A proteomics platform to address the dynamic characterization of native and modified proteins - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement Access content directly
Conference Poster Year : 2022

A proteomics platform to address the dynamic characterization of native and modified proteins

Abstract

MSPP (Mass Spectrometry Proteomics Platform) from IPSiM laboratory manages technological facilities for proteomics analyses including global large-scale studies of native and modified proteomes, large-scale and targeted quantitative analyses and targeted studies of low-abundant proteins. The platform is more specialized in analysis of membrane proteins in response to (a)biotic stresses. MSPP disposes of a nanoHPLC coupled online with a high resolution mass spectrometer (Exploris 240-ThermoFisher) and dedicated softwares (Maxquant, Skyline) that allows to characterize and quantify native and modified proteomes. In identification, large-scale approach allows us to identify up to 3500 proteins in a single run, whereas targeted-scale approach using Parallel Reaction Monitoring (PRM) is dedicated to identify low-abundant proteins (fmol). In more details, for biochemical preparation of samples, the platform manages (i) fractionation of complex protein mixtures by electrophoresis (ii) in gel or in solution enzymatic digestion of proteins, (iii) phosphorylated and ubiquitinylated peptides enrichment. For quantification, large scale Label-Free quantification is used and allows to determine relative quantitative variations between proteomes and PRM gives access to semi-absolute quantification using labelled internal standard peptides. Then, after data acquisition and processing, bioinformatical analysis, that allows protein identification and quantification, are carried out with commercial and open access softwares, implemented with home-made data processing chains for quantification studies. This poster will present three proteomics projects handled by MSPP including (i) a global proteomic approach with large scale label free quantification to identify potential Arabidospis potential client proteins for NFU2 using a mutant line, (ii) a targeted proteomics strategy to characterize and quantified tomato ethylene receptors, that are low-abundant membrane proteins, during fruit ripening, (iii) a strategy for identification of ubiquitinated proteins. Another perspective of development is peptidomic and preliminary results, on phloem peptidomes analysis to identify critical peptides in iron signaling homeostasis are presented in N. Berger poster’s (S1-P14
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Dates and versions

hal-04179721 , version 1 (10-08-2023)

Identifiers

  • HAL Id : hal-04179721 , version 1

Cite

Sonia Hem, Valérie Rofidal, Nathalie Berger, Vincent Demolombe - Liozu, Véronique Santoni-Kervella. A proteomics platform to address the dynamic characterization of native and modified proteins. 13th International Conference of the French Society of Plant Biology, Aug 2022, Montpellier (34000), France. ⟨hal-04179721⟩
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