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Proteomics

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...

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Dual-modality Molecular Cartography: Integrating Multiplex mRNA Detection with Protein Imaging Mass Cytometry

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Published on: November 14, 2025

Dual-modality Molecular Cartography: Integrating Multiplex mRNA Detection with Protein Imaging Mass Cytometry.

Sammy Ferri-Borgogno¹, Danielle L Stolley², Basant T Gamal³

¹Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center; SFerri@mdanderson.org.

Journal of Visualized Experiments : Jove

|December 1, 2025

Summary

This study integrates protein imaging mass cytometry (IMC) with mRNA in situ hybridization (ISH) to simultaneously analyze spatial proteomics and transcriptomics. This novel approach enhances understanding of cellular communication and microenvironment interactions.

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Multiplexed Barcoding Image Analysis for Immunoprofiling and Spatial Mapping Characterization in the Single-Cell Analysis of Paraffin Tissue Samples

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Quantitation of Protein Expression and Co-localization Using Multiplexed Immuno-histochemical Staining and Multispectral Imaging

Quantitation of Protein Expression and Co-localization Using Multiplexed Immuno-histochemical Staining and Multispectral Imaging

Published on: April 8, 2016

Area of Science:

Biotechnology
Molecular Biology
Cell Biology

Background:

Simultaneous detection of protein and mRNA provides insights into cellular priming and environmental interactions.
Higher-plexed imaging enables spatial transcriptomics and spatial proteomics on a single tissue section, avoiding redundancy.
Existing technologies often focus on either mRNA or protein, with limited simultaneous analysis.

Purpose of the Study:

To integrate protein imaging mass cytometry (IMC) with mRNA in situ hybridization (ISH) for simultaneous spatial analysis.
To overcome limitations of antibody-only detection for secreted or challenging protein markers.
To provide a robust method for understanding cellular communication within microenvironments.

Main Methods:

Utilizing metal probes for combined IMC and mRNA ISH on a single tissue section.
Focusing on protein analysis as central analytes, complemented by mRNA detection.
Implementing a protocol that minimizes spectral spillover and autofluorescence issues.

Main Results:

Enabled simultaneous spatial analysis of protein and mRNA.
Facilitated detection of challenging protein markers and secreted proteins.
Reduced need for compensation and post-processing compared to fluorescent methods.

Conclusions:

The integrated IMC-ISH protocol offers a powerful tool for studying cellular microenvironments.
This method enhances the understanding of cellular communication by analyzing both protein and mRNA expression spatially.
It overcomes technical limitations of existing multi-analyte detection systems.