The term proteome, refers to proteins that are encoded and expressed by a genome, and was first suggested in 1994 by Marc Wilkins. Wilkins defines proteomics as "the study of proteins, how they're modified, when and where they're expressed, how they're involved in the metabolic pathways and how they interact with each other." We can then define proteomics as the large-scale study of proteins, usually by biochemical methods. One of the unique features of proteomics studies is the ability to analyze the post-translation modification of proteins. Phosphorlyation, glycosylation and sulphation as well as many other modifications are extremely important for protein function.

The most significant breakthrough in proteomics has been the use of mass spectrometric identification of gel-separated proteins, which extends analysis far beyond the mere display of proteins. Mass spectrometry has essentially replaced the classical technique of Edman degradation, even in traditional protein chemistry, because it is much more sensitive, can deal with protein mixtures, and offers much higher output.

Two main approaches are employed to mass spectrometric protein identification. In the 'peptide-mass mapping' approach, the mass spectrum of an eluted peptide mixture is determine, which results in a 'peptide-mass fingerprint' of the protein being studied. This is usually achieved by use of MALDI-TOF. The second method for protein identification relies on fragmentation of individual peptides in the mixture to gain sequence information. In this method, the peptides are ionized by 'electrospray ionization' directly from the liquid phase. The peptide ions are sprayed into a 'tandem mass spectrometer' which has the ability to resolve peptides in a mixture, isolate one species at a time, and dissociate it into amino or carboxy-terminal-containing fragments. Once members of a multi-protein complex have been identified by mass spectrometry, their function is studied by pertinent assays.