Cancer is a disease of the genome, but many processes downstream of the genome can affect the tumor phenotype. Using proteogenomics data from the Clinical Proteomic Tumor Analysis Consortium (CPTAC), I will present examples on how proeogenomic integration can expand our knowledge on cancer genes, prioritize cancer drivers, clarify puzzling genomic observations, and correct misinterpreted gene functions. I will also discuss our recent works on using proteogenomics to identify tumor antigens and understand immune evasion mechanisms.