Table 4. Number of Peptides Unmatched, Mismatched and Correctly Matched at Various Significance Levels by X!Tandem, OMSSA and Crux when Either the b-, y-Ion Series, 50%, or 25% of the Ions in the Query Available for Precursor Charge State +1 and Including Neutral Mass Losses.

	OMSSA				X!Tandem				Crux
significancea	bb	y	50	25	b	y	50	25	b	y	50	25
Unmtchc	0	0	1	73	79	72	73	295	0	0	0	0
Mismtchd	0	0	0	4	6	15	13	10	0	0	0	0
0	160	48	71	492	237	138	316	1133	0	2	9	60
1	84	62	72	182	109	113	170	284	93	131	151	322
2	87	86	85	184	149	156	133	228	229	196	243	302
3	100	99	87	178	122	113	166	229	215	155	188	218
4	94	88	106	160	96	98	104	140	154	169	180	183
5	90	89	88	167	105	109	157	136	167	140	188	209
6	64	77	81	133	137	139	109	120	188	173	190	273
7	94	73	86	113	104	105	122	146	167	196	209	326
8	93	90	74	106	89	103	127	131	168	226	244	365
≥9	6984	7138	7099	6058	6617	6689	6360	4998	6469	6462	6248	5592
Prop >6e	92.2	94.0	93.5	81.7	88.5	89.6	85.6	68.7	89.1	89.9	87.8	83.5

^aSignificance threshold (t) for matched to be considered significant at E- or p-value < 1 × 10^–t.

^bb-, y-ion series, 50%, or 25% of the ions in the query are available.

^cUnmatched: the program does not provide a match with the program setting.

^dMismatched: the program provided an incorrect match.

^ePercentage of the matches that have E- or p-value < 1 × 10^–6.