Journal Highlight: Are formalin‐fixed and paraffin‐embedded tissues fit for proteomic analysis?

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  • Published: Apr 2, 2019
  • Author: separationsNOW
  • Channels: Proteomics & Genomics
thumbnail image: Journal Highlight: Are formalin‐fixed and paraffin‐embedded tissues fit for proteomic analysis?

Several published workflows for FFPE‐tissue have been evaluated by fit‐for‐purpose proteomics technologies, showing that many protein modifications and cross‐links remain after treatment, limiting the value of the technique.

Bayer, M., Angenendt, L., Schliemann, C., et al. (2019). Are formalin‐fixed and paraffin‐embedded tissues fit for proteomic analysis? Journal of Mass Spectrometry online

Abstract: Formalin‐fixed and paraffin‐embedded (FFPE)‐tissue archives are potential treasure troves in the search for clinically interesting specimens. However, while the FFPE‐treatment provides excellent conservation of the three‐dimensional structure of the tissue and prevents degradation over decades, it also introduces numerous non‐specific and irreversible protein modifications. In this study, we have evaluated several published workflows for FFPE‐tissue by fit‐for‐purpose proteomics technologies. We demonstrate that many protein modifications and cross‐links remain after treatment and conclude that the proteomics of FFPE‐tissue is of value, but clear‐cut limitations must be kept in mind. The analysis of abundant proteins in FFPE is straightforward, but confident identification of low‐level proteins and/or biologically relevant modifications is seriously hampered by the FFPE‐treatment. Peptide assignment should only be performed on high quality spectra, even if this is at the cost of lower numbers of protein IDs. As Yergey and Coorssen stated in 2015: "Data quality is considered the primary criterion, and we thus emphasize that the standards of Analytical Chemistry must apply throughout any proteomic analysis."

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