Training in metabolomics research. II. Processing and statistical analysis of metabolomics data, metabolite identification, pathway analysis, applications of metabolomics and its future

Stephen Barnes; H Paul Benton; Krista Casazza; Sara J Cooper; Xiangqin Cui; Xiuxia Du; Jeffrey Engler; Janusz H Kabarowski; Shuzhao Li; Wimal Pathmasiri; Jeevan K Prasain; Matthew B Renfrow; Hemant K Tiwari

doi:10.1002/jms.3780

Training in metabolomics research. II. Processing and statistical analysis of metabolomics data, metabolite identification, pathway analysis, applications of metabolomics and its future

J Mass Spectrom. 2016 Aug;51(8):535-548. doi: 10.1002/jms.3780.

Authors

Stephen Barnes^{1

2

3}, H Paul Benton⁴, Krista Casazza⁵, Sara J Cooper⁶, Xiangqin Cui⁷, Xiuxia Du⁸, Jeffrey Engler¹, Janusz H Kabarowski⁹, Shuzhao Li¹⁰, Wimal Pathmasiri¹¹, Jeevan K Prasain^{2

3}, Matthew B Renfrow¹, Hemant K Tiwari⁷

Affiliations

¹ Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
² Department of Pharmacology and Toxicology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
³ Targeted Metabolomics and Proteomics Laboratory, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
⁴ Scripps Research Institute, La Jolla, CA, 92307, USA.
⁵ Department of Pediatrics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
⁶ HudsonAlpha Institute, Huntsville, AL, 35806, USA.
⁷ Section on Statistical Genetics, School of Public Health, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
⁸ Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, NC, 28223, USA.
⁹ Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
¹⁰ Department of Medicine, Emory University, Atlanta, GA, 30322, USA.
¹¹ RTI International, Research Triangle Park, NC, 27709, USA.

Abstract

Metabolomics, a systems biology discipline representing analysis of known and unknown pathways of metabolism, has grown tremendously over the past 20 years. Because of its comprehensive nature, metabolomics requires careful consideration of the question(s) being asked, the scale needed to answer the question(s), collection and storage of the sample specimens, methods for extraction of the metabolites from biological matrices, the analytical method(s) to be employed and the quality control of the analyses, how collected data are correlated, the statistical methods to determine metabolites undergoing significant change, putative identification of metabolites and the use of stable isotopes to aid in verifying metabolite identity and establishing pathway connections and fluxes. This second part of a comprehensive description of the methods of metabolomics focuses on data analysis, emerging methods in metabolomics and the future of this discipline. Copyright © 2016 John Wiley & Sons, Ltd.

Keywords: data pre-processing; imaging metabolomics; isotopic labeling; multivariate analysis; pathway; univariate analysis.

MeSH terms

Animals
Chromatography, Liquid
Gas Chromatography-Mass Spectrometry
Humans
Isotopes
Mass Spectrometry / methods*
Metabolomics* / education
Metabolomics* / methods

Substances

Isotopes

Abstract

MeSH terms

Substances

Grants and funding