The development of cancer is a pathological process involving multiple environmental carcinogenic factors and genetic alterations. For decades, cancer researchers have focused on genomic and transcriptomic analyses. The completion of the Human Genome Project has opened the door to the post-genome era and oncoproteomics. Proteins play a critical role in tumorigenesis and influence the differences between normal cells and malignant cells. This report proposes the concept that cancer is a proteomic disease. This concept is based on examining protein expression profiles, post-translational modifications, and protein-protein interactions in carcinogenesis using recent advances in comparative, functional and structural proteomics. This approach provides a new way of viewing carcinogenesis, presents new clues in biomarker discovery for cancer diagnosis and therapy, and reveals important scientific findings and their significance to clinical applications.