Session: Parallel session 1 - environmental analysis

Exploring extraction methods for a comprehensive metabolomic and proteomic analysis of potato tubers using high resolution mass spectrometry

Pierre OTUSZEWSKI^1,2, Liyuan CHEN², Pierre CARLIER¹, Nicolas SZYDLOWSKI², Christian ROLANDO¹, Christophe D'HULST², Ahmed MAZZAH¹, Fabrice BRAY¹

¹MSAP - Miniaturisation pour la Synthèse, l'Analyse et la Protéomique; CNRS; Université de Lille , Lille, France
²UGSF - Unité de Glycobiologie Structurale et Fonctionnelle; CNRS; Université de Lille , Lille , France

Metabolomics allows the identification of a wide range of metabolites. Exploring the diversity of these molecules requires a methodological workflow that can comprehensively extract, detect, and identify them. Likewise, proteome analysis is often needed for a complete understanding of a biological system. This study explores three extraction methods capable of providing the best extraction of metabolites and proteins in a plant system. Each of these techniques was tested on lyophilized potato tuber powder, with the aim of understanding the behavior of potato cultivars when exposed to cold storage.

Three extraction methods were compared in this study: (i) Matyash (MTBE/MeOH/H2O), (ii) Bligh and Dyer (CHCl3/MeOH/H2O), and (iii) MeOH extraction. The Matyash method produced a two-phase solution and an insoluble pellet containing proteins. The Bligh and Dyer method also produced a two-phase solution, but the insoluble fraction is located between the two phases. Finally, the methanol extraction method produced a single-phase solution and the insoluble pellet. Direct injection on a FTICR MS and LC-MS/MS Orbitrap were used for metabolomics and proteomics analyses, respectively. DataAnalysis, Metaboanalyst and MaxQuant were used for metabolomic and proteomic data treatment.

Principal component analysis on metabolomic data showed differences between the apolar and polar phase analyses. Also, these results suggest that the Bligh and Dyer extraction seems to be less suitable for the analysis of polar metabolites. More than 500 different proteins were detected in each sample from each extraction method. Nevertheless, the Bligh and Dyer method resulted in fewer detected proteins compared to the other two methods. For this reason, this method seems less suitable for the analysis of a large number of samples and for the project. The Matyash methods is currently applied to 10 potato cultivars to rationalize their cold storage properties.