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Enhanced Spatial Proteomics and Metabolomics from a Single Tissue Section Using MALDI-MSI and LCM-microPOTS

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
PubMed
Summary
This summary is machine-generated.

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.

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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.