{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Hendriks TFE"],"funding":["Interreg Vlaanderen-Nederland","Dutch Research Council (NWO)","Fonds Wetenschappelijk Onderzoek","NWO-STEM"],"pagination":["42660"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12663239"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["15(1)"],"pubmed_abstract":["Understanding tissue complexity requires spatially resolved multi-omics data at single-cell resolution. Here, we present a workflow integrating high-resolution matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) with Xenium spatial transcriptomics (SPT) on a single tissue section. This strategy ensures pixel-scale spatial correspondence between metabolic and transcriptomic features, avoiding misalignment issues of serial sections, where even minor offsets result in sampling different cells. We investigated MALDI-MSI compatibility with downstream SPT revealing that the number of transcripts per cell decreased by ~ 30% after MSI, whilst cell recovery and cell-type assignments are preserved. Validated using mouse brain and demonstrated using human glioblastoma ti"],"journal":["Scientific reports"],"pubmed_title":["One section, two worlds: single-cell integration of MALDI-MSI and spatial transcriptomics on the same single tissue section."],"pmcid":["PMC12663239"],"funding_grant_id":["TBM T001919N","19013","Molecular Brain Tumor Detector"],"pubmed_authors":["Visvikis T","Heeren RMA","Eijkel GB","Cuypers E","Balluff B","Hendriks TFE"],"additional_accession":[]},"is_claimable":false,"name":"One section, two worlds: single-cell integration of MALDI-MSI and spatial transcriptomics on the same single tissue section.","description":"Understanding tissue complexity requires spatially resolved multi-omics data at single-cell resolution. Here, we present a workflow integrating high-resolution matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) with Xenium spatial transcriptomics (SPT) on a single tissue section. This strategy ensures pixel-scale spatial correspondence between metabolic and transcriptomic features, avoiding misalignment issues of serial sections, where even minor offsets result in sampling different cells. We investigated MALDI-MSI compatibility with downstream SPT revealing that the number of transcripts per cell decreased by ~ 30% after MSI, whilst cell recovery and cell-type assignments are preserved. Validated using mouse brain and demonstrated using human glioblastoma ti","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Nov","modification":"2026-06-05T21:35:14.514Z","creation":"2026-05-22T03:12:24.23Z"},"accession":"S-EPMC12663239","cross_references":{"pubmed":["41315396"],"doi":["10.1038/s41598-025-26735-1"]}}