Tissue Pressure (psi) Buffera Extraction condition % Protein Extractionc Unique Peptide IDs Unique Protein IDs Frozen, 30 d 14.7* EB1 On ice, 2.5 h 100% 10237 4727 Frozen, 30 d 14.7 * EB1 100°C+80°Cb 100% 9964 4581 FFPE, 30 d 14.7 * EB1 100°C+80°Cb 17% 5565 3449 FFPE, 30 d 40,000 EB1 100°C+80°Cb 77% 9621 5192 Frozen, 1 y 14.7* EB2 95°C, 3 min 100% 5872 3415 FFPE, 1 y 14.7* EB2 95°C, 1 h 18% 107 107 FFPE, 1 y 40,000 EB2 95°C, 1 h 79% 5180 3492

Table 3: MS analysis for Fresh and FFPE mouse liver extracted at atmospheric or elevated hydrostatic pressure. FFPE mouse liver was homogenized in extraction buffer and heated with or without elevated pressure. Fresh-frozen tissue from was extracted either at atmospheric pressure using the indicated extraction condition, or on ice for 2.5 h. *atmospheric pressure. aEB1: 50 mM Tris-HCl, pH 7, with 2% added [1]; EB2: 100 mM Tris HCl, pH 8, 100 mM DTT, 4% SDS [2]. bTissue was heated at 100°C for 30 min, then the temperature was lowered to 80°C for 2 h. cThe amount of protein extracted from fresh frozen tissue was set to 100%.