Novel biomarker identification and drug target validation are highly complex and resource-intensive processes, requiring an integral use of various tools, approaches and information. The recently developed proteomic technology features high-throughput parallel analysis of thousands of proteins in individual patients and amount populations and thus opens up the possibility of providing more details at a global level on the molecular mechanisms. With regularly updated public databases, bioinformatics can contribute to these processes by providing functional information of target candidates and correlating this information to the biological pathways. In this review, we outline recent advances of bioinformatic application in proteomic research on biomarker discovery and drug target validation. Specifically, we highlight how bioinformatics can facilitate the proteomic studies of biomarker identification and drug target validation.