Key Concepts of Section 3.6

• Proteomics is the systematic study of the amounts (and changes in the amounts), modifications, interactions, localization, and functions of all or subsets of all proteins in biological systems at the whole-organism, tissue, cellular, and subcellular levels.

• Proteomics provides insights into the fundamental organization of proteins within cells and how that organization is influenced by the state of the cells (e.g., differentiation into distinct cell types; responses to stress, disease, and drugs).

• A wide variety of methods are used for proteomic analyses, including two-dimensional gel electrophoresis, density-gradient centrifugation, and mass spectrometry (particularly LC-MS/MS).

• Proteomics has helped begin to identify the proteomes of organelles (“organelle proteome profiling”) as well as the organization of individual proteins into multiprotein complexes (see Figure 3-48).

• Phosphoproteomics is a specialized application of proteomics that identifies the collection of phosphorylated proteins (phosphoproteome) in cells and characterizes how the level of phosphorylation of these proteins varies as the state of the cells changes.