Techniques of Protein Extraction from FFPE Tissue/Cells for Mass Spectrometry

Antigen Retrieval Immunohistochemistry

“…In addition to ourselves, most investigators have emphasized high-temperature heating as the critical factor for protein extraction (Chu et al 2005;Prieto et al 2005;Yamashita and Okada 2005b;Fowler CB et al 2010). Jiang et al (2007) compared the efficiency of protein extraction from FFPE tissue between heating (at 100C for 30 min) and non-heating protocols and demonstrated that the protein concentration from the heated sample was much higher than that obtained by the non-heating sample (10.9 vs 0.82 mg/mL).…”

“…There is now general agreement that in any study of fixed tissues, protein extraction and preparation are the most critical steps for proteomics studies (Saravanan and Rose 2004;Fowler CB et al 2010). Satisfactory extraction of proteins from FFPE tissue requires not only a sufficient quantity to meet all test needs but also high quality to represent the true protein expression profile of the cell/tissue examined.…”

“…Extraction of nucleic acids and proteins from FFPE tissues has been successfully accomplished in recent years, particularly after adaptation of heat-induced AR methods (Goelz et al 1985;Dubeau et al 1986;Shibata et al 1988;Frank et al 1996;Masuda et al 1999;Coombs et al 1999;Shi et al 2002;Shi and Taylor 2010c;Fowler CB et al 2010). The use of an AR approach was initiated based on evidence that formalin-induced modification of protein and of nucleic acid is similar von Hippel 1977a, 1977b;Masuda et al 1999;Shi et al 2001).…”

“…Further development by combining elevated hydrostatic pressure may increase extraction to 80% to 95% of proteins in FFPE tissue sections. Ikeda et al 1998;Shi et al 2006;Fowler CB et al 2007;Fowler CB et al 2008;Fowler CB et al 2010 IMS Boiling AR pretreatment is being adopted to achieve satisfactory results of IMS in recent years. On the basis of comparing different AR solutions, Gustafsson et al (2010) summarized that the citrate acid AR method is an important step in being able to fully analyze the proteome for FFPE tissue.…”

“…Finally, and by no means least, there is a growing body of recent literature with respect to use of AR methods for extraction of molecules (DNA, RNA, and proteins) from FFPE tissues that has further extended the utility of archival tissues and promises to allow the combination of proteomics and IHC in a true molecular morphology approach. So effective have these AR-based approaches become that investigators are now actively exploring the possible advantages of FFPE tissues in terms of preservation of both morphology and molecules in cell/tissue samples, in comparison to other methods of sample preparation (Frank et al 1996;Masuda et al 1999;Sato et al 2001;Shi et al 2002;Shi et al 2006;Palmer-Toy et al 2005;Becker et al 2007;Guo et al 2007;Jiang et al 2007;Addis et al 2009;Fowler CB et al 2010;Shi and Taylor 2010c).…”