Metabolomic Profiling of Plant Tissues

  • José L. Rambla
  • M. P. López-Gresa
  • J. M. Bellés
  • Antonio GranellEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1284)


Metabolomics is a powerful discipline aimed at a comprehensive and global analysis of the metabolites present in a cell, tissue, or organism, and to which increasing attention has been paid in the last few years. Given the high diversity in physical and chemical properties of plant metabolites, not a single method is able to analyze them all.

Here we describe two techniques for the profiling of two quite different groups of metabolites: polar and semi-polar secondary metabolites, including many of those involved in plant response to biotic and abiotic stress, and volatile compounds, which include those responsible of most of our perception of food flavor. According to these techniques, polar and semi-polar metabolites are extracted in methanol, separated by liquid chromatography (UPLC), and detected by a UV–VIS detector (PDA) and a time-of-flight (ToF) mass spectrometer. Volatile compounds, on the other hand, are extracted by headspace solid phase microextraction (HS-SPME), and separated and detected by gas chromatography coupled to mass spectrometry (GC-MS).

Key words

Volatile compounds Semi-polar metabolites Gas chromatography Liquid chromatography Mass spectrometry SPME 


  1. 1.
    Lisec J, Schauer N, Kopka J et al (2006) Gas chromatography mass spectrometry-based metabolite profiling in plants. Nat Protoc 1:387–396CrossRefPubMedGoogle Scholar
  2. 2.
    Kim HK, Chou YH, Verpoorte R (2010) NMR-based metabolomic analysis of plants. Nat Protoc 5:536–549CrossRefPubMedGoogle Scholar
  3. 3.
    Heinig U, Aharoni A (2014) Analysis of steroidal alkaloids and saponins in Solanaceae plant extracts using UPLC-qTOF mass spectrometry. Methods Mol Biol 1153:171–185CrossRefPubMedGoogle Scholar
  4. 4.
    Fantini E, Falcone G, Frusciante S et al (2013) Dissection of tomato lycopene biosynthesis through virus-induced gene silencing. Plant Physiol 163:986–998CrossRefPubMedCentralPubMedGoogle Scholar
  5. 5.
    Moco S, Bino RJ, Vorst O et al (2006) A liquid chromatography mass spectrometry based metabolome database for tomato. Plant Physiol 141:1205–1218CrossRefPubMedCentralPubMedGoogle Scholar
  6. 6.
    González-Mas MC, Rambla JL, Alamar MC et al (2011) Comparative analysis of the volatile fraction of fruit juice from different Citrus species. PLoS One 6:e22016CrossRefPubMedCentralPubMedGoogle Scholar
  7. 7.
    Araguez I, Hoffmann T, Osorio S et al (2013) Eugenol production in achenes and receptacles of strawberry fruits is catalyzed by synthases exhibiting distinct kinetics. Plant Physiol 163:946–958CrossRefPubMedCentralPubMedGoogle Scholar
  8. 8.
    Tikunov Y, Lommen A, de Vos CHR et al (2005) A novel approach for nontargeted data analysis for metabolomics. Large-scale profiling of tomato fruit volatiles. Plant Physiol 139:1125–1137CrossRefPubMedCentralPubMedGoogle Scholar
  9. 9.
    Sánchez G, Besada C, Badenes ML et al (2012) A non-targeted approach unravels the volatile network in peach fruit. PLoS One 7:e38992CrossRefPubMedCentralPubMedGoogle Scholar
  10. 10.
    Besada C, Salvador A, Sdiri S et al (2013) A combination of physiological and chemometrics analyses reveals the main associations between quality and ripening traits and volatiles in two loquat cultivars. Metabolomics 9:324–336CrossRefGoogle Scholar
  11. 11.
    Trapero-Mozos A, Gómez-Gómez L, Rubio-Moraga A et al (2012) Changes in volatiles during grape maturation of two autochthon Castilla-La Mancha varieties: Airen and Tempranillo. FEBS J 279:77–78Google Scholar
  12. 12.
    Besada C, Sánchez G, Salvador A et al (2013) Volatile compounds associated to the loss of astringency in persimmon fruits revealed by untargeted GC-MS analysis. Metabolomics 9:157–172CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • José L. Rambla
    • 1
  • M. P. López-Gresa
    • 1
  • J. M. Bellés
    • 1
  • Antonio Granell
    • 1
    Email author
  1. 1.Instituto de Biología Molecular y Celular de PlantasCSIC - Universidad Politécnica de ValenciaValenciaSpain

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