Untargeted Analysis of Semipolar Compounds by LC-MS and Targeted Analysis of Fatty Acids by GC-MS/GC-FID: From Plant Cultivation to Extract Preparation

  • Camille Bénard
  • Sébastien Acket
  • Yannick Rossez
  • Olivier Fernandez
  • Thierry Berton
  • Yves Gibon
  • Cécile Cabasson
Part of the Methods in Molecular Biology book series (MIMB, volume 1778)


The way plants are grown and samples are harvested, prepared, and extracted has a profound impact on the output of a metabolomics experiment. In this chapter, we detail the experimental procedures from plant cultivation to extract preparation, in order to avoid difficulties that could result in contamination or undesired changes of the analytes. Two plant organs are mentioned as examples: tomato fruits (Solanum lycopersicum) and flax seeds (Linum usitatissimum). Extractions designed for the untargeted analysis of semipolar compounds by liquid chromatography–mass spectrometry (LC-MS) and targeted analysis of fatty acids by gas chromatography–mass spectrometry (GC-MS) or gas chromatography with flame ionization detector (GC-FID) are described.

Key words

Plant cultivation Sample preparation Sample harvest Fatty acids Specialized compounds Tomato Flax seeds 



C. Bénard thanks Patricia Ballias and Mickael Maucourt for fruitful technical discussions and Dr. Stéphane Bernillon for reviewing the manuscript and providing helpful comments. This work was supported by the projects MetaboHUB-ANR-11-INBS-0010, PHENOME-ANR-11-INBS-0012, SUNRISE-ANR-11-BTBR-0005, the Regional Council of Picardie, and by the European Union which cofunded equipment utilized within CPER 2007-2020.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Camille Bénard
    • 1
    • 2
    • 3
  • Sébastien Acket
    • 4
  • Yannick Rossez
    • 4
  • Olivier Fernandez
    • 2
  • Thierry Berton
    • 2
    • 3
  • Yves Gibon
    • 2
    • 3
  • Cécile Cabasson
    • 3
    • 5
  1. 1.Service de Pharmacologie et Immunoanalyse (SPI), MetaboHUB-Paris, CEA, INRAUniversité Paris SaclayGif-sur-Yvette CedexFrance
  2. 2.UMR 1332 Biologie du Fruit et Pathologie, Centre INRA de Nouvelle Aquitaine-Bordeaux, INRAUniv. BordeauxVillenave d’OrnonFrance
  3. 3.Plateforme Métabolome Bordeaux, PHENOME, MetaboHUB, Centre INRA de Nouvelle Aquitaine-Bordeaux, INRA, CNRSUniv. BordeauxVillenave d’OrnonFrance
  4. 4.Sorbonne Universités, Université de Technologie de CompiègneUMR CNRS 7025, Génie Enzymatique et CellulaireCompiègne CedexFrance
  5. 5.UMR 1332 Biologie du Fruit et PathologieCentre INRA de Nouvelle-Aquitaine Bordeaux, INRA, Univ. BordeauxVillenave d’OrnonFrance

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