ABSTRACT: Proteomics emerged in the beginning of the 1990s due to the need for new methods for protein analysis. Proteomics is a much newer discipline than genomics, and confronts similar challenges to those that genomics researchers faced in the implementation of large-scale sequencing programs. The definition of proteomics as the use of quantitative protein-level measurements of gene expression to characterize biological processes and decipher the mechanisms of gene expression control fits in with any biological approach. In the present study, proteomics is discussed and defined in parallel with genomics, given that many authors integrate proteomics in the context of functional genomics. In this Theme Section, several facets of proteomics in marine ecology were adressed: capacity, or what can be done, utility, the technology possibilities, and how to use the data obtained. As with any new and interesting technology, the expectations often exceed reality. The applications of proteomics, the advantages and disadvantages, as well as a few limitations are discussed.
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