Studying Plant Specialized Metabolites Using Computational Metabolomics Strategies

Lana Mutabdžija; Akhona Myoli; Niek F de Jonge; Tito Damiani; Robin Schmid; Justin J J van der Hooft; Fidele Tugizimana; Tomáš Pluskal

doi:10.1007/978-1-0716-3782-1_7

Studying Plant Specialized Metabolites Using Computational Metabolomics Strategies

Methods Mol Biol. 2024:2788:97-136. doi: 10.1007/978-1-0716-3782-1_7.

Authors

Lana Mutabdžija^{1

2}, Akhona Myoli³, Niek F de Jonge⁴, Tito Damiani¹, Robin Schmid¹, Justin J J van der Hooft^{3

4}, Fidele Tugizimana^{3

5}, Tomáš Pluskal⁶

Affiliations

¹ Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czechia.
² Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czechia.
³ Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa.
⁴ Bioinformatics Group, Wageningen University & Research, Wageningen, the Netherlands.
⁵ International Research and Development Division, Omnia Group, Ltd, Johannesburg, South Africa.
⁶ Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czechia. tomas.pluskal@uochb.cas.cz.

PMID: 38656511
DOI: 10.1007/978-1-0716-3782-1_7

Abstract

Plant specialized metabolites have diversified vastly over the course of plant evolution, and they are considered key players in complex interactions between plants and their environment. The chemical diversity of these metabolites has been widely explored and utilized in agriculture and crop enhancement, the food industry, and drug development, among other areas. However, the immensity of the plant metabolome can make its exploration challenging. Here we describe a protocol for exploring plant specialized metabolites that combines high-resolution mass spectrometry and computational metabolomics strategies, including molecular networking, identification of structural motifs, as well as prediction of chemical structures and metabolite classes.

Keywords: GNPS; MS2LDA; MS2Query; MZmine; Molecular networking; Plant metabolomics; SIRIUS; Specialized metabolites.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology / methods
Mass Spectrometry* / methods
Metabolome*
Metabolomics* / methods
Plants* / metabolism