Table 2.
MS analysis of FFPE and matched fresh-frozen mouse liver tissue. 1-year old FFPE mouse liver was homogenized in extraction buffer and heated with or without elevated pressure. Fresh-frozen tissue was extracted either at atmospheric pressure using the indicated extraction conditions, or on ice for 2.5 h
| Tissue | Pressure (psi) | Buffer a | Extraction conditions | %Protein Extraction b | Unique Peptide IDs | Unique Protein IDs |
|---|---|---|---|---|---|---|
| Frozen, 1 y | 14.7 | Tris/DTT | 95 °C, 3 min | 100% | 5872 | 3415 |
| FFPE, 1 y | 14.7 | Tris/DTT | 95 °C, 1h | 18% | 107 | 107 |
| FFPE, 1 y | 40,000 | Tris/DTT | 95 °C, 1h | 79% | 5180 | 3492 |
a
Extraction buffer: 100 mM Tris-HCl, pH 8, 100 mM DTT, 2% (w/v) SDS [40].
b
The amount of protein extracted from fresh frozen tissue was set to 100%.