Biological/bioinformatics databases are essential for medical and biological studies. They integrate and organize biologically related information in a structured format and provide researchers with easy access to a variety of relevant data. This review presents an overview of publicly available databases relevant to proteomics studies in cancer research. They include gene/protein expression databases, gene mutation and single nucleotide polymorphisms databases, tumor antigen databases, protein–protein interaction, and biological pathway databases. Automated information retrieval from these databases enables efficient large-scale proteomics data analysis.