title: Characterization of poplar metabotypes via mass difference enrichment analysis.
abstract: Instrumentation technology for metabolomics has advanced drastically in recent years in terms of sensitivity and specificity. Despite these technical advances, data analytical strategies are still in their infancy in comparison with other 'omics'. Plants are known to possess an immense diversity of secondary metabolites. Typically, more than 70% of metabolomics data are not amenable to systems biological interpretation because of poor database coverage. Here, we propose a new general strategy for mass-spectrometry-based metabolomics that incorporates all exact mass features with known sum formulas into the evaluation and interpretation of metabolomics studies. We extend the use of mass differences, commonly used for feature annotation, by redefining them as variables that reflect the remaining 'omic' domains. The strategy uses exact mass difference network analyses exemplified for the metabolomic description of two grey poplar (Populus × canescens) genotypes that differ in their capability to emit isoprene. This strategy established a direct connection between the metabotype and the non-isoprene-emitting phenotype, as mass differences pertaining to prenylation reactions were over-represented in non-isoprene-emitting poplars. Not only was the analysis of mass differences able to grasp the known chemical biology of poplar, but it also improved the interpretability of yet unknown biochemical relationships.
authors.affiliation: Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München (HMGU), Neuherberg, Germany.
authors.forename: Franco
authors.initials: F
authors.lastname: Moritz
authors.affiliation: Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München (HMGU), Neuherberg, Germany.|Research Unit Environmental Simulation, Institute of Biochemical Plant Pathology, Helmholtz Zentrum München (HMGU), Neuherberg, Germany.
authors.forename: Moritz
authors.initials: M
authors.lastname: Kaling
authors.affiliation: Research Unit Environmental Simulation, Institute of Biochemical Plant Pathology, Helmholtz Zentrum München (HMGU), Neuherberg, Germany.
authors.forename: Jörg-Peter
authors.identifier: http://orcid.org/0000-0002-9825-867X
authors.initials: JP
authors.lastname: Schnitzler
authors.affiliation: Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München (HMGU), Neuherberg, Germany.|Chair of Analytical Food Chemistry, Technische Universität München (TUM), Freising, Germany.
authors.forename: Philippe
authors.initials: P
authors.lastname: Schmitt-Kopplin
mesh_terms: D002070:Butadienes / Q000378:metabolism*; D005583:Fourier Analysis; D005838:Genotype; D045782:Hemiterpenes / Q000235:genetics / Q000378:metabolism*; D053858:Metabolic Networks and Pathways; D055442:Metabolome; D055432:Metabolomics / Q000379:methods*; D018384:Oxidative Stress; D010420:Pentanes / Q000378:metabolism*; D010728:Phosphoenolpyruvate / Q000378:metabolism; D032107:Populus / Q000235:genetics / Q000378:metabolism*; D054876:Prenylation; D015203:Reproducibility of Results; D053719:Tandem Mass Spectrometry
chemical_list: D002070:Butadienes; D045782:Hemiterpenes; D010420:Pentanes; C005059:isoprene; D010728:Phosphoenolpyruvate
keywords: Populus × canescens; mass difference analysis; metabolomics; networks; systems chemical biology