Quantitative Proteomics of the Cancer Cell Line Encyclopedia Reveals Coordinated Post-Transcriptional Pathway Regulation

Cell lines are widely used for examining normal biological function and disease. To date, large-scale profiling of cell line collections including the Cancer Cell Line Encyclopedia (CCLE) has focused primarily on genetic information while deep interrogation of the proteome has remained out of reach. Here we expand the CCLE through quantitative profiling of thousands of proteins by mass spectrometry across 375 cell lines from diverse lineages. At present this is the largest single collection of deep proteomics experiments reported on any human model. We present several analyses as example applications of these data including relationships to mutations and surprising regulation patterns within the electron transport chain. We observe unexpected correlations within and between pathways that are largely absent from RNA, and provide a correlation network to explore these structured expression patterns. These data in conjunction with the wider CCLE are a unique resource to explore cellular behavior