Skip to main content
Science Areas
Environmental Transformations and Interactions

Capturing Localized Protein and Metabolic Information from a Single Tissue Section

A new workflow enables spatially resolved analysis of both metabolites and proteins using different mass spectrometry modalities on the exact same tissue section, preserving true cell- and region-specific molecular information.

Photo of a cross section of several plants growing in soil and it displays roots below the surface of the soil

A team from the Environmental Molecular Sciences Laboratory developed a new workflow called metabolome-informed proteome imaging from the same tissue section. (Image by Oleh Malshakov, iStock)

The Science

Revealing how proteins and end products of biological activity (metabolites) change within specific tissue functional units during development or in response to environmental factors is beneficial for understanding localized biological processes and the biological roles of the molecules. However, there is no single technique that can capture both proteins and metabolites from the same tissue section because of their vastly different chemical structures, reactivity, and mass, requiring different sample-preparation protocols and instrumentation. A team from the Environmental Molecular Sciences Laboratory (EMSL), a Department of Energy Office of Science user facility at Pacific Northwest National Laboratory, developed a new workflow called metabolome-informed proteome imaging from the same tissue section (MIPI-STS) to analyze the same tissue section using spatial metabolomics and proteomics by modifying sample preparation so that analyses would be compatible with both techniques. Data from poplar root tissue show that, in this multimodal workflow where spatial metabolomics is first performed and then spatial proteomics, results are comparable to those obtained if the modalities are used individually in their most optimal settings and sample conditions. No loss of protein content or the delocalization of metabolites from their native locations were observed with the new workflow.

 

A graphic depicting the flow of how metabolome-informed proteome imaging from the same tissue section (MIPII-STS) works.
A team of researchers from the Environmental Molecular Sciences Laboratory developed a workflow for analyzing the metabolome and proteome from a single tissue section using matrix-assisted laser desorption/ionization and laser capture microdissection-based sample collection, respectively. The team accomplished this feat by adapting sample preparation to be compatible with different mass spectrometry modality requirements. (Image courtesy of Analytical Chemistry)

The Impact

The MIPI-STS workflow is the first of its kind to enable comprehensive analysis of the proteome and metabolome from the exact same cells or functional zones in a given tissue. By analyzing the exact same tissue section, researchers can ensure that concurrent metabolomic and proteomic processes are captured, in contrast to current approaches, in which serial sections or technical replicates are analyzed. Although researchers developed the workflow on plant root tissue sections, it is readily transferable to other environmental and biological specimens to capture molecular processes occurring at distinct hotspots and moments within tissues.

Summary

Spatial mass spectrometry-based multiomics workflows commonly require multiple independent tissue sections to analyze metabolite and protein compositions. This poses a significant challenge for preserving individual cellular- and region-specific molecular fidelity, as variations between tissue sections can compromise accurate molecular correlation. Scientists at EMSL developed a workflow for comprehensive multiomics profiling from a single tissue section using different mass spectrometry modalities. The team enhanced the functionality of an electrically insulated substrate by employing a metal-assisted approach that enables MIPI-STS. This strategy enables metabolite imaging using matrix-assisted laser desorption/ionization mass spectrometry imaging without damaging the tissue and supports subsequent proteome analysis via laser capture microdissection-based microdroplet processing in one experiment (or pot) for trace samples. The new MIPI-STS workflow enables high-resolution molecular profiling across multiple omics layers from the same tissue section, enabling more accurate cross-omics integration and providing a comprehensive view of biological processes and a deeper understanding of biological activity at the systems level.

Contacts

Dusan Velickovic
EMSL | PNNL
dusan.velickovic@pnnl.gov 

Marija Velickovic
EMSL | PNNL
marija.velickovic@pnnl.gov 

Funding

This research was performed on a project award (https://www.osti.gov/award-doi-service/biblio/10.46936/intm.proj.2024.61353/60012581) from the Environmental Molecular Sciences Laboratory, a DOE Office of Science User Facility sponsored by the Biological and Environmental Research program under Contract DE-AC05-76RL01830.

Publication

M. Veličković, et al. “Enhanced Spatial Proteomics and Metabolomics from a Single Tissue Section Using MALDI-MSI and LCM-microPOTS Platforms.” Analytical Chemistry 97, 44, 24715–24723 (2025). [DOI: 10.1021/acs.analchem.5c05005]