MetaboAnalystR 3.0: Toward an Optimized Workflow for Global Metabolomics

By Zhiqian Pang, Jasmine Chong, Shuzhao Li, Jianguo Xia. Metabolites, 2020

474 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/b9c57457202a41ecb4933097f85795982a274dae

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In Molecular Biology

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  2. Zhiqiang Pang

In Spectroscopy

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  2. Zhiqiang Pang

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