"Proteomics" is a word coined in 1994 by Marc Wilkins as an alternative to “the protein complement of the genome” (1). Proteomics is still defined in various ways (2), from “the large-scale analysis of the proteome” to “the simultaneous study of all proteins in the cell.” In this chapter, we define it as the study of proteins and their interactions. Proteomics is a new field—only 10 years old—and the rapid evolution of this field is due in large part to many improvements in mass spectrometry (MS) that have occurred during the past several years. Mass spectrometers do one thing—they measure mass. In proteomics, the mass gives information on the protein identity, its chemical modifications, and its structure. Every mass spectrometer has three main components: a source, an analyzer, and a detector. Mass spectrometers measure masses of charged species, so the source must be able to produce ions, the analyzer must be able to separate these ions based on their mass (or, more accurately, mass-to-charge ratio), and the detector must be able to detect charged particles and then amplify the response to give a measurable signal. In 2002, the award for the Nobel Prize in chemistry was given to two scientists (John Fenn and Koichi Tanaka) responsible for the development of two ionization techniques that have revolutionized biomedical mass spectrometry in general, and proteomics in particular. These two techniques, electrospray (3) and MALDI (matrix-assisted laser desorption ionization) (4) mass spectrometry, were groundbreaking in that they allow the vaporization and ionization (and thus the analysis) of relatively large, non-volatile biomolecules such as proteins and peptides. In addition, simultaneous improvements to and development of mass analyzers and detectors have greatly increased the use of mass spectrometry for biological studies.
