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Yeast Systems Biology pp 233–245Cite as

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

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 2049))

Abstract

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.

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Abbreviations

ACN:

Acetonitrile

AIF:

All ion fragmentation

AM:

Accurate mass

CID:

Collision induced dissociation

EIC:

Extracted ion chromatogram

HILIC:

Hydrophilic interaction liquid chromatography

LC-MS:

Liquid chromatography–mass spectrometry

MeOH:

Methanol

MS/MS:

Tandem mass spectrometry

RT:

Retention time

References

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Acknowledgments

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).

Author information

Authors and Affiliations

  1. Gunma University Initiative for Advanced Research (GIAR), Gunma University, Maebashi, Japan

    Romanas Chaleckis, Isabel Meister & Craig E. Wheelock

  2. Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden

    Romanas Chaleckis, Isabel Meister, Shama Naz & Craig E. Wheelock

  3. Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan

    Kazuto Ohashi

Authors
  1. Romanas Chaleckis
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  2. Kazuto Ohashi
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  3. Isabel Meister
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  4. Shama Naz
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  5. Craig E. Wheelock
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Corresponding author

Correspondence to Romanas Chaleckis .

Editor information

Editors and Affiliations

  1. Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK

    Stephen G. Oliver

  2. Genetadi Biotech, Parque Tecnológico de Bizkaia, Biscay, Spain

    Juan I. Castrillo

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Chaleckis, R., Ohashi, K., Meister, I., Naz, S., Wheelock, C.E. (2019). Metabolomic Analysis of Yeast and Human Cells: Latest Advances and Challenges. In: Oliver, S.G., Castrillo, J.I. (eds) Yeast Systems Biology. Methods in Molecular Biology, vol 2049. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9736-7_14

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  • DOI: https://doi.org/10.1007/978-1-4939-9736-7_14

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9735-0

  • Online ISBN: 978-1-4939-9736-7

  • eBook Packages: Springer Protocols

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