Dix, M.M. et al. Cell 150, 426–440 (2012).

During apoptosis, or programmed cell death, a substantial portion of the proteome is chewed up by caspases in a process regulated at least in part by phosphorylation. However, the global relationship between proteolysis and phosphorylation in apoptosis has not been well studied. Dix et al. applied a quantitative method called PROTOMAP (protein topography and migration analysis platform) to investigate the global apoptotic phosphoproteome of mammalian cells. PROTOMAP uses SDS-PAGE to determine the size and topography of SILAC-labeled proteins, followed by in-gel digestion, phosphopeptide enrichment, and peptide identification and quantification by mass spectrometry. The output is a quantitative 'peptograph' that highlights phosphorylation sites on the topographical map of cleaved proteins. Dix et al. discovered ∼500 apoptosis-specific phosphorylation events that were enriched on cleaved proteins and at caspase cleavage sites.