As the sequence analysis of the Human Genome is essentially completed, the focus in biomedical research has moved from genes and genomes to proteins and proteomes and to the analyses of their functions. DNA sequence data provide limited information as to the potential expression of a particular protein. The dynamics of a physiological process, such as how gene product expression is controlled, when genes are turned on/off, and how protein function is regulated by posttranslational modifications and/or interactions with other gene products, largely remain to be elucidated. In recent years, mass spectrometry has emerged as one of the most powerful tools in proteomics study. Advances in MS instrumentation and adoption of new separation techniques with interrogation of protein databases make it possible rapid and unambiguous identification of large suites of proteins. The technique also allows for sequence analysis of the unknowns as well as structural characterization of posttranslational modifications.