Single-cell MALDI-MSI datasets of breast cancer and glioblastoma cell lines for ionScell validation

This dataset contains MALDI-MSI single-cell datasets acquired from cytospin-deposited human cell lines analyzed using a Bruker MALDI rapifleX mass spectrometer. Data were exported in imzML + ibd formats and generated for the development and validation of the ionScell single-cell MSI pipeline. The datasets include four individual cell line acquisitions: AU565 (HER2-positive breast cancer) MDA-MB-231 (triple-negative breast cancer) MCF7 (luminal breast cancer) NCH82 (glioblastoma) Cells were deposited on conductive ITO slides using cytospin preparation to obtain monolayer distributions before MALDI-MSI acquisition. Acquisitions were performed in both positive and negative ionization modes. In addition to single cell line datasets, two mixed-cell datasets are provided: Binary mixed population: AU565 + NCH82 Ternary mixed population: AU565 + NCH82 + MDA-MB-231 For each mixed dataset, acquisitions were performed in positive and negative ionization modes. These datasets were generated to evaluate automated single-cell segmentation, spectral extraction, molecular subpopulation detection and cell-type discrimination using the ionScell workflow. Files are provided in standard imzML/ibd format for interoperability with MSI software platforms such as SCiLS Lab, Cardinal, pyimzML, and ionScell. Methods Sample preparation: cytospin-deposited cells on ITO-coated slides Matrix: Norharmane using HTX sprayer and OR HTX Sublimate Instrument: Bruker MALDI TimsToF flex Acquisition modes: positive and negative ionization Data format: centroid imzML + ibd Spatial resolution: 10 µm mass range : 350-1100 m/z