As in other high-throughput techniques, proteomics is in the rapid phase of development, with perhaps greater current attention to the technological advances than in the field of DNA microarrays. Proteomics is devoted to large-scale analysis of the proteome, which is the protein counterpart of the transcriptome. The proteome represents the result of gene expression, translation and protein degradation, and governs the phenotype of the cell, perhaps more than the transcriptome. Like the transcriptome, the pro-teome shows qualitative and quantitative changes during pathologic processes.

Proteomic analysis started with conventional technologies such as two-dimensional gel electrophoresis coupled with mass spectrometry.4 Two classes of proteome array-based methodologies are distinguished by the nature of the arrayed molecules: protein or protein-binding particles (DNA, RNA, antibody, or other ligand). In one type of protein array, a large amount of protein is spotted on a solid support at a defined location and tested to characterize either a biochemical activity or a molecular interaction. Protein microarrays may be comprised of antibodies, whole cell or microdissected cellular lysates, recombinant proteins, small molecule drugs, or phage or antibody-like molecules. Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), often referred to as gel-based pro-teomics, multidimensional chromatography, and protein biochips, in combination with mass spectrometry, are among the proteomic tools that are currently available for analysis of the proteome.

Proteomics encompasses many platform technologies for protein separation and identification, for determining biomolecular interactions, function, and regulation, and for annotating, storing, and distributing protein information. Today, the application of novel technologies from proteomics to the study of cancer is slowly shifting to the analysis of clinically relevant samples such as biopsy specimens and fluids. In the future, serum proteomic pattern analysis might be applied to medical screening as a supplement to diagnostic testing.

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