Journal
METABOLITES
Volume 10, Issue 5, Pages -Publisher
MDPI
DOI: 10.3390/metabo10050186
Keywords
global metabolomics; peak detection; batch effects; pathway activity prediction
Categories
Funding
- Genome Canada
- Genome Quebec
- U.S. National Institutes of Health [U01 CA235493]
- Natural Sciences and Engineering Research Council of Canada (NSERC)
- Canada Research Chairs (CRC) Program
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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 similar to 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.
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