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To deparaffinize paraffin tissue for protein extraction, ensure thorough deparaffinization to prevent residual paraffin from hindering protein recovery. Extend xylene incubation times or increase washes, and follow with ethanol washes to remove residual xylene and paraffin [1][4]. Inadequate rehydration after xylene treatment can also affect protein yield; ensure complete removal of organic solvents and proper rehydration [1]. Heat-induced antigen retrieval techniques using buffers like SDS-containing Laemmli buffer or Tris-HCl with 2% SDS can improve protein extraction from formalin-fixed paraffin-embedded tissues, enhancing protein solubilization [2][3][5]. Optimizing lysis buffer and incubation conditions in the Wessel and Flügge method may further improve protein yields [6].

Reference

[1] Addis, M. F., Tanca, A., Pagnozzi, D., Crobu, S., Fanciulli, G., Cossu-rocca, P., & Uzzau, S. (2009). Generation of high‐quality protein extracts from formalin‐fixed, paraffin‐embedded tissues. PROTEOMICS, 9.

[2] Scicchitano, M., Dalmas, D. A., Boyce, R., Thomas, H. C., & Frazier, K. S. (2009). Protein Extraction of Formalin-fixed, Paraffin-embedded Tissue Enables Robust Proteomic Profiles by Mass Spectrometry. Journal of Histochemistry & Cytochemistry, 57, 849 - 860.

[3] Klopfleisch, R., Weiss, A., & Gruber, A. D. (2011). Excavation of a buried treasure--DNA, mRNA, miRNA and protein analysis in formalin fixed, paraffin embedded tissues.. Histology and histopathology, 26 6, 797-810 .

[4] Shi, S., Taylor, C., Fowler, C., & Mason, J. (2013). Complete solubilization of formalin‐fixed, paraffin‐embedded tissue may improve proteomic studies. PROTEOMICS – Clinical Applications, 7.

[5] Mansour, A., Khalil, P. A., Bejjani, N. A., Chatila, R., Dagher-Hamalian, C., & Faour, W. H. (2017). An optimized xylene-free protein extraction method adapted to formalin-fixed paraffin embedded tissue sections for western blot analysis.. Histology and histopathology, 32 3, 307-313 .

[6] Mitsa, G., Guo, Q., Gonçalves, C., Preston, S. E. J., Lacasse, V., Aguilar-Mahecha, A., Benlimame, N., Basik, M., Spatz, A., Batist, G., Miller, W. H., Rincón, S. V. d., Zahedi, R., & Borchers, C. (2022). A Non-Hazardous Deparaffinization Protocol Enables Quantitative Proteomics of Core Needle Biopsy-Sized Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue Specimens. International Journal of Molecular Sciences, 23.