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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Dissertation
Topics in mass spectrometry based structure determination
TL;DR: This thesis presents a constant memory space algorithm (DIOPHANTINE), and an output sensitive dynamic programming based algorithm (DP++), outperforming state-of-the-art methods both for integer type and float type problems.
Engineering and Evolution of the Complete Reductive Glycine Pathway in Saccharomyces cerevisiae for Formate and CO2 Assimilation
TL;DR: In this article , the authors adopted a growth-coupled selection scheme for modular implementation of the Reductive Glycine Pathway (RGP) and subsequent Adaptive Laboratory Evolution (ALE) to enable formate and CO2 assimilation for biomass formation in yeast.
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Preferential mineral N form uptake by sugarcane genotypes contrasting in nitrogen use efficiency
TL;DR: In this paper , the preferential uptake of ammonium and nitrate in sugarcane genotypes contrasting with NUE under controlled conditions was evaluated under three time points: 0, 24, and 72 h after 15 N-fertilization.
Journal ArticleDOI
Comparative Primary Metabolite Profiling of Setaria viridis Reveals Potential Markers to Water Limitation
Fernanda Alves de Freitas Guedes,Luana Beatriz dos Santos Nascimento,Mara Priscila Costa,Andrew Macrae,Marcio Alves-Ferreira,Camila Caldana,Fernanda Reinert +6 more
TL;DR: In this paper , the primary metabolic profile of Setaria viridis was assessed in response to three water levels, i.e., five-day-old seedlings were submitted to water-limiting conditions for 25 days when samples were harvested.
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Circulating Metabolites as Potential Biomarkers for the Early Detection and Prognosis Surveillance of Gastric and Colon Cancers
TL;DR: In this article , the authors aimed to discriminate GI cancers from non-cancers and even allow the classification of cancer subtypes by assessing the alterations in metabolites for a specific cancer type.
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