We performed the first proteogenomic study on a prospectively collected colon cancer cohort. Comparative proteomic and phosphoproteomic analysis of paired tumor and normal adjacent tissues produced a catalog of colon cancer-associated proteins and phosphosites, including known and putative new biomarkers, drug targets, and cancer/testis antigens. Proteogenomic integration not only prioritized genomically inferred targets, such as copy-number drivers and mutation-derived neoantigens, but also yielded novel findings. Phosphoproteomics data associated Rb phosphorylation with increased proliferation and decreased apoptosis in colon cancer, which explains why this classical tumor suppressor is amplified in colon tumors and suggests a rationale for targeting Rb phosphorylation in colon cancer. Proteomics identified an association between decreased CD8 T cell infiltration and increased glycolysis in microsatellite instability-high (MSI-H) tumors, suggesting glycolysis as a potential target to overcome the resistance of MSI-H tumors to immune checkpoint blockade. Proteogenomics presents new avenues for biological discoveries and therapeutic development. Display omitted •Systematic identification of colon cancer-associated proteins and phosphosites•Proteomics-supported neoantigens and cancer/testis antigens in 78% of the tumors•Rb phosphorylation is an oncogenic driver and a putative target in colon cancer•Glycolysis inhibition may render MSI tumors more sensitive to checkpoint blockade A systematic proteogenomic analysis of colon cancer reveals vulnerabilities of potential clinical value inaccessible from genomic assessment alone.