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Subcellular Fractionation01:32

Subcellular Fractionation

The homogenate obtained after cell lysis contains various membrane-bound organelles that can be further separated into pure fractions by subcellular fractionation. These isolates are used to study specific cellular components, analyze localized protein activity, and are even employed in diagnostics. Fractionation is typically achieved using centrifugation methods, the most common being density-gradient and differential centrifugation.
Differential Centrifugation
Differential centrifugation is...
Proteomics01:33

Proteomics

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 proteomics...

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Related Experiment Video

Updated: Jul 17, 2026

A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions
09:00

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
PubMed
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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High-Resolution Complexome Profiling by Cryoslicing BN-MS Analysis
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High-Resolution Complexome Profiling by Cryoslicing BN-MS Analysis

Published on: October 15, 2019

Related Experiment Videos

Last Updated: Jul 17, 2026

A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions
09:00

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
09:33

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.