Quantitative, High-Resolution Proteomics for Data-Driven Systems Biology
Annu Rev Biochem. May 2011
Cox J, Mann M.
Systems biology requires comprehensive data at all molecular levels. Mass spectrometry (MS)-based proteomics has emerged as a powerful and universal method for the global measurement of proteins. In the most widespread format, it uses liquid chromatography (LC) coupled to high-resolution tandem mass spectrometry (MS/MS) to identify and quantify peptides at a large scale. This peptide intensity information is the basic quantitative proteomic data type. It is used to quantify proteins between different proteome states, including the temporal variation of the proteome, to determine the complete primary structure of proteins including posttranslational modifications, to localize proteins to organelles, and to determine protein interactions. Here, we describe the principles of analysis and the areas of biology where proteomics can make unique contributions. The large-scale nature of proteomics data and its high accuracy pose special opportunities as well as challenges in systems biology that are largely untapped so far. Expected final online publication date for the Annual Review of Biochemistry Volume 80 is June 02, 2011. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.