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Updated: Jul 17, 2026

A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions

A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions

Published on: April 18, 2025

NicheProt: Cell-type-resolved proteomics of tissue compartments.

Yi-Chien Wu¹, Dylan Schwartz¹, Elie Abi Khalil¹

¹Department of Pharmaceutical Sciences, Retzky College of Pharmacy, University of Illinois Chicago, Chicago, IL, USA.

Science Advances

|July 15, 2026

Summary

Researchers developed NicheProt, a novel method for cell-type-specific spatial proteomics in intact tissues. This technique identified distinct dendritic cell phenotypes in mouse spleen, revealing new cellular subtypes and their functions.

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Last Updated: Jul 17, 2026

A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions

A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions

Published on: April 18, 2025

High-Resolution Complexome Profiling by Cryoslicing BN-MS Analysis

High-Resolution Complexome Profiling by Cryoslicing BN-MS Analysis

Published on: October 15, 2019

Area of Science:

Proteomics
Cell Biology
Immunology

Background:

Spatial proteomics reveals cellular functions in tissues.
Laser capture microdissection-mass spectrometry lacks cell-type specificity.
Understanding cell-type-specific molecular functions in distinct tissue niches is crucial.

Purpose of the Study:

To present NicheProt, a 3D microscopy-guided, photobleaching-mediated cell barcoding method.
To enable cell-type and microregion-resolved proteomic analysis in intact tissues.
To identify distinct cell phenotypes within specific tissue compartments.

Main Methods:

Developed NicheProt: a 3D optical microscopy-guided, photobleaching-mediated cell barcoding approach.
Utilized sequential bottom-up proteomic analysis.
Applied the method to analyze CD11c+ dendritic cells in inflamed mouse spleen.

Main Results:

Successfully isolated intact, specific cell types from defined microanatomical niches.
Defined two distinct CD11c+ dendritic cell phenotypes based on spatial location.
Identified proteomic signatures differing in 54 proteins between these two cell populations.

Conclusions:

NicheProt facilitates cell-type and microregion-resolved proteomic analysis.
The method enables the discovery of previously unrecognized cell subtypes.
This approach aids in understanding the functional roles of distinct cell subtypes in tissue compartments.