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Protein extraction from FFPE sections of mouse liver was increased 3.33-fold by pressure cycling technology (PCT) and reached the same level as protein extraction from frozen sections. After PCT-assisted processing of FFPE liver samples followed by SWATH-MS-based comprehensive quantification, the peak areas of 88.4% of peptides agreed with those from matched fresh samples within a 1.5-fold range. For membrane proteins, this percentage was remarkably increased from 49.1 to 93.8% by PCT. Compared to the conventional method using urea buffer, the present method using phase-transfer surfactant (PTS) buffer at 95\u00a0\u00b0C showed better agreement of peptide peak areas between FFPE and fresh samples. When our method using PCT and PTS buffer at 95\u00a0\u00b0C was applied to a bile duct ligation (BDL) disease model, the BDL\/control expression ratios for 80.0% of peptides agreed within a 1.2-fold range between FFPE and fresh samples. This heat-compatible FFPE-PCT-SWATH proteomics technology using PTS is suitable for quantitative studies of pathological molecular mechanisms and biomarker discovery utilizing widely available FFPE samples.<\/jats:p>","DOI":"10.1038\/s41598-020-68245-2","type":"journal-article","created":{"date-parts":[[2020,7,9]],"date-time":"2020-07-09T10:06:38Z","timestamp":1594289198000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":26,"title":["Establishment and validation of highly accurate formalin-fixed paraffin-embedded quantitative proteomics by heat-compatible pressure cycling technology using phase-transfer surfactant and SWATH-MS"],"prefix":"10.1038","volume":"10","author":[{"given":"Yasuo","family":"Uchida","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hayate","family":"Sasaki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tetsuya","family":"Terasaki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,7,9]]},"reference":[{"key":"68245_CR1","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1002\/pmic.201300311","volume":"14","author":"C Steiner","year":"2014","unstructured":"Steiner, C. et al. 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