Proteomics is the next step in the study of biological systems and is loosely defined as the global analysis of proteins in a protein complex, organelle, cell, tissue or complete organism. The term proteomics was coined to make an analogy with genomics, the study of the genes. Proteomics, however, is much more complicated than genomics, mostly because while an organism’s genome is rather constant, the proteome differs from cell to cell and constantly changes through its biochemical interactions with the genome and the environment. One organism has radically different protein expression in different parts of its body, at different stages of its life cycle and different environmental conditions.

The level of transcription of a gene gives only a rough estimate of its level of expression into a protein. An mRNA produced in abundance may be degraded rapidly or translated inefficiently, resulting in a small amount of protein. Second, many proteins experience post-translational modifications (PTMs) that can profoundly affect their activities. For instance, a protein may not be active until it becomes phosphorylated. Third, transcripts give rise to more than one protein, through alternative splicing or alternative post-translational modifications. Finally, many proteins form complexes with other proteins or RNA molecules, and only function in the presence of these other molecules. Altogether, this leads to an enormous number of possible proteoforms.


Since proteins play a central role in the life of an organism, proteomics is instrumental in finding novel biomarkers, such as markers that indicate a particular disease and could thus be used for early diagnosis.

The key technology to study proteins at a large scale is mass spectrometry.


Further reading & teaching material

Introductory book about the concepts of protein mass spectrometry: 

Reviews on mass spectrometry based proteomics:

Book chapters on quantitative proteomics:

Advanced reading material:

A lot of information on proteomics and mass spectrometry can be found on the websites of the American Society for Mass Spectrometry (ASMS) and the Human Proteome Organization (HUPO). See also this useful links page.