The number of subjects that can be recruited in proteomics studies and the number of proteomics parameter that can be measured has increased rapidly over the past decade and is likely to continue to expand. Proteomics-based approaches, which examine the expressed proteins of a tissue or cell type, complement the genome initiatives and are increasingly used to address biomedical questions. Proteins are the main functional output, and the genetic code cannot always indicate which proteins are expressed, in what quantity, and in what form. For example- post translational modifications of proteins such as phosphorylation or glycosylation, are very important in determining protein function. Similarly, the effects of environmental factors or muligenic processes such as ageing or disease cannot be assessed simply by examination of the genome alone. This review describes the underlying technology and illustrates several areas of biomedical research, ranging from pathogenesis of neurological disorders to drug and vaccine design, in which potential clinical application are being explored.