Protocol abstract

Nature Protocols 1, 387 - 396 (2006)
Published online: 27 June 2006 | Corrected online: 5 August 2015 | doi:10.1038/nprot.2006.59

There is a Corrigendum (September 2015) associated with this Protocol.

Gas chromatography mass spectrometry–based metabolite profiling in plants

Jan Lisec1,2, Nicolas Schauer1,2, Joachim Kopka1, Lothar Willmitzer1 & Alisdair R Fernie1

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.

  1. Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
  2. These authors contributed equally to this work.

Correspondence to: Alisdair R Fernie1 e-mail: