The term proteome, coined in 1994 as a linguistic equivalent to the concept of genome, is used to describe the complete set of proteins that is expressed, and modified following expression, by the entire genome in the lifetime of a cell. It is also used in a less universal sense to describe the complement of proteins expressed by a cell at any one time.

Proteomics refers to the study of the proteome using technologies of large-scale protein separation and identification. The nomenclature is catching on. The generation of messenger RNA expression profiles is referred to as transcriptomics, as these are based around the process of transcription. And the complement of mRNAs transcribed from a cell's genome is called the transcriptome.

The company Ciphergen, based in Palo Alto, California, is trying to popularize the term phenomics to describe the technology of automated functional analysis of proteins. The word derives from phenotype — the observable characteristics conferred by a gene. Some enthusiastic researchers in the field are even starting to refer to the whole operation of molecular analysis of a cell, extending from DNA through RNA to protein, as operomics.