Highlights d Comprehensive LUAD proteogenomics exposes multi-omic clusters and immune subtypes d Phosphoproteomics identifies candidate ALK-fusion diagnostic markers and targets d Candidate drug targets: PTPN11 (EGFR), SOS1 (KRAS), neutrophil degranulation (STK11) d Phospho and acetyl modifications denote tumor-specific markers and druggable proteins

Highlights d Integrated proteogenomic characterization in 103 ccRCC cases d Delineation of chromosomal translocation events leading to chromosome 3p loss d Tumor-specific proteomic/phosphoproteomic alterations unrevealed by mRNA analysis d Immune-based subtypes of ccRCC defined by mRNA, proteome, and phosphoproteome

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Highlights d Proteogenomic characterization reveals the functional impact of genomic alterations d Phosphoproteomics uncovers putative therapeutic targets downstream of KRAS d Multiomics links endothelial cell remodeling and glycolysis to immune exclusion d Proteomics and glycoproteomics reveal candidates for early detection or intervention