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

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

Key words

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

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

Notes

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).

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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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