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Assay Tools for Metabolomics

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Genetics Meets Metabolomics

Abstract

Metabolomics deals with a comprehensive evaluation of metabolites, which reflect all functional activities, transient effects, and also endpoints of processes in biological systems. Metabolomics provides a snapshot of the physiological state, which is determined by the sum of its genetic composition, regulation of gene expression, protein function, and environmental influence. Successful metabolomic analyses rely on proper experimental design, standardized sample processing, versatile analytical methods, and large scale bioinformatics. This chapter provides an overview on practical aspects of metabolomics including aims, experimental design, as well as methods for sample processing and analytics. It will introduce the reader to the analytical tools like gas and liquid chromatography coupled to mass spectrometry. Moreover, different types of metabolomics such as profiling, non-targeted and targeted metabolomics, which contribute to versatile analyses of the metabolism, will also be discussed. Additionally, details will be provided on the application of metabolomics in human and animal studies.

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Abbreviations

AMU:

Atomic mass unit

APCI:

Atmospheric pressure chemical ionization

APPI:

Atmospheric pressure photoionization

BMI:

Body mass index

CE:

Capillary electrophoresis

CE-MS:

Capillary electrophoresis mass spectrometry

CI:

Chemical ionization

CID:

Collision-induced dissociation

EI:

Electron impact ionization

ESI:

Electrospray ionization

FIA:

Flow injection analysis

FIA-MS:

Flow injection analysis mass spectrometry

FT-ICR-MS:

Fourier transform ion cyclotron resonance mass spectrometry

FT-IR:

Fourier transform infrared spectrometry

GC:

Gas chromatography

GC-MS:

Gas chromatography mass spectrometry

GWAS:

Genome-wide association studies

HMDB:

Human metabolome database

HPLC:

High performance liquid chromatography

IUPAC:

International union of pure and applied chemistry

KEGG:

Kyoto encyclopedia of genes and genomes

LC:

Liquid chromatography

LC-MS:

Liquid chromatography mass spectrometry

LC-MS/MS:

Liquid chromatography tandem mass spectrometry

LIMS:

Laboratory information and management system

LLOQ:

Lower limit of quantification

LOD:

Limit of detection

LOQ:

Limit of quantification

m/z:

Mass to charge ratio

MRI:

Magnetic resonance imaging

MRM:

Multiple reaction monitoring

MS:

Mass spectrometry

MS/MS:

Tandem mass spectrometry

NMR:

Nuclear magnetic resonance

PBS:

Phosphate buffered saline

PCA:

Principal component analysis

PCI/NCI:

Positive chemical ionization/negative chemical ionization

RF:

Random forest

RP18:

Reversed phase C18 alkyl chain modified silica

SIM:

Single ion monitoring

SOP:

Standard operating procedure

SPE:

Solid phase extraction

SRM:

Selected reaction monitoring

UHPLC:

Ultra high performance liquid chromatography

UHPLC-MS:

Ultra high performance liquid chromatography mass spectrometry

ULOQ:

Upper limit of quantification

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Authors and Affiliations

  1. Helmholtz Zentrum München, Institute of Experimental Genetics, Genome Analysis Center, Ingolstädter Landstraße 1, Neuherberg, Bavaria, 85764, Germany

    Anna Artati Ph.D., Cornelia Prehn Ph.D., Gabriele Möller Ph.D. & Jerzy Adamski Ph.D., M.Sc.

Authors
  1. Anna Artati Ph.D.
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  2. Cornelia Prehn Ph.D.
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  3. Gabriele Möller Ph.D.
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  4. Jerzy Adamski Ph.D., M.Sc.
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Corresponding author

Correspondence to Jerzy Adamski Ph.D., M.Sc. .

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Editors and Affiliations

  1. Qatar Foundation-Education City, Weill Cornell Medical College in Qatar, Education City – Qatar Foundation, Doha, 24144, Qatar

    Karsten Suhre

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Artati, A., Prehn, C., Möller, G., Adamski, J. (2012). Assay Tools for Metabolomics. In: Suhre, K. (eds) Genetics Meets Metabolomics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-1689-0_3

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