Are formalin-fixed and paraffin-embedded tissues fit for proteomic analysis? - PubMed (original) (raw)
doi: 10.1002/jms.4347. Epub 2019 Apr 10.
Affiliations
- PMID: 30828905
- DOI: 10.1002/jms.4347
Are formalin-fixed and paraffin-embedded tissues fit for proteomic analysis?
Malte Bayer et al. J Mass Spectrom. 2020 Aug.
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 nonspecific 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."
Keywords: FFPE-tissue; cross-links; formaldehyde-induced modifications; proteomics.
© 2019 John Wiley & Sons, Ltd.
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