Transfer posterior error probability estimation for peptide identification

Table 2 Results achieved with the three methods for estimating variant FDRs on simulated data, with the FDR control level at 1%

n	iCombined FDR			iSeparate FDR			iTransfer FDR
	Ave.#I.D.s	Est.error(%)		Ave.#I.D.s	Est.error(%)		Ave.#I.D.s	Est.error(%)
	(false/all)	Mean	SD	(false/all)	Mean	SD	(false/all)	Mean	SD
1	10.22/10.70	-94.36	5.13	0.21/0.55	-16.95	34.64	0.00/0.25	0.00	0.02
5	10.76/13.09	-80.95	8.84	0.30/2.05	-11.09	20.57	0.00/1.24	0.01	0.07
10	10.09/14.87	-66.43	9.50	0.60/4.17	-12.92	11.63	0.00/2.50	0.04	0.14
20	10.90/20.57	-51.64	9.08	0.72/ 8.07	-8.86	6.31	0.00/5.30	0.08	0.19
50	10.53/34.44	-29.25	6.87	0.73/19.07	-3.60	2.57	0.00/13.28	0.20	0.27
100	10.67/58.64	-17.09	4.54	0.73/38.27	-1.43	1.25	0.00/27.40	0.42	0.35

Note: n, the number of variant mass spectra; Ave.#I.D.s, average number of false/all identifications of variant peptides from the target database at 1% estimated FDR; Est.error, the difference between the estimated FDR and the real FDR; Mean and SD, mean and standard deviation of the Est.error as percentage