One section, two worlds: single-cell integration of MALDI-MSI and spatial transcriptomics on the same single tissue section.

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

SUBMITTER: Hendriks TFE 

PROVIDER: S-EPMC12663239 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature