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This textbook is a comprehensive guide in the context of overall strategies which can be adopted to address the different aspects of large-scale protein analysis. Proteomics is a rapidly growing field of molecular biology that is concerned with the systematic, highthroughput approach to protein expression analysis of a cell or an organism. Typical results of proteomics studies are inventories of the protein content of differentially expressed proteins across multiple conditions. The emergence of proteomics, the large-scale analysis of proteins, has been inspired by the realization that the final product of a gene is inherently more complex and closer to function than the gene itself. Shortfalls in the ability of bioinformatics to predict both the existence and function of genes have also illustrated the need for protein analysis. Proteomics enables the understanding the structure, function and interactions of the entire protein content in a specific organism.