This article has been reviewed according to Science X's editorial process and policies. Editors have highlighted the following attributes while ensuring the content's credibility: 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 molecules. However, no single technique 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.
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. 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).
The work is published in the journal Analytical Chemistry. The workflow analyzes the same tissue section using spatial metabolomics and proteomics by modifying sample preparation so analyses are compatible with both techniques. Data from poplar root tissue show that, in this multimodal workflow in which spatial metabolomics is performed first and then spatial proteomics, results are comparable to those obtained when the modalities are used individually in their optimal settings and sample conditions.
No loss of protein content or delocalization of metabolites from their native locations was observed with the new workflow. 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. Marija Veličković et al, Enhanced Spatial Proteomics and Metabolomics from a Single Tissue Section Using MALDI-MSI and LCM-microPOTS Platforms, Analytical Chemistry (2025). DOI: 10.1021/acs.analchem.5c05005 Journal information: Analytical Chemistry Provided by Environmental Molecular Sciences Laboratory BSc Life Sciences & Ecology.
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