Proteomics without polyacrylamide: qualitative and quantitative uses of tandem mass spectrometry in proteome analysis

Proteomics can be thought of as an attempt to understand the information encoded in genomic sequences from the perspective of proteins; i.e. the structure, function and regulation of biological processes at the protein level. In practice it stands in stark contrast to the hypothesis-driven serial approach practiced in the last century that was so successful for protein chemists and is built on the basic understanding of protein physicochemical properties developed during that era. Proteomics attempts to study biological processes comprehensively or globally by systematic parallel analysis of proteins expressed in a cell. While there are many analytical techniques in use and under development in proteomics, mass spectrometry is currently one of the field's most important discovery-based tools. This article will review some of the current approaches for qualitative and quantitative uses of tandem mass spectrometry in the field of proteomics specifically avoiding a discussion of the use of gel electrophoresis prior to mass spectrometry.