Using MetaboAnalyst 5.0 for LC-HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data

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 well-established MetaboAnalyst platform (www.metaboanalyst.ca). This protocol extends the previous 2011 Nature Protocol by providing stepwise instructions on how to use MetaboAnalyst 5.0 to: optimize parameters for LC-HRMS spectra processing; obtain functional insights from peak list data; integrate metabolomics data with transcriptomics data or combine multiple metabolomics datasets; conduct exploratory statistical analysis with complex metadata. Parameter optimization may take similar to 2 h to complete depending on the server load, and the remaining three stages may be executed in similar to 60 min.

Automated summary

Liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) is widely used in global metabolomics studies, but there are still challenges in data processing, statistical analysis, and functional interpretation. To overcome these barriers, the MetaboAnalyst platform has been updated to provide step-by-step instructions.