Untargeted Spatial Metabolomics and Spatial Proteomics on the Same Tissue Section.

Area of Science:

• Biochemistry
• Proteomics
• Metabolomics

Background:

• Existing spatial multiomic workflows often require serial sections or have incompatible substrate needs.
• Desorption electrospray ionization-mass spectrometry imaging (DESI-MSI) offers a potential solution for on-tissue metabolite profiling.

Purpose of the Study:

• To develop and validate a novel, integrated spatial multiomic workflow.
• To enable simultaneous spatial metabolomics and proteomics from the same tissue section.

Main Methods:

• Utilized DESI-MSI for on-tissue spatial metabolomics on a rat brain section.
• Employed METASPACE for metabolite annotation and generated a segmentation map.
• Performed downstream spatial proteomics on selected regions of interest (ROIs) from the same tissue section.

Main Results:

• Identified 160 metabolite annotations with DESI-MSI (≤20% FDR).
• Quantified 3888–4717 proteins per ROI (200 μm × 200 μm) using spatial proteomics.
• Demonstrated correlation between ceramide localization and SMPD3 protein abundance.
• Showcased protein abundance resolving metabolite isomeric ambiguity.

Conclusions:

• The integrated DESI-MSI workflow allows for complementary spatial and molecular information from a single tissue section.
• This approach optimizes spatial proteomics assays by minimizing sample disruption and substrate limitations.
• The workflow facilitates deeper understanding of tissue molecular architecture and function.