Proteomics refer to the study of all the proteins of an organism, an organ, a cell and even a cell compartment. Proteins are the direct result of genome expression, so two organisms with totally different appearances can have the same genome, it is the proteins that differentiate them and give them specific characteristics.
There are several techniques for detecting the presence of specific proteins in a sample. The most common are immunodetection techniques, which rely on the affinity of an antibody for its specific antigen. Thus, an assay that uses an antibody directed against a protein will indicate the presence or absence of that protein. This is the case, for example, with ELISA or Western blot techniques.
There is a wide variety of proteins in and secreted from cells that are constantly synthesized, modified and degraded. This diversity contributes to the complex mechanisms that occur intra- and extracellularly. The identification of proteins present in a sample is therefore one of the keys to understanding how cells work.
For this purpose, various analytical methods such as MALDI-ToF or LC-MS/MS, which combine chromatography and mass spectrometry, make it possible to identify proteins in the presence and characterize their phosphorylation or ubiquitination states.
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The conjugation of proteins or peptides with linkers is very useful for detection as well as for studying structure and interactions with other molecules. For example, linkers may be fluorescent for imaging analysis, or may be used to produce antibody-drug conjugates (ADC).
Quantitative proteomic analyses are used to determine the amount of a given protein in a sample. Immunochemical techniques can be used, such as the ELISA method or the Western Blot. Analytical techniques such as quantitative mass spectrometry (mass measurement) or microarray (measurement of interaction with other molecules such as peptides) are also possible.
The three-dimensional structure of a protein has a direct link to its function, which is why structural analyses of proteins are important. One of the methods commonly used to determine the three-dimensional structure of proteins is the X-ray analysis of protein crystals. This method gives very precise information on the structure of proteins.