This unit reviews the new discipline of proteomics, which includes any large-scale protein-based systematic analysis of the proteome or defined sub-proteome from a cell, tissue, or entire organism. Proteomics originated in the mid-1990 s due to two key enabling advances, availability of complete genome sequences, and mass spectrometry advances that allowed high sensitivity identifications of proteins. Proteome analyses can be broadly categorized into three types of studies: quantitative protein profile comparisons, analysis of protein-protein interactions, and compositional analysis of simple proteomes or subproteomes such as organelles or large protein complexes. The complexity of different types of proteomes, the merits of targeted versus global proteome studies, and the advantages of alternative separation and analysis technologies are discussed.