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

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.”

Proteomic Workflows for High-Quality Quantitative Proteome and Post-Translational Modification Analysis of Clinically Relevant Samples from Formalin-Fixed Paraffin-Embedded Archives

“…1,3−5 The tissue fixation by formalin allows the three-dimensional structure to be preserved, and the blocks can be stored at room temperature (RT) for decades without any significant alteration of the confined macromolecules. 1,2,6,7 Because storage of these blocks is much simpler and less expensive compared to fresh frozen tissues, the vast majority of scientifically relevant samples in biobanks such as tissue biopsies and surgically resected tumor tissues are stored as FFPE blocks. 6−8 The often high number of available FFPE samples enables statistical power, facilitating biomarker discovery and validation by increasing the understanding of disease biology.…”

Chronic Occupational Exposure to Ionizing Radiation Induces Alterations in the Structure and Metabolism of the Heart: A Proteomic Analysis of Human Formalin-Fixed Paraffin-Embedded (FFPE) Cardiac Tissue

“…FFPE tissue is an ideal source of analytical material for clinical investigations due to its stability in long-term storage [7][8][9][10][11][12][13]. The technical improvement of proteome analysis using FFPE material is a prerequisite for the successful elucidation of biological pathways.…”

Targeted Protein Profiling of In Vivo NIPP-Treated Tissues Using DigiWest Technology

“…Therefore, clinical samples are immediately fixed with formalin and embedded in paraffin wax. Formalin cross-links form a protein grid that preserves the tissue structure and prevents protein degradation [31]. Subsequent paraffin embedding facilitates the handling of samples and sectioning of the tissue into thin slices for staining and microscopical assessment.…”