Table 1.

Summary of peptides identified with a PeptideProphet P score ≥0.9

Peptide	Counts	Percentage
Total assignment above threshold	800,507
Total correct assignment	791,069
Total incorrect assignment	9,438
Spectrum assignment false discovery rate	0.012
Total distinct peptides	13,779	100.00
Distinct peptides mapped to human genome	13,461	97.69
Possible proteins implicated in mapping	10,674
Simple reduced proteins	4,084
Simple reduced genes	3,580
Unambiguously mapped proteins	1,590
Total distinct peptides, presented in ≥2 samples	9,170	66.55
Total singleton distinct peptides	4,609	33.45
Cys-containing distinct peptides	3,709	26.92
Trp-containing distinct peptides	2,067	15.00
Lys-containing distinct peptides	8,392	60.90
Total distinct peptides from colon cancer versus normal	5,958
Total distinct peptides from breast cancer versus normal	8,874
Total distinct peptides from pancreatic cancer versus normal	7,753
Total distinct peptides from ovarian cancer versus normal	5,368
Total distinct peptides in all four reference sets	2,897	21.02
Total distinct peptides in three reference sets	1,534	11.13
Total distinct peptides in two reference sets	2,415	17.53