Metabolomic Analysis of Yeast and Human Cells: Latest Advances and Challenges

  • Romanas ChaleckisEmail author
  • Kazuto Ohashi
  • Isabel Meister
  • Shama Naz
  • Craig E. Wheelock
Part of the Methods in Molecular Biology book series (MIMB, volume 2049)


Liquid chromatography–mass spectrometry (LC-MS) based nontargeted metabolomics has been applied to a wide range of biological samples and can provide information on thousands of compounds. However, reliable identification of the compounds remains a challenge affecting result interpretation. In this protocol, we describe comparable yeast cell and whole blood metabolome sample preparation for extracting similar compound groups, and we present a LC-MS method using the all ion fragmentation (AIF) approach for the purposes of increasing accuracy in metabolite annotation. Our method enables database-dependent targeted as well as nontargeted metabolomics analysis from the same data acquisition, while simultaneously improving the accuracy in metabolite identification to increase the quality of the resulting biological information.

Key words

Metabolomics Liquid chromatography–mass spectrometry (LC-MS) All ion fragmentation (AIF) Metabolite annotation 





All ion fragmentation


Accurate mass


Collision induced dissociation


Extracted ion chromatogram


Hydrophilic interaction liquid chromatography


Liquid chromatography–mass spectrometry




Tandem mass spectrometry


Retention time



We acknowledge the support of the Gunma University Initiative for Advanced Research (GIAR). This work was supported in part by The Environment Research and Technology Development Fund (ERTDF) (Grant No 5-1752). CEW was supported by the Swedish Heart Lung Foundation (HLF 20150640).


  1. 1.
    Kell DB, Oliver SG (2016) The metabolome 18 years on: a concept comes of age. Metabolomics 12:148. Scholar
  2. 2.
    Beger RD, Dunn W, Schmidt MA et al (2016) Metabolomics enables precision medicine: “a white paper, community perspective”. Metabolomics 12:149. Scholar
  3. 3.
    Chaleckis R, Ebe M, Pluskal T et al (2014) Unexpected similarities between the Schizosaccharomyces and human blood metabolomes, and novel human metabolites. Mol BioSyst 10:2538–2551. Scholar
  4. 4.
    Sumner LW, Amberg A, Barrett D et al (2007) Proposed minimum reporting standards for chemical analysis chemical analysis working group (CAWG) metabolomics standards initiative (MSI). Metabolomics 3:211–221. Scholar
  5. 5.
    Pluskal T, Nakamura T, Villar-Briones A, Yanagida M (2010) Metabolic profiling of the fission yeast S. pombe: quantification of compounds under different temperatures and genetic perturbation. Mol BioSyst 6:182–198. Scholar
  6. 6.
    Plumb RS, Johnson KA, Rainville P et al (2006) UPLC/MS(E); a new approach for generating molecular fragment information for biomarker structure elucidation. Rapid Commun Mass Spectrom 20:1989–1994. Scholar
  7. 7.
    Naz S, Gallart-Ayala H, Reinke SN et al (2017) Development of a liquid chromatography-high resolution mass spectrometry metabolomics method with high specificity for metabolite identification using all ion fragmentation acquisition. Anal Chem 89:7933–7942. Scholar
  8. 8.
    Volani C, Caprioli G, Calderisi G et al (2017) Pre-analytic evaluation of volumetric absorptive microsampling and integration in a mass spectrometry-based metabolomics workflow. Anal Bioanal Chem 32:338–314. Scholar
  9. 9.
    Tsugawa H, Cajka T, Kind T et al (2015) MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis. Nat Methods 12:523–526. Scholar
  10. 10.
    Pluskal T, Castillo S, Villar-Briones A, Oresic M (2010) MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinformatics 11:395. Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Romanas Chaleckis
    • 1
    • 2
    Email author
  • Kazuto Ohashi
    • 3
  • Isabel Meister
    • 1
    • 2
  • Shama Naz
    • 2
  • Craig E. Wheelock
    • 1
    • 2
  1. 1.Gunma University Initiative for Advanced Research (GIAR)Gunma UniversityMaebashiJapan
  2. 2.Division of Physiological Chemistry II, Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
  3. 3.Institute for Molecular and Cellular RegulationGunma UniversityMaebashiJapan

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