Document Type

Article

Publication Date

5-7-2020

Keywords

JGM

JAX Source

Metabolites 2020 May 7; 10(5):E186

Volume

10

Issue

5

ISSN

2218-1989

PMID

32392884

DOI

https://doi.org/10.3390/metabo10050186

Abstract

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 20~100X 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.

Comments

This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license.

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