Introduction to Proteomics

What is Proteomics?

Proteome refers to all the proteins expressed by a genome or a cell or tissue. Proteome is a dynamic concept. It is to explore the mode of action, functional mechanism, regulation and control of proteins as well as the mutual relationship within the protein population at the overall protein level of tissues and cells, so as to comprehensively and deeply understand the disease process, cell physiological and pathological process and regulatory network, and reveal the basic rules of life activities. At the same time, it also provides theoretical basis for many application fields such as clinical diagnosis, drug screening, new drug development and medical treatment.

The Relationship Between Proteomics and Genomics

The important genetic information encoded and stored in the genome depends on the expression of proteins, so the proteome corresponds to the genome, and both are the concept of expressing the whole.

The genome is complete in almost all cells. An organism has only one genome. The different cells that make up the organism share the same genome that exists in its nucleus. Proteins, on the other hand, are highly cell-specific. Cells in different tissues express only different subsets of their proteome. Even the same cell expresses different proteins at different times. Because the conditions and degree of gene expression in the genome change with time and space. Therefore, the types and quantities of proteins as expression products of genes vary with time and space conditions.

If the genome is a one-dimensional data chain of 3.2 billion base pairs strung together by A, G, T and C, then the proteome it encodes and translates can be assembled into the four dimensions (three dimensions plus time) of A whole living being. In this sense, the genome is a static repository of information. Proteomics, on the other hand, is dynamic. Each kind of life activity is the result of specific combination of protein population appearing in different time and space and exerting its biological function.

The formation of the proteome is more complicated than the genome. From transcription to translation, not only requires three levels of regulation, but protein synthesis also undergoes a series of environment-dependent modifications, such as phosphorylation and glycosylation.

Proteomics Research Methods

With the development of proteomics, proteomics research methods are becoming more and more mature. Proteomics research first requires protein separation. Protein separation mainly includes two-dimensional polyacrylamide gel electrophoresis and chromatography. After obtaining the protein sample, it may be necessary to identify the protein in the obtained mixed sample or perform a quantitative analysis of the specific protein. The commonly used protein identification methods mainly include peptide fingerprinting technology and combined chromatography-mass spectrometry analysis. Common techniques for protein quantification are labeled-based protein quantification and labeled-free protein quantification. The common labeled-based protein quantification methods include TMT and SILAC. Labeled-free quantitative methods are all kinds of analysis methods based on mass spectrometry, including SRM, MRM, SWATH, etc. At present, mass spectrometry is the most commonly used analysis technique in proteomics. In addition to the above analysis items, most other analysis contents of proteomics, such as protein modification analysis and protein sequencing analysis, require mass spectrometry technology.