MetaboAnalystR 3.0: Toward an Optimized Workflow for Global Metabolomics

Liquid chromatography coupled to high-resolution mass spectrometry platforms are increasingly employed to comprehensively measure metabolome changes in systems biology and complex diseases. Over the past decade, several powerful computational pipelines have been developed for spectral processing, an...

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Bibliographic Details
Published in:Metabolites Vol. 10; no. 5; p. 186
Main Authors: Pang, Zhiqiang, Chong, Jasmine, Li, Shuzhao, Xia, Jianguo
Format: Journal Article
Language:English
Published: Switzerland MDPI 07.05.2020
MDPI AG
Subjects:
batch effects
global metabolomics
pathway activity prediction
peak detection
peak detection
pathway activity prediction
global metabolomics
batch effects
ISSN:2218-1989, 2218-1989
Online Access:Get full text
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Summary:Liquid chromatography coupled to high-resolution mass spectrometry platforms are increasingly employed to comprehensively measure metabolome changes in systems biology and complex diseases. Over the past decade, several powerful computational pipelines have been developed for spectral processing, annotation, and analysis. However, significant obstacles remain with regard to parameter settings, computational efficiencies, batch effects, and functional interpretations. Here, we introduce MetaboAnalystR 3.0, a significantly improved pipeline with three key new features: (1) efficient parameter optimization for peak picking; (2) automated batch effect correction; and (3) more accurate pathway activity prediction. Our benchmark studies showed that this workflow was 20~100× faster compared to other well-established workflows and produced more biologically meaningful results. In summary, MetaboAnalystR 3.0 offers an efficient pipeline to support high-throughput global metabolomics in the open-source R environment.
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ISSN:2218-1989
2218-1989
DOI:10.3390/metabo10050186