomics and system biology are imbricated. Quantitative cell-wide monitoring of cellular processes and the analysis of this information is the basis for systems biology. Establishing the most comprehensive protein-parts list is an essential prerequisite prior to analysis of the cell-wide dynamics of proteins, their post-translational modifications, their complex network interactions and interpretation of these data as a whole. High-quality genome annotation is, thus, a crucial basis. Proteogenomics consists of high-throughput identification and characterization of proteins by extra-large shotgun MS/MS approaches and the integration of these data with genomic data. Discovery of the remaining unannotated genes, defining translational start sites, listing signal peptide processing events and post-translational modifications, are tasks that can currently be carried out at a full-genomic scale as soon as the genomic sequence is available. Proteomics is increasingly being used at the primary stage of genome annotation and such an approach may become standard in the near future for genome projects. Advantageously, the same experimental proteomic datasets may be used to characterize the speci...Continue Reading

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Citations

Oct 28, 2010·The Journal of Biological Chemistry·Alain DedieuJean Armengaud
Jan 11, 2012·Molecular & Cellular Proteomics : MCP·Gérémy ClairCatherine Duport
Nov 30, 2011·Molecular & Cellular Proteomics : MCP·Joseph Alexander Christie-OlezaJean Armengaud
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Jan 21, 2014·Journal of Proteomics·Jean ArmengaudErica M Hartmann
Jul 6, 2014·Clinical Proteomics·Emily S Boja, Henry Rodriguez
Dec 1, 2012·Expert Review of Proteomics·Jean ArmengaudCatherine Duport
Dec 15, 2015·Expert Review of Proteomics·Marie Locard-PauletJean Armengaud
Sep 30, 2015·Proteomics·Joseph A Christie-Oleza, Jean Armengaud
Dec 24, 2015·Frontiers in Bioengineering and Biotechnology·Cuauhtemoc Licona-CassaniEsteban Marcellin
Jan 17, 2012·Proteomics·Tzu-Chiao Chao, Nicole Hansmeier
Jun 21, 2012·Environmental Microbiology·Joseph Alexander Christie-OlezaJean Armengaud
Jun 20, 2012·Environmental Microbiology·Jean Armengaud
Apr 21, 2012·Journal of Proteomics·Ganesh Kumar AgrawalRandeep Rakwal
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