Application of Mass Spectrometry for Identification of Biomarkers in Formaldehyde-Fixed Paraffin Embedded Specimens

Mass Spectrometry (MS) has recently been utilized for the identification of biomarkers in peripheral blood and in urine, whereas its application in tissue samples remains limited. In this review article, we introduce a novel application of MS using archived Formalin-Fixed Paraffin-Embedded (FFPE) tissue. This method addresses the significant technical challenges for protein ionization, including amino acid residue modification of proteins. While various immunochemical pretreatments for enhancing the ionization signal of peptides have been reported, significant developments have yet to be achieved. We performed a simplified chemical pretreatment method for preparing tissue sections involving heating in acetonitrile-containing buffer under airtight and pressurized conditions. Analysis revealed that the number and intensity of ionized peptide peaks obtained from pretreated tissue were significantly higher than from untreated (control) tissue. This highly sensitive treatment may enable MALDI-MS and LC/MS (liquid chromatography/MS) analyses of archived pathological FFPE samples in the hospital, leading to the identification of new biomarkers.