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Enhanced Spatial Proteomics and Metabolomics from a Single Tissue Section Using MALDI-MSI and LCM-microPOTS Platforms
Marija Veličković1, Le Z Day1, Kevin J Zemaitis1
1Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.
Analytical Chemistry
|October 31, 2025
Summary
Researchers developed novel single tissue section (STS) workflows for spatial multiomics, enabling simultaneous metabolite and protein analysis. This preserves molecular fidelity and enhances tissue biology insights.
Area of Science:
- Biochemistry
- Molecular Biology
- Analytical Chemistry
Background:
- Spatially resolved mass spectrometry (MS)-based multiomics are crucial for understanding tissue biology.
- Current methods often require multiple tissue sections, risking molecular data correlation due to inter-section variability.
- Preserving cell- or region-specific molecular fidelity is a significant challenge in multiomics tissue analysis.
Purpose of the Study:
- To develop workflows for comprehensive multiomics profiling from a single tissue section (STS).
- To enable both spatial metabolomics and proteomics from STS using different MS modalities.
- To overcome limitations of multi-section approaches and improve molecular data correlation.
Main Methods:
- Developed metal-assisted, electrically insulated substrates for STS multiomics.
- Utilized matrix-assisted laser desorption/ionization-MS imaging (MALDI-MSI) for metabolite imaging.
- Employed laser capture microdissection (LCM) coupled with microdroplet preparation for subsequent proteome profiling.
- Investigated copper and gold-coated PEN substrates with different MS instruments (timsTOF, FTICR).
Main Results:
- Successfully performed untargeted spatial metabolomics and proteomics from a single poplar root tissue section.
- Detected >140 metabolites and 6571 unique proteins using copper-backed PEN slides with MALDI-timsTOF-MS.
- Profiled >170 metabolites and identified 6542 unique proteins using gold-coated PEN slides with MALDI-FTICR-MS.
- Achieved results comparable to independent omics analyses, demonstrating workflow efficacy.
Conclusions:
- The developed STS workflows enable high-resolution, multi-omics profiling from a single tissue section.
- These methods preserve molecular fidelity and offer new opportunities for correlative multi-omics studies.
- The approach enhances the ability to reveal complex biological insights within tissues.
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