MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights

Abstract

Since its first release over a decade ago, the MetaboAnalyst web-based platform has become widely used for comprehensive metabolomics data analysis and interpretation. Here we introduce MetaboAnalyst version 5.0, aiming to narrow the gap from raw data to functional insights for global metabolomics based on high-resolution mass spectrometry (HRMS). Three modules have been developed to help achieve this goal, including: (i) a LC–MS Spectra Processing module which offers an easy-to-use pipeline that can perform automated parameter optimization and resumable analysis to significantly lower the barriers to LC-MS1 spectra processing; (ii) a Functional Analysis module which expands the previous MS Peaks to Pathways module to allow users to intuitively select any peak groups of interest and evaluate their enrichment of potential functions as defined by metabolic pathways and metabolite sets; (iii) a Functional Meta-Analysis module to combine multiple global metabolomics datasets obtained under complementary conditions or from similar studies to arrive at comprehensive functional insights. There are many other new functions including weighted joint-pathway analysis, data-driven network analysis, batch effect correction, merging technical replicates, improved compound name matching, etc. The web interface, graphics and underlying codebase have also been refactored to improve performance and user experience. At the end of an analysis session, users can now easily switch to other compatible modules for a more streamlined data analysis. MetaboAnalyst 5.0 is freely available at https://www.metaboanalyst.ca.

Adenosine deaminase modulates metabolic remodeling and orchestrates joint destruction in rheumatoid arthritis

“…Three independent serum metabolomics datasets of RA patients 72 , 74 , 75 were taken from the published literature and the deregulated metabolite levels were compared with our metabolomics dataset of RA patients. Metaboanalyst 5.0 100 was used for the pathway analysis of the deregulated list of metabolites. The pathways listed in all three studies were overlapped with significant pathways of our metabolomics dataset for correlation using Venn Diagram tool ( http://bioinformatics.psb.ugent.be/webtools/Venn/ ).…”

Common Muscle Metabolic Signatures Highlight Arginine and Lysine Metabolism as Potential Therapeutic Targets to Combat Unhealthy Aging

“…Statistical data analysis including principal component analysis (PCA) of individual data sets was performed using the tool MetaboAnalyst 5.0 [ 73 ] using default parameters if not indicated otherwise. Data filtering was performed by the Interquartile Range (IQR) method.…”

“…Metabolites with a mean decrease accuracy > 0 were selected and used to build a heatmap with MetaboAnalyst 5.0 and default heatmap parameters. This subset of metabolites was also used for quantitative enrichment analysis using the Enrichment Analysis module of MetaboAnalyst 5.0 [ 73 ] with the pathway-based KEGG metabolite set library (containing 84 metabolite sets based on human metabolic pathways). The metabolite classes of random forest selected metabolites were displayed as pie charts using GraphPad Prism 8.4.3 (GraphPad Software).…”

“…To identify a common metabolite signature in all three data sets, statistical meta-analysis was performed using the Statistical Meta-Analysis module of MetaboAnalyst 5.0 [ 73 ]. In all data sets, the control samples were designated as ‘desirable’, while the remaining samples were designated as ‘undesirable’.…”

Metabolomics in Bone Research

“…To comprehensively identify metabolic pathways that are affected during bones diseases, we conducted an integrating enrichment and pathway topology analysis from the data of Table 1 by using Metabo Analyst 5.0 [94]. For this, we used the metabolites that are reported as significantly altered in osteoporosis, arthritis, and osteosarcoma.…”