Computational Systems Biology Methods and Protocols.7z

Chapter 16

Metabolomics: A High-Throughput Platform for Metabolite

Profile Exploration

Jing Cheng, Wenxian Lan, Guangyong Zheng, and Xianfu Gao

Abstract

Metabolomics aims to quantitatively measure small-molecule metabolites in biological samples, such as
bodily fluids (e.g., urine, blood, and saliva), tissues, and breathe exhalation, which reflects metabolic
responses of a living system to pathophysiological stimuli or genetic modification. In the past decade,
metabolomics has made notable progresses in providing useful systematic insights into the underlying
mechanisms and offering potential biomarkers of many diseases. Metabolomics is a complementary manner
of genomics and transcriptomics, and bridges the gap between genotype and phenotype, which reflects the
functional output of a biological system interplaying with environmental factors. Recently, the technology
of metabolomics study has been developed quickly. This review will discuss the whole pipeline of metabo-
lomics study, including experimental design, sample collection and preparation, sample detection and data
analysis, as well as mechanism interpretation, which can help understand metabolic effects and metabolite
function for living organism in system level.

KeywordsMetabolomics, Metabolite profile, Metabolic response, Biomarker, Underlying

mechanism

1 Introduction

In the past decade, metabolomics, as a vital component of systems

biology, has made notable progresses in providing systematic

insights into the underlying mechanisms of biological processes

and presenting potential biomarkers of many diseases such as can-

cer, obesity, and type 2 diabetes. Metabolomics aims to quantita-

tively measure endogenous small molecular metabolites (typically

<1500 Da) containing substrates, intermediates, and products

(e.g., carbohydrates, fatty acids, organic acids, amino acids, nucleo-

tides, steroids, and lipids) in a biological sample. Accurate measure-

ment of variations of small molecular metabolites reflects multi-

parametric metabolic responses of a living system to

Tao Huang (ed.),Computational Systems Biology: Methods and Protocols, Methods in Molecular Biology, vol. 1754,
https://doi.org/10.1007/978-1-4939-7717-8_16,©Springer Science+Business Media, LLC, part of Springer Nature 2018

Jing Cheng and Wenxian Lan contributed equally to this work.

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