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

J Proteome Res. 2011 Oct 7;10(10):4855-68. doi: 10.1021/pr200672n. Epub 2011 Sep 14.


Formalin-fixed (FF) autopsy tissue comprises the bulk of existing Multiple Sclerosis (MSc) pathology archives, providing a rich pool of material for biomarker discovery and disease characterization. Here, we present the development of a heat-induced extraction protocol for the proteomic analysis of FF brain tissue, its application to the study of lesion remyelination and its failure in MSc. A 4-round extraction strategy was optimized using FF tissue leading to a 35% increase in the number of proteins identified compared to a single extraction; and a 65% increase in proteins identified with ≥4 peptides. Histological staining of sections with oil red O and luxol fast blue-periodic acid Schiff, required to characterize MSc lesions was found to have minimal effect on LC-MS/MS. The application of the optimized protocol to chronic demyelinated and remyelinated FF MSc lesions and the adjacent periplaque white matter, isolated through laser guided manual dissection from 3 patients, identified 428 unique proteins (0.2% FDR) using LC-MS/MS. Comparison of the lesion types using iTRAQ and 2-D LC-MS/MS revealed 82 differentially expressed proteins. Protein quantitation by iTRAQ and spectral counting was well-correlated (r(s)= 0.7653; p < 10(-30)). The data generated from this work illustrates the scope of the methodology and provides insights into the pathogenesis of MSc and remyelination.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Autopsy
  • Azo Compounds / pharmacology
  • Chromatography / methods
  • Chromatography, Liquid / methods
  • Female
  • Humans
  • Inflammation
  • Isotopes / chemistry
  • Male
  • Middle Aged
  • Multiple Sclerosis / metabolism*
  • Myelin Sheath / chemistry
  • Periodic Acid / pharmacology
  • Proteomics / methods*


  • Azo Compounds
  • Isotopes
  • Periodic Acid
  • oil red O