Evaluation of open search methods based on theoretical mass spectra comparison

BMC Bioinformatics

Table 2 Number of PSMs obtained by Strategy2 according to shift SPC

Min *shift SPC*	\(\Delta m {= 0}\)		\(\Delta m < {0}\)		\(\Delta m > {0}\)		Total
Min *shift SPC*	#target	#decoy	#target	#decoy	#target	#decoy	#target	#decoy	FDR(%)
7	14,207	17,401	145,801	86,218	122,479	69,298	282,487	17,2917	37.97
9	5132	4787	145,756	86,183	122,465	69,287	273,353	160,257	36.96
11	1944	1793	144,795	85,247	121,833	68,671	268,572	155,711	36.7
13	721	343	139,895	80,327	119,006	65,901	259,622	146,571	36.08
15	496	187	116,674	61,154	110,457	58,923	227,627	120,264	34.57
17	341	42	58,584	130,53	55,297	130,52	114,222	26,147	18.63
19	250	36	37,840	1681	35,439	1647	73,529	3364	4.37
21	201	12	29,675	271	27,908	251	57,784	534	0.92
23	160	10	24,262	87	22,881	82	47,303	179	0.38
25	131	5	20,036	35	18,910	36	39,077	76	0.19
27	108	4	16,686	18	15,792	14	32,586	36	0.11
29	92	2	13,835	12	13,120	9	27,047	23	0.08
31	67	2	11,345	4	10,801	5	22,213	11	0.05
33	54	0	9314	2	8888	3	18,256	5	0.03
35	44	0	7608	2	7296	2	14,948	4	0.03
37	39	0	6231	2	5989	2	12,259	4	0.03
39	17	0	5008	1	4832	1	9857	2	0.02

The best PSMs provided by SpecOMS are separated into three groups based on \(\Delta m\), and subdivided in each group by the origin of the hit (target or decoy database). An FDR < 1% is reached whenever shift SPC is greater than or equal to 21 (row in bold). Only results for odd minimum shift SPC are displayed here: indeed, shift SPC is always even, since a match always involves both a b-ion and a y-ion after realignment. The results we obtain are thus the same for consecutive odd and even shift SPC (except for a few exceptions due to overlapping masses)

ISSN: 1471-2105