Large-scale DNA sequencing has stimulated the development of proteomics by providing a sequence infrastructure for protein analysis. Rapid and automated protein identification can be achieved by searching protein and nucleotide sequence databases directly with data generated by mass spectrometry. A high-throughput and large-scale approach to identifying proteins has been the result. These technological changes have advanced protein expression studies and the identification of proteins in complexes, two types of studies that are essential in deciphering the networks of proteins that are involved in biological processes.