The sequencing of complete genomes is providing an enormous resource for understanding the biology of organisms (1 ). A complete genome sequence, however, will still leave many unanswered questions about the basic biology of the organism. Which open reading frames are authentic genes? What genes express highly abundant proteins in the cell? How well do the observed physical properties of a protein agree with the predictions of the genomic sequence? Which proteins are covalently processed? Analysis of the proteins encoded in the genome or “the proteome” can answer many of these questions, and will help in understanding the physiology of the organism.
