A huge amount of formalin-fixed paraffin-embedded (FFPE) tissues have been reserved in hospitals and medical research centers. Until recent years those materials have been utilized only for limited purposes such as DNA analyses and immunohistochemistry verification studies. We have developed application of Liquid Tissue technology, which solubilizes proteins in FFPE tissue samples, for biomarker discovery and verification. An use of human FFPE tissues has a great advantage because of their already known clinical outcomes. AS a protocol in Tokyo Medical University Hospital, tumor blocks are formalin-fixed immediately after their surgical excision. We have been experiencing a promising results from proteomic analyses of FFPE tissues following their laser microdissection (LMD), LT solubilization, and trypsin digestion. A standard preparation protocol for FFPE samples will be presented for further proteomic analyses, and some recent results obtained from discovery cancer biomarkers investigations and their verification/validation using multiple-reaction monitoring (MRM) MS-based assays will be exemplified.
