MetaboAnalyst 6.0: towards a unified platform for metabolomics data processing, analysis and interpretation

Abstract

We introduce MetaboAnalyst version 6.0 as a unified platform for processing, analyzing, and interpreting data from targeted as well as untargeted metabolomics studies using liquid chromatography - mass spectrometry (LC–MS). The two main objectives in developing version 6.0 are to support tandem MS (MS2) data processing and annotation, as well as to support the analysis of data from exposomics studies and related experiments. Key features of MetaboAnalyst 6.0 include: (i) a significantly enhanced Spectra Processing module with support for MS2 data and the asari algorithm; (ii) a MS2 Peak Annotation module based on comprehensive MS2 reference databases with fragment-level annotation; (iii) a new Statistical Analysis module dedicated for handling complex study design with multiple factors or phenotypic descriptors; (iv) a Causal Analysis module for estimating metabolite - phenotype causal relations based on two-sample Mendelian randomization, and (v) a Dose-Response Analysis module for benchmark dose calculations. In addition, we have also improved MetaboAnalyst's visualization functions, updated its compound database and metabolite sets, and significantly expanded its pathway analysis support to around 130 species. MetaboAnalyst 6.0 is freely available at https://www.metaboanalyst.ca.

MetaboAnalystR 4.0: a unified LC-MS workflow for global metabolomics

“…MetaboAnalystR can also directly incorporate raw spectral processing results (such as MSP and MGF files) generated from other well-established tools into its workflow for downstream analysis. Finally, MetaboAnalystR 4.0 is the backend of the MetaboAnalyst 6.0 web application 52 , which has been developed to support users who are not comfortable with the R command-line interface.…”

Stable Isotope Tracing Analysis in Cancer Research: Advancements and Challenges in Identifying Dysregulated Cancer Metabolism and Treatment Strategies

“…Using these tools for targeted metabolite analysis usually requires a file containing targeted metabolite mass-to-charge ratio, metabolite retention times, or MRM scan parameters to retrieve peaks from raw data files. For MS-based untargeted metabolomics data analysis, open-source platforms like XCMS, MetaboAnalyst, MS-DIAL, and MZmine provide comprehensive solutions for the peak detection, alignment, normalization, and annotation of MS data [73,[82][83][84]. More specifically for stable isotope tracing data analysis, software tools such as X13CMS, Dy-naMet, geoRge, HiResTEC, MetTracer, and others offer a global analysis of 13 C enrichment in metabolites [85][86][87][88][89].…”

HumanIslets: An integrated platform for human islet data access and analysis

“…This resource continues to evolve through the ongoing collection of datasets outlined in this report, and by the addition of new data types for additional analyses. Examples of the latter, include donor genotyping; genetically predicted ancestry, and genetic risk scores for diabetes; 55,56 prohormone processing; 57,58 metabolomics; 59 and the pancreatic accumulation of environmental contaminants 60,61 and lipids, 62 among other data types that will be added in the future. In time, we hope to allow all ADI IsletCore islet and tissue recipients to provide/upload data for integration.…”