What is proteomics?

Proteomics is the large-scale study of proteomes. A proteome is a set of proteins produced in an organism, system, or biological context. We may refer to, for instance, the proteome of a species (for example, Homo sapiens) or an organ (for example, the liver). The proteome is not constant; it differs from cell to cell and changes over time. To some degree, the proteome reflects the underlying transcriptome. However, protein activity (often assessed by the reaction rate of the processes in which the protein is involved) is also modulated by many factors in addition to the expression level of the relevant gene.

Proteomics is used to investigate:

  • when and where proteins are expressed
  • rates of protein production, degradation, and steady-state abundance
  • how proteins are modified (for example, post-translational modifications (PTMs) such as phosphorylation)
  • the movement of proteins between subcellular compartments
  • the involvement of proteins in metabolic pathways
  • how proteins interact with one another

Proteomics can provide significant biological information for many biological problems, such as:

  • which proteins interact with a particular protein of interest (for example, the tumour suppressor protein p53)? (Human example)
  • which proteins are localised to a subcellular compartment (for example, the mitochondrion)? (Human example)
  • which proteins are involved in a biological process (for example, circadian rhythm)? (Human example)
Figure 1 Areas of proteomics: Proteomic experiments generally collect data on three properties of proteins in a sample: location, abundance/turnover and post-translational modifications. Depending on the experimental design, researchers may be directly interested in these data, or may use them to infer additional information. For example, it may be possible to infer a protein’s interaction partners among others that are co-localised with it, or to assess whether a protein is active from its post-translational modifications.