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MS-CleanR: A Feature-Filtering Workflow for Untargeted LC–MS Based Metabolomics

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posted on 10.07.2020, 16:37 by Ophélie Fraisier-Vannier, Justine Chervin, Guillaume Cabanac, Virginie Puech, Sylvie Fournier, Virginie Durand, Aurélien Amiel, Olivier André, Omar Abdelaziz Benamar, Bernard Dumas, Hiroshi Tsugawa, Guillaume Marti
Untargeted metabolomics using liquid chromatography–mass spectrometry (LC–MS) is currently the gold-standard technique to determine the full chemical diversity in biological samples. However, this approach still has many limitations; notably, the difficulty of accurately estimating the number of unique metabolites profiled among the thousands of MS ion signals arising from chromatograms. Here, we describe a new workflow, MS-CleanR, based on the MS-DIAL/MS-FINDER suite, which tackles feature degeneracy and improves annotation rates. We show that implementation of MS-CleanR reduces the number of signals by nearly 80% while retaining 95% of unique metabolite features. Moreover, the annotation results from MS-FINDER can be ranked according to the database chosen by the user, which enhance identification accuracy. Application of MS-CleanR to the analysis of Arabidopsis thaliana grown in three different conditions fostered class separation resulting from multivariate data analysis and led to annotation of 75% of the final features. The full workflow was applied to metabolomic profiles from three strains of the leguminous plant Medicago truncatula that have different susceptibilities to the oomycete pathogen Aphanomyces euteiches. A group of glycosylated triterpenoids overrepresented in resistant lines were identified as candidate compounds conferring pathogen resistance. MS-CleanR is implemented through a Shiny interface for intuitive use by end-users (available at