2-D PAGE and MS analysis of proteins from formalin-fixed, paraffin-embedded tissues

Proteomics. 2009 Sep;9(18):4329-39. doi: 10.1002/pmic.200900010.


In the past decade, encouraging results have been obtained in extraction and analysis of proteins from formalin-fixed, paraffin-embedded (FFPE) tissues. However, 2-D PAGE protein maps with satisfactory proteomic information and comparability to fresh tissues have never been described to date. In the present study, we report 2-D PAGE separation and MS identification of full-length proteins extracted from FFPE skeletal muscle tissue. The 2-D protein profiles obtained from FFPE tissues could be matched to those achieved from frozen tissues replicates. Up to 250 spots were clearly detected in 2-D maps of proteins from FFPE tissue following standard mass-compatible silver staining. Protein spots from both FFPE and frozen tissue 2-D gels were excised, subjected to in situ hydrolysis, and identified by MS analysis. Matched spots produced matched protein identifications. Moreover, 2-D protein maps from FFPE tissues were successfully subjected to Western immunoblotting, producing comparable results to fresh-frozen tissues. In conclusion, this study provides evidence that, when adequately extracted, full-length proteins from FFPE tissues might be suitable to 2-D PAGE-MS analysis, allowing differential proteomic studies on the vast existing archives of healthy and pathological-fixed tissues.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Electrophoresis, Gel, Two-Dimensional / methods*
  • Formaldehyde / chemistry
  • Hydrolysis
  • Immunoblotting
  • Isoelectric Point
  • Mass Spectrometry / methods*
  • Muscle Proteins / analysis
  • Muscle, Skeletal / chemistry
  • Paraffin Embedding / methods*
  • Proteins / analysis*
  • Sheep
  • Silver Staining
  • Specimen Handling / methods*


  • Muscle Proteins
  • Proteins
  • Formaldehyde