UNIT 23.5 Peptide Extraction from Formalin-Fixed Paraffin-Embedded Tissue

  1. Katherine J. Heaton1,
  2. Stephen R. Master2

Published Online: 1 AUG 2011

DOI: 10.1002/0471140864.ps2305s65

Current Protocols in Protein Science

Current Protocols in Protein Science

How to Cite

Heaton, K. J. and Master, S. R. 2011. Peptide Extraction from Formalin-Fixed Paraffin-Embedded Tissue. Current Protocols in Protein Science. 65:23.5:23.5.1–23.5.19.

Author Information

  1. 1

    Phoenix S&T, Chester, Pennsylvania

  2. 2

    University of Pennsylvania, Philadelphia, Pennsylvania

Publication History

  1. Published Online: 1 AUG 2011
  2. Published Print: AUG 2011


This unit describes how to extract tryptic peptides from formalin-fixed, paraffin-embedded (FFPE) tissues for analysis using nano-reverse-phase liquid chromatography/tandem mass spectrometry (nRPLC-MS/MS). The tissues are deparaffinized in the first protocol. Following deparaffinization, the cells are harvested via one of two methods: needle dissection or laser capture microdissection (LCM). Needle dissection is performed using hydrated, unstained tissue, whereas LCM is performed with dehydrated, hematoxylin-stained tissue. Heat is applied to the collected cells to reverse the cross-links that have formed during the formalin fixation process. Finally, the cells are digested using filter-aided sample preparation, in which buffers are exchanged throughout the process. An alternate protocol using commercially available Liquid Tissue is also described. These samples are then ready for mass spectrometric analysis. Curr. Protoc. Protein Sci. 65:23.5.1-23.5.19. © 2011 by John Wiley & Sons, Inc.


  • FFPE;
  • proteomics;
  • FASP;
  • antigen retrieval;
  • protein extraction