Proteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of cells.
The term "proteomics" was first coined in 1997 to make an analogy with genomics, the study of the genes. The word "proteome" is a blend of "protein" and "genome", and was coined by Marc Wilkins in 1994 while working on the concept as a PhD student.
The proteome is the entire complement of proteins, It is now known that mRNA is not always translated into protein, and the amount of protein produced for a given amount of mRNA depends on the gene it is transcribed from and on the current physiological state of the cell. Proteomics confirms the presence of the protein and provides a direct measure of the quantity present.
Scientists are very interested in proteomics because it gives a much
better understanding of an organism than genomics. First, 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, as mentioned above many proteins experience
post-translational modifications that profoundly affect their
activities; for example some proteins are not active until they become
Methods such as phosphoproteomics and glycoproteomics
are used to study post-translational modifications. Third, many
transcripts give rise to more than one protein, through alternative
splicing or alternative post-translational modifications. Fourth, many
proteins form complexes with other proteins or RNA molecules, and only
function in the presence of these other molecules. Finally, protein
degradation rate plays an important role in protein content.
Not only does the translation from mRNA cause differences, many proteins are also subjected to a wide variety of chemical modifications after translation. A lot of these post-translational modifications are critical to the protein's function.
One such modification is phosphorylation, which happens to many enzymes and structural proteins in the process of cell signaling. The addition of a phosphate to particular amino acids—most commonly serine and threonine mediated by serine/threonine kinases, or more rarely tyrosine mediated by tyrosine kinases—causes a protein to become a target for binding or interacting with a distinct set of other proteins that recognize the phosphorylated domain.
Because protein phosphorylation is one of the most-studied protein modifications many "proteomic" efforts are geared to determining the set of phosphorylated proteins in a particular cell or tissue-type under particular circumstances. This alerts the scientist to the signaling pathways that may be active in that instance.
Ubiquitin is a small protein that can be affixed to certain protein substrates by enzymes called E3 ubiquitin ligases. Determining which proteins are poly-ubiquitinated can be helpful in understanding how protein pathways are regulated. This is therefore an additional legitimate "proteomic" study. Similarly, once it is determined what substrates are ubiquitinated by each ligase, determining the set of ligases expressed in a particular cell type will be helpful.
Listing all the protein modifications that might be studied in a "Proteomics" project would require a discussion of most of biochemistry; therefore, a short list will serve here to illustrate the complexity of the problem.
In addition to phosphorylation and ubiquitination, proteins can be subjected to (among others) methylation, acetylation, glycosylation, oxidation and nitrosylation. Some proteins undergo ALL of these modifications, often in time-dependent combinations, aptly illustrating the potential complexity one has to deal with when studying protein structure and function.
Distinct proteins are made under distinct settings
Even if one is studying a particular cell type, that cell may make different sets of proteins at different times, or under different conditions. Furthermore, as mentioned, any one protein can undergo a wide range of post-translational modifications.
Therefore a "proteomics" study can become quite complex very quickly, even if the object of the study is very restricted. In more ambitious settings, such as when a biomarker for a tumor is sought - when the proteomics scientist is obliged to study sera samples from multiple cancer patients - the amount of complexity that must be dealt with is as great as in any modern biological project.
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