proteomic analysis of FFPE tissue

A synopsis of the review of M.B. O’Rourke and M.P. Padula, Biotechniques 60:229-238 (May 2016) doi 10.2144/000114414

  • a number of researchers have successfully performed proteomic analysis of FFPE tissue
  • formaldehyde makes methylene crosslinks between amino and sulfhydryl groups to arginine, asparagine, glutamine, histidine, tryptophan, tyrosine
  • heating at 95°C or more reverses sufficient cross links to allow protein identifications
  • SDS appears helpful in reversing cross links but must be removed before mass spectrometry analysis
  • the authors have not seen evidence that reducing agents help
  • removal of paraffin with xylene or similar is also required
  • current search engines cannot identify peptides cross linked with methylene bridges

Successful analyses here have used a commercial kit.