Elemental formula annotation of polar and lipophilic metabolites using 13C, 15N and 34S isotope labelling, in combination with high‐resolution mass spectrometry

Summary 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 labell...

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Bibliographic Details
Published in:The Plant journal : for cell and molecular biology 2011-10, Vol.68 (2), p.364-376
Main Authors: Giavalisco, Patrick, Li, Yan, Matthes, Annemarie, Eckhardt, Aenne, Hubberten, Hans‐Michael, Hesse, Holger, Segu, Shruthi, Hummel, Jan, Köhl, Karin, Willmitzer, Lothar
Format: Article
Language:English
Subjects:
Arabidopsis thaliana
Biological and medical sciences
Diverse techniques
Fundamental and applied biological sciences. Psychology
isotope labelling
Isotopes
Mass spectrometry
Metabolites
metabolomics
Molecular and cellular biology
Plant biology
Plant physiology and development
Proteins
proteomics
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Summary:Summary 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 13C, 15N and 34S 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.
ISSN:0960-7412
1365-313X
DOI:10.1111/j.1365-313X.2011.04682.x