The proteome is defined as the entire collection of proteins, in their modified and active forms that are present in a cell at any one time. It is changes in the proteome, much more so than any change in the genome, that is reflected by changes in the environment. The purpose behind the study of proteomics is that many cells, whether in tissues in a whole organism or as single cells in a fluctuating environment, are defined not by the presence of a gene in the DNA, but by the expression of those genes in the form of proteins in their many varying forms. Such changes as tissue types, carbon sources, stage in life of the cell, or even temperature can alter the expression level of a given protein, or can alter the post-translational modification of the protein such that it is secreted instead of attached to the plasma membrane, or can alter the half-life of a protein.
There's also a Massachusetts-based company called Proteome (www.proteome.com) that offers complete (well, as complete as can be) protein databases for several organisms: yeast (S. cerevisiae and S. pombe), roundworms (C. elegans), and, most recently added, humans. The company provides this service free to academic users, and for a small fee to corporations and independent users. The databases are organized in such a way that one can search by gene name, protein function, or by sequence.

Personally, I've found it invaluable as a research tool.


Other sources:

http://www.sdu.dk/Nat/CPA/index.html -- Centre for Proteome Analysis, University of Southern Denmark, Odense, Denmark
http://www.ebi.ac.uk/proteome/ -- European Bioinformatics Institute, Hinxton, Cambridge, UK
http://www.proteome.co.uk/ -- Proteome Sciences, Cobham, Surrey, UK

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