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

Publication Type:Journal Article
Year of Publication:2011
Authors:Giavalisco, P, Li, Y, Matthes, A, Eckhardt, A, Hubberten, H-M, Hesse, H, Segu, S, Hummel, J, Köhl, K, Willmitzer, L
Journal:The Plant Journal
Volume:68
Issue:2
Date Published:2011
ISBN Number:1365-313X
Keywords:Arabidopsis thaliana, isotope labelling, mass spectrometry, metabolomics, proteomics
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 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.

URL:http://dx.doi.org/10.1111/j.1365-313X.2011.04682.x
Short Title:The Plant Journal
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Scratchpads developed and conceived by (alphabetical): Ed Baker, Katherine Bouton Alice Heaton Dimitris Koureas, Laurence Livermore, Dave Roberts, Simon Rycroft, Ben Scott, Vince Smith