Elemental formula annotation of polar and lipophilic metabolites using 13C, 15N and 34S isotope labelling, in combination with high-resolution mass spectrometry
Patrick Giavalisco,Yan Li,Annemarie Matthes,Aenne Eckhardt,Hans-Michael Hubberten,Holger Hesse,Shruthi Segu,Jan Hummel,Karin Köhl,Lothar Willmitzer +9 more
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TLDR
A comprehensive multi-isotope labelling-based strategy using fully labelled plant tissues, in combination with a fractionated metabolite extraction protocol, which can be applied in either an automated database-dependent or a database-independent analysis of the plant polar metabolome and lipidome.Abstract:
The unbiased and comprehensive analysis of metabolites in any organism presents a major challenge if proper peak annotation and unambiguous assignment of the biological origin of the peaks are required. Here we provide a comprehensive multi-isotope labelling-based strategy using fully labelled (13) C, (15) N and (34) S plant tissues, in combination with a fractionated metabolite extraction protocol. The extraction procedure allows for the simultaneous extraction of polar, semi-polar and hydrophobic metabolites, as well as for the extraction of proteins and starch. After labelling and extraction, the metabolites and lipids were analysed using a high-resolution mass spectrometer providing accurate MS and all-ion fragmentation data, providing an unambiguous readout for every detectable isotope-labelled peak. The isotope labelling assisted peak annotation process employed can be applied in either an automated database-dependent or a database-independent analysis of the plant polar metabolome and lipidome. As a proof of concept, the developed methods and technologies were applied and validated using Arabidopsis thaliana leaf and root extracts. Along with a large repository of assigned elemental compositions, which is provided, we show, using selected examples, the accuracy and reliability of the developed workflow.read more
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Acyl-Lipid Metabolism
Younghua Li-Beisson,Basil S. Shorrosh,Fred Beisson,Mats X. Andersson,Vincent Arondel,Philip D. Bates,Sébastien Baud,David Bird,Debono Allan George,Timothy P. Durrett,Rochus Franke,Ian A. Graham,Kenta Katayama,Amélie A. Kelly,Tony R. Larson,Jonathan E. Markham,Martine Miquel,Isabel Molina,Ikuo Nishida,Owen Rowland,Lacey Samuels,Katherine M. Schmid,Hajime Wada,Ruth Welti,Changcheng Xu,Rémi Zallot,John B. Ohlrogge +26 more
TL;DR: This chapter focuses on the metabolic pathways that are associated with the biosynthesis and degradation of the acyl lipids that represent their major form of carbon and energy storage in Arabidopsis.
Journal ArticleDOI
Toward Merging Untargeted and Targeted Methods in Mass Spectrometry-Based Metabolomics and Lipidomics.
TL;DR: This work focuses on the application of mass spectrometry to the treatment of metabolomics and Lipidomics with a focus on the characterization of the role of phosphorous in the biosynthetic pathway.
Journal ArticleDOI
Comprehensive analysis of lipids in biological systems by liquid chromatography-mass spectrometry
Tomas Cajka,Oliver Fiehn +1 more
TL;DR: This review focuses on state of the art in LC-MS-based lipidomics, covering all the steps of global lipidomic profiling, and concludes that phospholipids followed by sphingomyelins, di- and tri-acylglycerols, and ceramides were the most frequently targeted lipid species.
Journal ArticleDOI
Comprehensive Dissection of Spatiotemporal Metabolic Shifts in Primary, Secondary, and Lipid Metabolism during Developmental Senescence in Arabidopsis
Mutsumi Watanabe,Salma Balazadeh,Takayuki Tohge,Alexander Erban,Patrick Giavalisco,Joachim Kopka,Bernd Mueller-Roeber,Alisdair R. Fernie,Rainer Hoefgen +8 more
TL;DR: The metabolome data and the approach provided here can serve as a blueprint for the analysis of traits and conditions linking crop yield and senescence as well as provide clues to source-sink relations.
Journal ArticleDOI
Mass spectrometry-based plant metabolomics: Metabolite responses to abiotic stress.
Tiago F. Jorge,João A. Rodrigues,Camila Caldana,Romy Schmidt,Joost T. van Dongen,Jane Thomas-Oates,Carla António +6 more
TL;DR: Recent applications of metabolomics are described and its increasing application to study plant responses to environmental (stress-) factors, including drought, salt, low oxygen caused by waterlogging or flooding of the soil, temperature, light and oxidative stress are described.
References
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Journal ArticleDOI
Towards the plant metabolome and beyond
TL;DR: Current innovations in small-molecule analysis have created the ability to rapidly identify and quantify numerous compounds, and these data are creating new opportunities for understanding plant metabolism and for plant metabolic engineering.
Journal ArticleDOI
A Topological Map of the Compartmentalized Arabidopsis thaliana Leaf Metabolome
Stephan Krueger,Patrick Giavalisco,Leonard Krall,Marie-Caroline Steinhauser,Dirk Büssis,Bjoern Usadel,Ulf-Ingo Flügge,Alisdair R. Fernie,Lothar Willmitzer,Dirk Steinhauser +9 more
TL;DR: This complex data set does not only contain a rich repository of metabolic information, but due to thorough validation and testing by statistical methods, represents an initial step in the analysis of metabolite dynamics and fluxes within and between subcellular compartments.
Journal ArticleDOI
GC-EI-TOF-MS analysis of in vivo carbon-partitioning into soluble metabolite pools of higher plants by monitoring isotope dilution after 13CO2 labelling
TL;DR: The established GC-EI-TOF-MS method for the profiling of soluble polar metabolites from plant tissue was employed for the kinetic metabolic phenotyping of higher plants and Simplifying data reduction schemes comprising calculation of (13)C-enrichment from mass isotopomer distributions and of initial (13C-dilution rates were employed.
Journal ArticleDOI
Metabolic systems biology
TL;DR: The placement of metabolic systems biology in the context of broader scientific developments, its foundational concepts, some of its current uses, and some of the expected future developments in the field are discussed.
Journal ArticleDOI
Stable isotope assisted assignment of elemental compositions for metabolomics.
Adrian D. Hegeman,Christopher F. Schulte,Qiu Cui,Ian A. Lewis,Edward L. Huttlin,Hamid R. Eghbalnia,Amy C. Harms,Eldon L. Ulrich,John L. Markley,Michael R. Sussman +9 more
TL;DR: It is demonstrated that metabolic labeling can be used to provide additional constraints for higher confidence formula assignments over an extended mass range by analyzing exact mass measurement data from the four extracts using two methods.
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