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Gas chromatography mass spectrometry–based metabolite profiling in plants

Nature Protocols volume 1, pages 387–396 (2006)Cite this article

A Corrigendum to this article was published on 27 August 2015

This article has been updated

Abstract

The concept of metabolite profiling has been around for decades, but technical innovations are now enabling it to be carried out on a large scale with respect to the number of both metabolites measured and experiments carried out. Here we provide a detailed protocol for gas chromatography mass spectrometry (GC-MS)-based metabolite profiling that offers a good balance of sensitivity and reliability, being considerably more sensitive than NMR and more robust than liquid chromatography–linked mass spectrometry. We summarize all steps from collecting plant material and sample handling to derivatization procedures, instrumentation settings and evaluating the resultant chromatograms. We also define the contribution of GC-MS–based metabolite profiling to the fields of diagnostics, gene annotation and systems biology. Using the protocol described here facilitates routine determination of the relative levels of 300–500 analytes of polar and nonpolar extracts in ∼400 experimental samples per week per machine.

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Figure 1: Experimental procedure for extract preparation.
Figure 2: Normalization.
Figure 3: Timeline of standard operating procedure.
Figure 4: Retention time variation within sample sets.
Figure 5: Example of a peak deconvolution error.
Figure 6: Median and box-plot spectra.
Figure 7: Spectra annotation correction process.

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  • 05 August 2015

    In the version of this article initially published, Figure 1 contained the words "metoxyamin hydrochloride." These words should have read "methoxyamine hydrochloride." The error has been corrected in the HTML and PDF versions of the article.

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Acknowledgements

We thank O. Fiehn and Ä. Eckhardt for intensive collegial discussions on all matters metabolomic.

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Author notes

  1. Jan Lisec and Nicolas Schauer: These authors contributed equally to this work.

Authors and Affiliations

  1. Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany

    Jan Lisec, Nicolas Schauer, Joachim Kopka, Lothar Willmitzer & Alisdair R Fernie

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Correspondence to Alisdair R Fernie.

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Lisec, J., Schauer, N., Kopka, J. et al. Gas chromatography mass spectrometry–based metabolite profiling in plants. Nat Protoc 1, 387–396 (2006). https://doi.org/10.1038/nprot.2006.59

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