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Related Experiment Video

Updated: May 29, 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

Comprehensive tissue processing strategy for quantitative proteomics of formalin-fixed multiple sclerosis lesions.

Linda Ly1, Michael H Barnett, Yuan Z Zheng

  • 1Central Clinical School, The University of Sydney, NSW, Australia.

Journal of Proteome Research
|August 30, 2011
PubMed
Summary

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Formalin-fixed autopsy tissue can be used for proteomic analysis in Multiple Sclerosis (MS) research. A new heat-induced extraction protocol enhances protein identification in MS brain tissue, aiding biomarker discovery.

Area of Science:

  • Neuroscience
  • Proteomics
  • Biochemistry

Background:

  • Formalin-fixed (FF) autopsy brain tissue is abundant in Multiple Sclerosis (MS) archives.
  • Existing archives offer potential for biomarker discovery and disease characterization.
  • Proteomic analysis of FF tissue is challenging but valuable for MS research.

Purpose of the Study:

  • To develop and optimize a heat-induced extraction protocol for proteomic analysis of FF brain tissue.
  • To apply this protocol to study lesion remyelination and its failure in MS.
  • To identify differentially expressed proteins in MS lesions and surrounding white matter.

Main Methods:

  • Optimized a 4-round heat-induced extraction strategy for FF brain tissue.
  • Utilized Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) for protein identification.

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Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue
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Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue

Published on: September 2, 2013

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Last Updated: May 29, 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

Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue
09:20

Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue

Published on: September 2, 2013

  • Employed iTRAQ and 2-D LC-MS/MS for differential protein expression analysis in laser-dissected MS lesions.

    • Main Results:

    • The optimized protocol increased protein identification by 35% and proteins with ≥4 peptides by 65% compared to single extraction.
    • Histological staining minimally affected LC-MS/MS results.
    • Identified 428 unique proteins in MS lesions and periplaque white matter, with 82 differentially expressed proteins between lesion types.

    Conclusions:

    • The developed heat-induced proteomic protocol is effective for analyzing FF MS brain tissue.
    • The methodology provides insights into the pathogenesis of MS and the mechanisms of remyelination.
    • This approach enhances the utility of existing FF autopsy tissue archives for MS research.