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

Plant J. 2011 Oct;68(2):364-76. doi: 10.1111/j.1365-313X.2011.04682.x. Epub 2011 Jul 26.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / chemistry
  • Arabidopsis / metabolism*
  • Carbon Isotopes
  • Chlorophyll / analogs & derivatives
  • Chlorophyll / chemistry
  • Databases, Factual
  • Fourier Analysis
  • Isotope Labeling
  • Lipids / analysis
  • Mass Spectrometry
  • Metabolomics / methods*
  • Nitrogen Isotopes
  • Plant Extracts / chemistry
  • Plant Extracts / isolation & purification*
  • Plant Leaves / chemistry
  • Plant Leaves / metabolism
  • Plant Roots / chemistry
  • Plant Roots / metabolism
  • Proteomics / methods*
  • Reproducibility of Results
  • Sulfur Isotopes


  • Carbon Isotopes
  • Lipids
  • Nitrogen Isotopes
  • Plant Extracts
  • Sulfur Isotopes
  • Chlorophyll
  • pheophorbide a