Table 1.

Influence of background removal on the recovery of BSA, ADH and TRF in MS/MS spectra of 100 fmol test samples. The original number of MS/MS spectra for the BSA (bovine serum albumine), ADH (yeast alcoholdehydrogenase) and TRF (human transferring) datasets (recorded on a DecaXP machine) are 2679, 2325 and 2608 respectively. The intensity threshold s (column 3) describes the search of the sequence ladder (length n in column 2) within the 15%, 20%, 25% or 30% top peaks (100% - all peaks are considered). The following three columns show the MS Cleaner output - number of spectra with background removal, number of unselected spectra and the MS Cleaner CPU time on a single-processor Windows XP computer (Pentium IV 2.4 GHz; to get exact measurements of computation time, we did not use the cluster version). The remaining four columns present the MASCOT output - the CPU time on the same machine, the protein score, the number of spectra matching peptides in a MASCOT search and the final sequence coverage. For each dataset, the first line shows the results for the case when MS Cleaner is not used for pre-processing and the MS/MS data is immediately interpreted by MASCOT.

protein	sequence ladder length n	intensity threshold s [%]	cleaned spectra	bad spectra	MS Cleaner time [min]	MASCOT time [min]	MASCOT score	queries matched	sequence coverage
BSA	0	100	-	-	-	61	586	89	55
	3	100	1664	1015	3.92	44	720	91	57
	3	15	390	2289	1.21	17	1991	84	52
	3	20	490	2189	1.40	21	2108	87	57
	3	25	601	2078	1.61	26	2114	89	57
	3	30	688	1991	1.75	29	2114	90	57
	4	100	940	1739	3.80	36	2108	91	57
	4	15	260	2419	0.91	12	1875	78	47
	4	20	321	2358	1.06	14	1911	80	47
	4	25	380	2299	1.25	18	2114	86	57
	4	30	441	2238	1.30	19	2114	89	57
	5	100	593	2086	3.82	26	2108	91	57
	5	15	174	2505	0.60	9	1579	60	41
	5	20	232	2447	0.85	11	1809	72	44
	5	25	281	2398	1.00	13	1963	81	49
	5	30	313	2366	0.85	14	2058	86	54
ADH	0	100	-	-	-	64	242	39	39
	3	100	1446	879	4.15	45	327	34	39
	3	15	269	2056	0.88	12	673	29	35
	3	20	347	1978	1.10	13	696	31	37
	3	25	440	1885	1.33	17	697	32	37
	3	30	697	1628	1.53	20	697	33	37
	4	100	902	1423	4.15	35	733	34	39
	4	15	173	2152	0.58	7	562	26	28
	4	20	216	2109	0.71	9	673	30	35
	4	25	271	2054	0.90	12	607	28	33
	4	30	325	2000	1.05	13	697	32	37
	5	100	594	1731	4.20	23	712	33	39
	5	15	94	2231	0.35	5	311	15	21
	5	20	125	2200	0.46	6	366	17	25
	5	25	145	2180	0.53	7	434	19	26
	5	30	186	2139	0.66	9	589	24	31
TRF	0	100	-	-	-	52	588	86	47
	3	100	1587	1021	3.57	42	768	87	49
	3	15	373	2235	1.00	17	1988	86	49
	3	20	485	2123	1.23	20	1988	86	49
	3	25	568	2040	1.36	24	1998	87	49
	3	30	639	1969	0.78	27	1998	87	49
	4	100	864	1744	3.62	34	1973	87	49
	4	15	231	2377	0.70	11	1987	81	49
	4	20	298	2310	0.86	13	1988	84	49
	4	25	360	2248	1.00	16	1988	85	49
	4	30	414	2194	1.12	19	1998	87	49
	5	100	540	2068	3.63	23	1973	87	49
	5	15	164	2444	0.55	9	1785	68	45
	5	20	194	2414	0.61	10	1890	74	47
	5	25	245	2363	0.75	12	1957	80	48
	5	30	286	2322	0.86	14	1968	84	48