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The ability to broadly identify and measure abundances for biological macromolecules, especially proteins, is essential for delineating complex cellular networks and pathways in systems biology studies. Enabled by the development in the late 1980s of two “soft” ionization methodss electrospray ionization (ESI) 1 and matrix-assisted laser desorption/ionization (MALDI) 2, 3 that prevent or limit fragmentation of large biomoleculessand the increasing availability of genomic sequence databases, mass spectrometry (MS) has become a major analytical tool for studying the array of proteins in an organism, tissue, or cell at a given time, ie, for proteomics. Such proteome-wide analysis provides a wealth of biological information, such as sequence, quantity, post-translational modifications (PTMs), interactions, activities, subcellular distributions, and structure of proteins, that is critical to the comprehensive understanding of a …