A reference to the complete set of proteins which can be expressed by the genetic material of an organism: "An emerging approach for targeted proteome analysis is called selected reaction monitoring; SRM, in which a mass spectrometer is programmed to detect signals from multiple specific proteins."

The entire set of proteins expressed by a genome, cell, tissue, or organism.

It is the set of expressed proteins in a given type of cells or an organism at a given time under specifically defined conditions.

The proteome is the totality of proteins (expressed genes) in an organism, tissue type or cell, and proteomics is now well-established as a term for studying the proteome.