Mass-Guided Single-Cell and 3D MALDI Imaging Spatial Omics in Biological Systems

Spatial omics has revolutionized our understanding of biological heterogeneity, yet matrixassisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) faces persistent challenges in detecting low-mass metabolites (<500 DA)  at single-cell and volumetric resolution. Traditional MSI workflows suffer from matrix interference, ion suppression in complex environments, and limited throughput for large-scale 3D organoid analysis — critical barriers for translating spatial metabolomics into routine pharma screening and clinical diagnostics. Here, we present advanced PRISM-MS (Precision Raster Imaging with Single-cell Mass spectrometry) which enables space-efficient single cell lipid and metabolite analysis [1] and a 3D MALDI imaging platform for advanced 3D spatial omics analysis of organoids [2]. These integrate mass-guided targeted rastering over large cell populations, increased sensitivity for small analytes, and multidimensional imaging (x, y, z, m/z, intensity) to achieve cellular spatial resolution (<10 μm) in 2D tissues and full volumetric reconstructions in organoids. We identified stimulus‑dependent cellular activation states and metabolically defined cell subpopulations in large cell populations as well as demonstrated molecular profiling of patient-derived colorectal cancer organoids.

[1] J. L. Cairns, J. Huber, A. Lewen, J. Jung, S. J. Maurer, T. Bausbacher, S. Schmidt, P. A. Levkin, D. Sevin, K. Göpfrich, P. Koch, O. Kann, C. Hopf, Mass-Guided Single-Cell MALDI Imaging of Low-Mass Metabolites Reveals Cellular Activation Markers. Adv. Sci. 2025, 12, 2410506. https://doi.org/10.1002/advs.202410506
[2] S. A. Iakab, J. Cordes, T. Enzlein, et al. “ From Sample to Mixed Reality: A Translational 3D MALDI Imaging Platform for Advanced 3D Spatial Omics Analysis of 3D Cell Culture Disease Models.” Adv. Sci. (2025): e16098. https://doi.org/10.1002/advs.202516098