Proteomics is a rapidly growing field of molecular biology that is concerned with the systematic, high-throughput approach to protein expression analysis of a cell or an organism. Typical results of proteomics studies are inventories of the protein content of differentially expressed proteins across multiple conditions.

The cell responds to internal and external changes by regulating the activity and level of its proteins; therefore changes in the proteome (a collection of all the proteins coded in our genes) provide a snapshot of the cell in action. Proteomics enables the understanding the structure, function and interactions of the entire protein content in a specific organism.

History of proteomics

The term “protein” was initially introduced in 1938 by the Swedish chemist Jöns Jakob Berzelius, an accomplished experimenter in the field of electrochemistry. He wanted to describe a particular class of macromolecules that are plentiful in living organisms and made up of linear chains of amino acids.

The first protein studies that can be called proteomics began in 1975 with the introduction of the two-dimensional gel and mapping of the proteins from the bacterium Escherichia coli, guinea pig and mouse. Albeit many proteins could be separated and visualized, they could not be identified.

The terms “proteome” and “proteomics” were coined in the early 1990s by Marc Wilkins, a student at Macquarie University, in order to mirror the terms “genomics” and “genome”, which represent the entire collection of genes in an organism.

Since the first use of the term “proteome”, its meaning and scope have narrowed. Post-translational modifications, alternative splice products, and proteins intractable to classic separation techniques have presented a challenge towards the realization of the conventional definition of the word.

Today, many different areas of study are explored by proteomics. Amongst them are protein-protein interaction studies, protein function, protein modifications, and protein localization studies. The fundamental goal of proteomics is not only to pinpoint all the proteins in a cell, but also to generate a complete three-dimensional map of the cell indicating their exact location.

In many ways, proteomics runs parallel to genomics. The starting point for genomics is a gene in order to make inferences about its products (i.e. proteins), whereas proteomics begins with the functionally modified protein and works back to the gene responsible for its production.

Types of proteomics

Proteomics studies whose goal is to map out the proteins present in a specific cellular organelle or the structure of protein complexes are known as structural proteomics. Structural analysis can aid in identification of the functions of newly discovered genes, show where drugs bind to proteins and where proteins interact with each other. Technologies employed in structural proteomics are X-ray crystallography and nuclear magnetic resonance spectroscopy.

The quantitative study of protein expression between samples that differ by certain variable is known as expression proteomics. This type of proteomics can help identify the main proteins found in a particular sample and proteins differentially expressed in related samples, e.g. when comparing diseased and healthy tissue. Technologies such as 2D-PAGE and mass spectrometry are used here.

Functional proteomics represents a wide-ranging term for many specific, directed proteomics methodologies. The characterization of protein-protein interactions are used to determine protein functions and to demonstrate how proteins assemble in larger complexes. In some cases, specific subproteomes are isolated by affinity chromatography for additional analysis.