Abstract
SUMMARY: Imaging mass spectrometry (imaging MS) has advanced spatial and single-cell metabolomics, but the reliance on MS1 data complicates the accurate identification of molecular structures, not being able to resolve isomeric and isobar molecules. This prevents application of conventional methods for overrepresentation analysis (ORA) and metabolite set enrichment analysis (MSEA). To address this, we introduce S2IsoMEr R package and a web app for METASPACE, which uses bootstrapping to propagate isomeric/isobaric ambiguities into the enrichment analysis. We demonstrate S2IsoMEr for single-cell metabolomics and the METASPACE web app for spatial metabolomics. AVAILABILITY AND IMPLEMENTATION: METASPACE web app can be used on existing and new datasets submitted to METASPACE (https://metaspace2020.org). The source code for the S2IsoMEr R package is available on GitHub (https://github.com/alexandrovteam/S2IsoMEr).