Table 1.

LC/MS analysis for a 5-protein FFPE tissue surrogate extrated under atmospheric or elevated hydrostatic pressure.

Condition	Lysozyme		Carbonic Anhydrase		RNAse A		BSA		Myoglobin
	Peptide hits*	% Sequence Coverage**	Peptide hits	% Sequence Coverage	Peptide hits	% Sequence Coverage	Peptide hits	% Sequence Coverage	Peptide hits	% Sequence Coverage
Native protein mixture	67/10	66%	25/10	56%	10/6	63%	34/23	54%	6/5	38%
FFPE; pH 4, 40 Kpsi	26/8	69%	9/7	36%	12/5	59%	21/12	26%	3/3	28%
FFPE; pH 4, 14.7 psi	4/1	15%	n.d		1/1	7%	n.d		n.d
FFPE; pH 8, 40 Kpsi	75/7	57%	12/7	30%	11/5	71%	23/15	29%	3/2	16%
FFPE; pH 8, 14.7 psi	n.d		n.d		n.d		n.d		n.d

Multi-protein FFPE tissue surrogates were extracted at 100°C for 30 min followed by 80°C for 2 h at either 40,000 psi or atmospheric pressure (14.7 psi) in 50 mM Tris- HCL, 2% (w/v) SDS buffer, pH 4 or 8. The extracts were washed extensively, and digested overnight with trypsin at 37°C in 50 mM NH₄HCO₃, pH 7.9 with 20% acetonitrile (v/v).

^*Peptide hits: total spectra/number of unique peptides.

^**% Sequence coverage: percent of theoretical tryptic peptides identified by LC/MS/MS. n.d.-none detected.