Temperature, Oil and Pressure (TOP) extraction: optimal sample preparation for proteomic analysis of formalin fixed paraffin embedded tissue

Formalin-fixed paraffin embedded (FFPE) is the clinical gold standard of tissue preservation globally. We present a novel method for optimal extraction of proteins from FFPE tissue samples. The method combines non-toxic, proteomic inert mineral oil for deparaffinization, followed by extraction using elevated temperature and pressure (121˚C; 15 psi). Our novel TOP (Temperature, Oil, and Pressure) proteome extraction is four times faster, less laborious and increases the protein yield. Furthermore, the TOP method is environmentally friendly, as opposed to traditional methods. Comparison of extracted protein by mass spectrometry based proteomics revealed that TOP is not sensitive to formalin over-fixation, unlike the traditional approach, a fact that makes it suitable in the clinical setting. We expect that the TOP proteome extraction platform will help to alleviate some of the difficulties proteomics is facing in the clinical setting.