Protocol for analysis of liquid chromatography-mass spectrometry metabolomics data using R to understand how metabolites affect disease

Hong Lin; Chunyan Hu; Shuangyuan Wang; Yu Xu; Min Xu; Yufang Bi; Jieli Lu

doi:10.1016/j.xpro.2023.102137

Protocol for analysis of liquid chromatography-mass spectrometry metabolomics data using R to understand how metabolites affect disease

STAR Protoc. 2023 Mar 17;4(1):102137. doi: 10.1016/j.xpro.2023.102137. Epub 2023 Feb 27.

Authors

Hong Lin¹, Chunyan Hu¹, Shuangyuan Wang¹, Yu Xu¹, Min Xu¹, Yufang Bi², Jieli Lu³

Affiliations

¹ Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai National Clinical Research Center for Endocrine and Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.
² Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai National Clinical Research Center for Endocrine and Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China. Electronic address: byf10784@rjh.com.cn.
³ Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai National Clinical Research Center for Endocrine and Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China. Electronic address: ljl11319@rjh.com.cn.

Abstract

Liquid-chromatography-mass-spectrometry-based metabolomics is widely used in prospective case-control studies for disease prediction. Given the large amount of clinical and metabolomics data involved, data integration and analyses are crucial to provide an accurate understanding of the disease. We provide a comprehensive analysis approach to explore associations among clinical risk factors, metabolites, and disease. We describe steps for performing Spearman correlation, conditional logistic regression, casual mediation, and variance partitioning to investigate the potential effects of metabolites on disease. For complete details on the use and execution of this protocol, please refer to Wang et al. (2022).¹.

Keywords: Bioinformatics; Health Sciences; Metabolism.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Case-Control Studies
Chromatography, Liquid / methods
Mass Spectrometry / methods
Metabolomics* / methods