Figure 1. Identification of proteins obtained in biological studies. Proteins from a study can be separated by one- or two-dimensional gel electrophoresis and proteins identified using MALDI-TOF and peptide mass mapping. Alternatively, peptides obtained by site-specific digestion of proteins isolated from polyacrylamide gels can be analysed using tandem mass spectrometry. The tandem mass spectrometry data can then be used to search a database. A third method is to digest a protein mixture proteolytically and use microcapillary high-performance liquid chromatography and tandem mass spectrometry to generate fragmentation for individual peptides contained in the mixture. Tandem mass spectra, representing the amino acid sequences of peptides from the protein(s) present, are then used to search sequence databases. Proteins are identified when tandem mass spectra are matched to individual protein sequences.