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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Lipidomics analysis unravels the effect of nitrogen fertilization on lipid metabolism in tea plant ( Camellia sinensis L.)
TL;DR: It is indicated that appropriate application of N fertilizer could balance the lipid metabolism and the formation of flavor/aroma origin compounds, which help to improve the quality of tea.
Journal ArticleDOI
Liquid chromatography high-resolution mass spectrometry for fatty acid profiling
Mariusz A. Bromke,Anton Hochmuth,Takayuki Tohge,Alisdair R. Fernie,Patrick Giavalisco,Asdrubal Burgos,Lothar Willmitzer,Yariv Brotman +7 more
TL;DR: This work has compared the analysis by LC-MS and GC-FID of two previously characterized Arabidopsis thaliana knock-out mutants for FAD6 and FAD7 desaturase genes, and suggests that because of higher sensitivity and selectivity theLC-MS-based method allows for a broader coverage and determination of novel fatty acids.
Journal ArticleDOI
Analysis of metabolic flux using dynamic labeling and metabolic modeling
Alisdair R. Fernie,J. A. Morgan +1 more
TL;DR: The conceptual basis of these complementary approaches, as well as their historical application in microbial, mammalian and plant sciences, is reviewed, and an update on technical developments in label distribution analyses is provided.
Journal ArticleDOI
RAPTOR Controls Developmental Growth Transitions by Altering the Hormonal and Metabolic Balance
Mohamed A. Salem,Mohamed A. Salem,Yan Li,Krzysztof Bajdzienko,Joachim Fisahn,Mutsumi Watanabe,Rainer Hoefgen,Mark Aurel Schöttler,Patrick Giavalisco +8 more
TL;DR: It is found that the Arabidopsis raptor1b mutation did not affect chloroplast development or photosynthetic electron transport efficiency; however, it resulted in decreased CO2 assimilation rate and increased stomatal conductance, indicating the tight interaction between TOR function and hormone synthesis and signaling in plants.
Journal ArticleDOI
Recent advances in stable isotope-enabled mass spectrometry-based plant metabolomics.
Dana M. Freund,Adrian D. Hegeman +1 more
TL;DR: This review examines stable isotopic labeling approaches that have been developed for labeling whole intact plants, plant tissues, or crude extracts of plant materials with stable isotopes.
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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