AI Insight
Researchers developed spatialMET, an open-source software framework that enables comprehensive analysis of mass spectrometry imaging data for spatially resolved metabolomics studies. The platform integrates preprocessing, spatial domain detection using an efficient clustering algorithm, and multiple downstream analyses including differential abundance testing and network analysis into a unified workflow. When tested on mouse lung cancer tissue samples containing hundreds of thousands of pixels, spatialMET successfully identified distinct tumor, stromal, and normal tissue regions and detected metabolic features that differed between these spatial domains.
Why it matters
Current mass spectrometry imaging analysis requires combining multiple proprietary software tools, limiting reproducibility and scalability. This open-source framework addresses these limitations by providing an end-to-end solution that can handle large datasets and runs on standard computing infrastructure, potentially accelerating spatial metabolomics research in cancer biology and other disease areas.
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⚠️ Preprint – Noch nicht peer-reviewed
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Mass spectrometry imaging (MSI) enables spatially resolved metabolomics in intact tissue sections, but analysis remains challenging at scale. Existing MSI workflows often require users to combine multiple software tools, while others rely on proprietary vendor software that limits interoperability and reproducibility. To address these challenges, we developed spatialMET, an open-source framework that provides an end-to-end workflow for MSI analysis. spatialMET provides a unified platform for preprocessing, spatial domain detection, and visualization. Downstream analyses include differential abundance testing, spatial autocorrelation and gradient analysis, dimensionality reduction, and correlation network analysis. Spatial domain detection uses hcdist, a C-based hierarchical clustering implementation that substantially reduces runtime and memory use relative to existing R-based approaches. spatialMET can be run through an interactive R Shiny application or as a standalone command-line workflow for larger datasets or high-performance computing environments. Applied to mouse small cell lung cancer MALDI-MSI data containing 284,673 pixels, spatialMET identified tumor-associated, stromal, and adjacent lung spatial domains that aligned with matched histology. Differential abundance analysis identified 117 m/z features that differed between tumor and stromal regions, while spatial autocorrelation analyses revealed spatially structured abundance patterns. Applying spatialMET to mouse lung adenocarcinoma data from an entire lung lobe containing 338,477 pixels further demonstrated scalability and captured spatial heterogeneity across tumor and surrounding lung tissue. In summary, spatialMET provides a scalable, open-source framework for end-to-end spatial metabolomics analysis, and it is distributed as a Docker container for reproducible deployment. Source code and installation instructions are available at https://github.com/biodatalab/spatialMET.
Source: spatialMET: an open and scalable framework for spatial metabolomics analysis