Untargeted GC-MS Metabolomics

  • Matthaios-Emmanouil P. Papadimitropoulos
  • Catherine G. Vasilopoulou
  • Christoniki Maga-Nteve
  • Maria I. Klapa
Part of the Methods in Molecular Biology book series (MIMB, volume 1738)


Untargeted metabolomics refers to the high-throughput analysis of the metabolic state of a biological system (e.g., tissue, biological fluid, cell culture) based on the concentration profile of all measurable free low molecular weight metabolites. Gas chromatography-mass spectrometry (GC-MS), being a highly sensitive and high-throughput analytical platform, has been proven a useful tool for untargeted studies of primary metabolism in a variety of applications. As an omic analysis, GC-MS metabolomics is a multistep procedure; thus, standardization of an untargeted GC-MS metabolomics protocol requires the integrated optimization of pre-analytical, analytical, and computational steps. The main difference of GC-MS metabolomics compared to other metabolomics analytical platforms, including liquid chromatography-MS, is the need for the derivatization of the metabolite extracts into volatile and thermally stable derivatives, the latter being quantified in the metabolic profiles. This analytical step requires special care in the optimization of the untargeted GC-MS metabolomics experimental protocol. Moreover, both the derivatization of the original sample and the compound fragmentation that takes place in GC-MS impose specialized GC-MS metabolomic data identification, quantification, normalization and filtering methods. In this chapter, we describe the integrated protocol of untargeted GC-MS metabolomics with both the analytical and computational steps, focusing on the GC-MS specific parts, and provide details on any sample depending differences.

Key words

Untargeted metabolomics Gas chromatography-mass spectrometry (GC-MS) metabolomics Metabolic profiling Metabolic network analysis Primary metabolism 


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Copyright information

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

Authors and Affiliations

  • Matthaios-Emmanouil P. Papadimitropoulos
    • 1
    • 2
  • Catherine G. Vasilopoulou
    • 1
    • 3
  • Christoniki Maga-Nteve
    • 1
    • 4
  • Maria I. Klapa
    • 1
    • 5
    • 6
  1. 1.Metabolic Engineering and Systems Biology LaboratoryInstitute of Chemical Engineering Sciences, Foundation for Research & Technology - Hellas (FORTH/ICE-HT)PatrasGreece
  2. 2.Division of Genetics, Cell & Developmental Biology, Department of BiologyUniversity of PatrasPatrasGreece
  3. 3.Human and Animal Physiology Laboratory, Department of BiologyUniversity of PatrasPatrasGreece
  4. 4.School of MedicineUniversity of PatrasPatrasGreece
  5. 5.Department of Chemical and Biomolecular EngineeringUniversity of MarylandCollege ParkUSA
  6. 6.Department of BioengineeringUniversity of MarylandCollege ParkUSA

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