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Proteomic research in biology : which questions can be asked ?
Yann Verdier, Maître de Conférences. Crédits : ESPCI ParisTechThese last years, technologies for proteome studies reach a development level allowing their use in a vast area of applications. For an example, the possibility to study proteins in interaction or to characterize post-traductional modifications of protein of interest offer prospects of comprehension, at the molecular level, a large number of physiological pathological mechanisms.
One of the most widely used strategies for studying molecular complexes consists in the purification of the protein of interest together their molecular partners, and then in their identification by a bottom-up approach. This latest needs the use of systems, ( e.g. nanochromatography) allowing the reduction of sample complexity, and the use of hight resolution mass spectrometer, allowing to distinguish between peptides of very close biochemical properties. We used this approach for the identification of the molecular partners of the fibrillar amyloïd beta peptide, which is over-expressed in the Alzheimer’s disease, and to identify the molecular partners of the already described actors of the anti-bacterial (IMD cascade) and anti-viral (siRNA) in the drosophila. These experiments showed that the complexes can include dozens of proteins. Although the capacity of analyze of actual mass spectrometers allows the identification of such a number of proteins, there is a large number of challenges for the more exhaustive description of such complexes, and a fortiori for the kinetic description of their evolution in response to a stimulation. These challenges include pre-analytical aspects, quantification strategies, but also validation criteria and the assessment of the biological significance of the data.
The characterization of post-traductional modifications is also a challenge. It is possible, by the exact masses determination, to determine the nature and the position of post-traductional modifications. However specific strategies of purification should often be used, such as specific labeling and chemical derivations, as illustrated by the examples of the characterization of the Tau catabolic forms, or the determination of the cysteines oxidation levels. In these studies, pre-analytical and post-analytical aspects (biological significance of the results) are fundamental.
The impressive technological developments of the latest years open the possibility to use proteomic tools to answer to a large number of biological questions. However, the correct formulation of these questions is fundamental to design pre-analytical and post-analytical strategies necessary to answer these questions.