Reversible protein phosphorylation is one of the most important forms of cellular regulation. For this reason, phosphoproteomic analysis of protein phosphorylation in cells is a powerful tool for evaluating the functional status of cells. The importance of protein kinase-regulated signal transduction pathways in human cancer has led to the development of drugs that inhibit protein kinases at the apex or intermediary levels of these pathways. Phosphoproteomic analysis of these signalling pathways will provide important insights into the operation and connectivity of these pathways that will facilitate the identification of the best targets for cancer therapies. Moreover, phosphoproteomic analysis of individual tumours will help match targeted cancer drugs to the appropriate patients.