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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High-resolution plant metabolomics: from mass spectral features to metabolites and from whole-cell analysis to subcellular metabolite distributions
TL;DR: In this review the different approaches for targeted and non-targeted metabolomics analysis will be described with special emphasis on mass spectrometry-based techniques, with particular attention to approaches which can be employed for the annotation of unknown compounds.
Journal ArticleDOI
Differential remodeling of the lipidome during cold acclimation in natural accessions of Arabidopsis thaliana
Thomas Degenkolbe,Patrick Giavalisco,Ellen Zuther,Bettina Seiwert,Dirk K. Hincha,Lothar Willmitzer +5 more
TL;DR: An alternative ecological genomics approach that relies on the natural genetic variation within a species, highly correlated with the freezing tolerance of the accessions, allowing the identification of possible marker lipids for plant freezing tolerance.
Journal ArticleDOI
Local Fatty Acid Channeling into Phospholipid Synthesis Drives Phagophore Expansion during Autophagy
TL;DR: This work illuminates how cells spatially tune synthesis and flux of phospholipids for autophagosome biogenesis during autophagy and delineates a pathway that expands the phagophore membrane by localized phospholIPid synthesis.
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Protocol: a fast, comprehensive and reproducible one-step extraction method for the rapid preparation of polar and semi-polar metabolites, lipids, proteins, starch and cell wall polymers from a single sample
TL;DR: The described extraction protocol provides a simple and straightforward method for the efficient extraction of lipids, metabolites and proteins from minute amounts of a single sample, enabling the targeted but also untargeted high-throughput analyses of diverse biological tissues and samples.
Journal ArticleDOI
Global Analysis of the Role of Autophagy in Cellular Metabolism and Energy Homeostasis in Arabidopsis Seedlings under Carbon Starvation
Tamar Avin-Wittenberg,Krzysztof Bajdzienko,Gal Wittenberg,Saleh Alseekh,Takayuki Tohge,Ralph Bock,Patrick Giavalisco,Alisdair R. Fernie +7 more
TL;DR: Significant differences between atg mutants and wild-type plants have been demonstrated, suggesting global effects of autophagy on central metabolism during carbon starvation as well as severe energy deprivation, resulting in a morphological phenotype.
References
More filters
Journal ArticleDOI
KEGG for linking genomes to life and the environment
Minoru Kanehisa,Michihiro Araki,Susumu Goto,Masahiro Hattori,Mika Hirakawa,Masumi Itoh,Toshiaki Katayama,Shuichi Kawashima,Shujiro Okuda,Toshiaki Tokimatsu,Yoshihiro Yamanishi +10 more
TL;DR: KEGG PATHWAY is now supplemented with a new global map of metabolic pathways, which is essentially a combined map of about 120 existing pathway maps, and the KEGG resource is being expanded to suit the needs for practical applications.
Journal ArticleDOI
XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification.
TL;DR: An LC/MS-based data analysis approach, XCMS, which incorporates novel nonlinear retention time alignment, matched filtration, peak detection, and peak matching, and is demonstrated using data sets from a previously reported enzyme knockout study and a large-scale study of plasma samples.
Journal ArticleDOI
MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data
TL;DR: A new generation of a popular open-source data processing toolbox, MZmine 2 is introduced, suitable for processing large batches of data and has been applied to both targeted and non-targeted metabolomic analyses.
Journal ArticleDOI
Mass spectrometry-based metabolomics.
TL;DR: This review presents an overview of the dynamically developing field of mass spectrometry-based metabolomics, a technique that analyzes all detectable analytes in a given sample with subsequent classification of samples and identification of differentially expressed metabolites, which define the sample classes.
Journal ArticleDOI
Lipid extraction by methyl-tert-butyl ether for high-throughput lipidomics
TL;DR: In this paper, the methyl-tert-butyl ether (MTBE) extraction method was used for shotgun profiling of lipid species, and the results showed that the MTBE protocol delivered similar or better recoveries of species of most major lipid classes compared with the "gold-standard" Folch or Bligh and Dyer recipes.
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