Table 1.

Summary of the results of a 2D-HPLC MS/MS analysis of the S. pombe proteome^*

Frac.	# of entries	Min. Prob.	Sensit	Error	#corr.	#incorr.
1	332	0.50	0.984	0.016	327	5
2	173	0.90	0.795	0.014	171	2
3	288	0.90	0.800	0.019	283	5
4	499	0.60	0.980	0.017	490	8
5	1009	0.10	1.000	0.013	996	13
6	1220	0.10	1.000	0.020	1196	24
7	1255	0.50	0.995	0.018	1233	23
8	1341	0.60	0.980	0.017	1317	23
9	1323	0.70	0.962	0.017	1302	23
10	1257	0.80	0.934	0.015	1238	19
11	1113	0.80	0.939	0.017	1095	19
12	991	0.70	0.959	0.020	971	20
13	1022	0.70	0.969	0.017	1005	17
14	1164	0.60	0.983	0.017	1145	20
15	1235	0.60	0.978	0.019	1212	23
16	1273	0.60	0.982	0.019	1249	24
17	1252	0.60	0.976	0.017	1231	21
18	1152	0.70	0.959	0.019	1130	22
19	976	0.70	0.941	0.020	957	20
20	918	0.70	0.946	0.020	899	18
21	929	0.70	0.960	0.019	912	18
22	723	0.80	0.912	0.016	712	12
23	525	0.80	0.899	0.019	515	10
24	302	0.80	0.924	0.020	296	6

^*Abbreviations and definitions: Frac., SCX fraction that was re-injected to RP HPLC-MS/MS; # of entries, number of protein database entries (proteins) identified; Min. Prob., minimum probability that a protein identification is correct at a protein FDR of 0.02 or less; Sensit, sensitivity of identification of proteins at a protein FDR of 0.02 or less, i.e. the number of proteins identified divided by the total predicted number of correct entries; Error = estimated protein FDR (0.02 or less, and dependent on the minimum protein probability, which in turn is specified in increments of 0.01 to 0.1, depending on the range; see Fig. 5D); #corr, number correct = estimated number of correct protein identifications at the given FDR (0.02 or less); #incorr., number incorrect = estimated number of incorrect protein identifications at the given FDR (0.02 or less)