title: Granger causality in integrated GC-MS and LC-MS metabolomics data reveals the interface of primary and secondary metabolism.
abstract: Metabolomicshas emerged as a key technique of modern life sciences in recent years. Two major techniques for metabolomics in the last 10 years are gas chromatography coupled to mass spectrometry (GC-MS) and liquid chromatography coupled to mass spectrometry (LC-MS). Each platform has a specific performance detecting subsets of metabolites. GC-MS in combination with derivatisation has a preference for small polar metabolites covering primary metabolism. In contrast, reversed phase LC-MS covers large hydrophobic metabolites predominant in secondary metabolism. Here, we present an integrative metabolomics platform providing a mean to reveal the interaction of primary and secondary metabolism in plants and other organisms. The strategy combines GC-MS and LC-MS analysis of the same sample, a novel alignment tool MetMAX and a statistical toolbox COVAIN for data integration and linkage of Granger Causality with metabolic modelling. For metabolic modelling we have implemented the combined GC-LC-MS metabolomics data covariance matrix and a stoichiometric matrix of the underlying biochemical reaction network. The changes in biochemical regulation are expressed as differential Jacobian matrices. Applying the Granger causality, a subset of secondary metabolites was detected with significant correlations to primary metabolites such as sugars and amino acids. These metabolic subsets were compiled into a stoichiometric matrix N. Using N the inverse calculation of a differential Jacobian J from metabolomics data was possible. Key points of regulation at the interface of primary and secondary metabolism were identified.
authors.affiliation: Department of Molecular Systems Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
authors.forename: Hannes
authors.initials: H
authors.lastname: Doerfler
authors.forename: David
authors.initials: D
authors.lastname: Lyon
authors.forename: Thomas
authors.initials: T
authors.lastname: Nägele
authors.forename: Xiaoliang
authors.initials: X
authors.lastname: Sun
authors.forename: Lena
authors.initials: L
authors.lastname: Fragner
authors.forename: Franz
authors.initials: F
authors.lastname: Hadacek
authors.forename: Volker
authors.initials: V
authors.lastname: Egelhofer
authors.forename: Wolfram
authors.initials: W
authors.lastname: Weckwerth
keywords: Cold acclimation; Differential Jacobian; Granger causality; Mass spectrometry; Metabolomics; Plant systems biology