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Metabolomics: From Fundamentals to Clinical Applications pp 19–44Cite as

Collection and Preparation of Clinical Samples for Metabolomics

Part of the Advances in Experimental Medicine and Biology book series (PMISB,volume 965)

Abstract

A wide range of biofluids (urine, serum, plasma, saliva, etc.) as well as cellular and tissue samples can be collected and investigated in clinical metabolomic studies. The choice of sample is dependent on the clinical question being investigated with biofluids typically studied to identify biomarkers, whereas tissues and primary/immortalised cells are typically studied to investigate mechanisms associated with pathophysiological processes. Methods applied to collect samples, quench metabolism and extract samples differ between sample types from simple collect, dilute and analyse methods for urine to complex washing, quenching and biphasic extraction methods for tissues. The range of sample collection and extraction methods are discussed with sample-specific considerations highlighted. Finally, methods for imaging of cells and tissues and for in vivo metabolomic analysis will also be introduced.

Keywords

  • Serum
  • Plasma
  • Urine
  • Human cells
  • Human tissues
  • Metabolic quenching
  • Extraction
  • Imaging

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Fig. 2.1
Fig. 2.2
Fig. 2.3

Abbreviations

ATCC:

American Type Culture Centre

BMI:

Body mass index

BSTFA:

N,O-Bis(trimethylsilyl)trifluoroacetamide

CHO:

Chinese hamster ovary

CSF:

Cerebrospinal fluid

DESI-MS:

Desorption electrospray ionisation-mass spectrometry

DNA:

Deoxyribonucleic acid

EDTA:

Ethylenediaminetetraacetic acid

ESI:

Electrospray ionisation

GC-MS:

Gas chromatography-mass spectrometry

HILIC:

Hydrophilic interaction chromatography

HS-SPME:

Headspace solid-phase microextraction

IPA:

Isopropyl alcohol

LC:

Liquid chromatography

LC-MS:

Liquid chromatography-mass spectrometry

LLE:

Liquid-liquid extraction

MALDI-MS:

Matrix-assisted laser desorption/ionisation and mass spectrometry

MSTFA:

N-Methyl-N-(trimethylsilyl) trifluoroacetamide

MTBE:

Methyl tert-butyl ether

NMR:

Nuclear magnetic resonance

PBS:

Phosphate-buffered saline

RNA:

Ribonucleic acid

SIMS:

Secondary ion mass spectrometry

SOP:

Standard operating procedure

SPE:

Solid-phase extraction

SPME:

Solid-phase microextraction

TCA:

Tricarboxylic acid

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  1. School of Biosciences and Phenome Centre Birmingham, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK

    Andrew J. Chetwynd, Warwick B. Dunn & Giovanny Rodriguez-Blanco

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  1. University of Campinas (UNICAMP) Institute of Chemistry Laboratory of Bioanalytics and Integrated Omics (LaBIOmics), Campinas, Brazil

    Alessandra Sussulini

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Chetwynd, A.J., Dunn, W.B., Rodriguez-Blanco, G. (2017). Collection and Preparation of Clinical Samples for Metabolomics. In: Sussulini, A. (eds) Metabolomics: From Fundamentals to Clinical Applications. Advances in Experimental Medicine and Biology(), vol 965. Springer, Cham. https://doi.org/10.1007/978-3-319-47656-8_2

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