Liquid-chromatography coupled with high-resolution mass spectrometry (LC-HRMS) has become a workhorse in global metabolomics studies with growing applications across biomedical and environmental sciences. However, outstanding bioinformatics challenges in terms of data processing, statistical analysis and functional interpretation remain critical barriers to the wider adoption of this technology. To help the user community overcome these barriers, we have made major updates to the

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... d MetaboAnalyst platform (www.metaboanalyst.ca). This protocol is part three of four and provides stepwise instructions on how to use MetaboAnalyst to integrate metabolomics data with transcriptomics data or to combine multiple metabolomics datasets.