What does this strategy enable?
SpaceM combines light microscopy, image segmentation, MALDI mass spectrometry imaging, and spatial registration to convert tissue- or culture-level ion images into per-cell metabolic profiles. The key methodological step is aligning optical cell information with MSI ablation coordinates so metabolite signals can be associated with individual cells while retaining morpho-spatial context.
Transferable workflow
Workflow
- 1
Acquire microscopy of the same cells
Record optical images that preserve cell morphology and spatial context before MALDI analysis.
- 2
Segment individual cells
Derive cell boundaries and image-derived features from the optical data.
- 3
Acquire MALDI mass spectrometry imaging
Collect spatially resolved metabolite signals across the same cellular field.
- 4
Register optical and MSI coordinate systems
Align cell masks with MALDI ablation locations so mass-spectral signals can be assigned to individual cells.
- 5
Construct per-cell metabolic profiles
Aggregate registered ion signals into a cell-by-metabolite matrix while retaining morphologic and spatial information.
- 6
Identify metabolic cell states
Analyze single-cell metabolic profiles to distinguish heterogeneous cell states and relate them to morphology or experimental conditions.
Connected resources
Tools used in this strategy
Strategy profile
Related objectives
Spatial metabolomics, Phenotype association
Components
Sample preparation, Data acquisition, Preprocessing and feature extraction, Metadata analysis, Statistical analysis, Biological validation
Sample types
Cells or cell pellets
Biological context
Broadly applicable
Ion mobility
Ion mobility not required
Scope and considerations
Designed for
- In situ metabolic profiling of heterogeneous cell populations at single-cell resolution.
- Linking metabolic states to cell morphology and spatial position.
Important requirements
- Compatible microscopy, cell segmentation, and MALDI-MSI measurements from the same spatial field.
- Accurate spatial registration between optical images and MSI coordinates.
Considerations
- Cell-level profiles depend on segmentation and registration accuracy.
- MALDI pixel size, analyte delocalization, and ion suppression can influence per-cell assignments.
Reusable resources
Publication
Rappez L, Stadler M, Triana S, et al. SpaceM reveals metabolic states of single cells. Nature Methods 18, 799-805 (2021).