n. The set of all proteins created and used by an organism.
Other Forms
In mid-1994, Marc Wilkins, a student at Australia's Macquarie University, struggled to find the right words while cobbling together a scientific paper to support his PhD thesis on rapidly identifying proteins. Wilkins found himself repeatedly writing, 'all proteins expressed by a genome, cell or tissue,' a phrase he didn't like. 'This was cumbersome, inelegant and made for a lot of extra typing,' explains Wilkins, who now works at Sydney's Proteome Systems. So he started playing with words that would communicate the protein equivalent of the genome. After discarding 'proteinome' and 'protome,' he settled on proteome, 'the one that seemed to work best and roll off the tongue nicely.'

In September 1994, Wilkins referred to the proteome at a scientific conference in Italy, and the word stuck.
—Jon Cohen, “The Proteomics Payoff,” Technology Review, October 01, 2001
'The human proteome has become the next frontier of modern biology,' said Peter Meldrum, president and chief executive of Myriad, a biotechnology company in Salt Lake City that is leading the venture. The proteome is a term referring to all the proteins in an organism, much as the genome refers to an organism's complete set of DNA, containing all the genes.
—Andrew Pollack, “3 Companies Will Try to Identify All Human Proteins,” The New York Times, April 05, 2001
1994 (earliest)
Proteome: the PROTEin complement expressed by a genOME, cell or tissue.
—Marc Wilkins, “2D Electrophoresis: from protein maps to genomes,” Proceedings of the International Meeting, September 05, 1994
Thanks to the Human Genome Project and related endeavors, many of us have at least some familiarity with the arcane jargon of genomics ("the study of genes"). However, there is a related field that you're probably going to hear a lot about over the next few years. It's called proteomics, "the study of proteins." Many scientists now believe that proteomics is medically more important than genomics. That's because genes themselves "only" serve one purpose: to hold the instructions for creating proteins. But proteins are the fundamental building blocks of the human body. All our tissues, muscles, bones, and other body bits and pieces are conglomerations of proteins. So it appears as though the biotechnology industry's attention for the next few years will be focussed on studying how proteins work and on cataloguing the complete human proteome.

To get the earliest citation for this term, I contacted Marc Wilkins, who graciously sent the following reply:
The actual physical slide that I used at the 1994 congress (this was before data projectors were used at conferences) was lost somewhere in my move between Australia and Europe in the mid 1990s. However, the slide was a very simple one… I thought it would be important and so it has stuck in my memory. The slide was one which proposed the concept of the proteome and defined the term. It just contained a definition of the proteome, probably a bit like this:

Proteome: the PROTEin complement expressed by a genOME, cell or tissue

The capitalisation was something which I used a lot during the introduction of this to audiences (and in publications).

The extension of this (proteomics) appeared in the vernacular pretty soon thereafter and, I think as you know, the proteome and proteomics spawned a rash of other 'omics'. So in some senses the introduction of the proteome was an intellectual tipping point whereby biologists started to move from studying one gene or protein at a time to studying the cell as an interconnected system of thousands of parts.
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