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Formalin-fixed paraffin-embedded (FFPE) tissue samples from surgical procedures and biopsies are often preserved in a formaldehyde solution to impede degradation of biopolymers. An estimated 520 million FFPE samples are currently biobanked in the United States. Nucleic acids and proteins react with formaldehyde to form hemi-aminal and aminal adduct crosslinks. Although an effective method for the preservation of biospecimen, most methods that characterize nucleic acids or proteins (e.g. sequence or mass spectrometry- based proteomics) require liberation of the biopolymers from crosslinks before analysis. Typically employed methods to remove adducts involve lengthy exposure to high temperatures and extreme pH which can erase labile chemical modifications. Our central hypothesis is that bifunctional aryl catalysts will expedite the removal of formaldehyde adducts through reduced temperatures which will ameliorate the recovery of proteins and their post-translational modifications in proteomics applications. FFPE tissue samples were simulated by culturing HeLa cells and fixing them with formaldehyde. Cell lysates were subjected to specific organocatalysts and temperatures for decrosslinking. The effectiveness of decrosslinking was evaluated by a combination of bottom-up and top-down protein mass spectrometry measurements. Figures of merit include the number of identified proteins, number of identified (modified) peptides, and sequence coverage.

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Purdue University / 2023

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Am Author