%0 Journal Article
%T Novel protein extraction approach using micro-sized chamber for evaluation of proteins eluted from formalin-fixed paraffin-embedded tissue sections
%A Keiichi Hatakeyama
%A Kanako Wakabayashi-Nakao
%A Yutaka Aoki
%A Shun-ichiro Ogura
%A Ken Yamaguchi
%A Takashi Nakajima
%A Taka-Aki Sato
%A Tohru Mochizuki
%A Isamu Hayashi
%J Proteome Science
%D 2012
%I BioMed Central
%R 10.1186/1477-5956-10-19
%X The standard method for storing clinical specimens in hospital tissue banks is in the form of formalin-fixed paraffin-embedded (FFPE) tissue samples, and these are both abundant and widely available for pathological diagnosis worldwide. Recently, FFPE tissue samples have been subjected to mass spectrometry (MS)-based proteomic analysis [1-4], and several studies in FFPE samples employed heat-induced antigen retrieval (HIAR) to improve protein identification [1,4-12]. These investigations have demonstrated the similarity of protein identification between FFPE and fresh/frozen tissue samples [4,9,12-15]. Thus, FFPE tissues are now considered an alternative to fresh/frozen tissues for protein biomarker discovery.Although several groups have reported the equivalence of proteomes derived from fresh/frozen and FFPE samples, the mechanism of protein extraction by HIAR is not entirely understood. HIAR was originally developed to improve the sensitivity of immunohistochemical methods [16,17], and is used to unmask epitopes in FFPE samples [18,19]. Recent MS imaging of FFPE tissues suggests that HIAR treatment also increases accessibility of proteins to trypsin [6,20]. However, these studies focused only on the retrieved proteins remaining in the FFPE tissue sections. Chu et al. have shown that HIAR treatment facilitates partial release of macromolecules (polypeptides, nucleic acids, and lipids) from FFPE tissues fixed on a glass slide [21]. In their study, the proteins released from FFPE samples by HIAR were not investigated or characterized by MS analysis.In this study, we report a novel antigen-retrieval method using a micro-sized chamber for identifying proteins eluted from FFPE tissue samples. FFPE colon cancer tissue sections fixed on a glass slide were treated by HIAR in a fabricated chamber. The method yielded improved protein identification compared to untreated samples, as assessed by MS/MS analysis using a nano-flow LC-ESI linear ion trap (LIT)-TOF mass spectromete
%K Antigen retrieval
%K Colon adenoma
%K Colon cancer
%K FFPE tissue
%K Gastric cancer
%K Heat-induced antigen retrieval
%K Mass spectrometry
%K Micro-sized chamber
%U http://www.proteomesci.com/content/10/1/19