A simple peak detection and label-free quantitation algorithm for chromatography-mass spectrometry

BMC Bioinformatics

Table 1 Summary of the numbers of peaks generated by AB3D, MZmine 2, MSight, SuperHirn and OpenMS for standard peptide mixture consisting of BSA peptides with different concentrations (96 amol, 480 amol, 2400 amol, 12 fmol, 60 fmol and 300 fmol) and peptides derived from four standard proteins such as beta galactosidase, phosphorylase b, myoglobin and cytochrome c with the same concentrations, and their replicates (n = 4) using Data set 1

BSA Conc.	N	AB3D			MZmine2			MSight			SuperHirn			OpenMS
BSA Conc.	N	Total	TP	FP	Total	TP	FP	Total	TP	FP	Total	TP	FP	Total	TP	FP
300 fmol	1	1,482	208	1,274	4,980	240	4,740	1,317	169	1,148	2,009	201	1,808	3,305	240	3,065
	2	1,458	205	1,253	4,901	246	4,655	1,155	175	980	1,896	202	1,694	3,393	240	3,153
	3	1,452	207	1,245	5,047	235	4,812	1,437	176	1,261	2,007	201	1,806	3,214	239	2,975
	4	1,415	214	1,201	4,875	239	4,636	1,333	173	1,160	1,919	205	1,714	3,052	228	2,824
	UKP		261			276			195			249			263
60 fmol	1	1,022	189	833	2,620	193	2,427	1,062	164	898	1,182	167	1,015	1,340	198	1,142
	2	1,033	185	848	2,521	185	2,336	1,047	166	881	1,257	173	1,084	1,264	193	1,071
	3	975	181	794	2,374	187	2,187	909	152	757	1,160	165	995	1,239	190	1,049
	4	950	181	769	2,318	186	2,132	833	154	679	1,187	167	1,020	1,153	185	968
	UKP		217			220			177			202			210
12 fmol	1	752	145	607	1,474	146	1,328	603	128	475	869	130	739	773	150	623
	2	742	148	594	1,449	150	1,299	513	121	392	858	140	718	754	147	607
	3	695	151	544	1,262	145	1,117	624	128	496	789	128	661	680	148	532
	4	673	154	519	1,234	143	1,091	518	122	396	752	130	622	642	141	501
	UKP		177			170			134			170			161
2400 amol	1	655	122	533	1,279	124	1,155	440	98	342	747	107	640	619	118	501
	2	653	115	538	1,193	113	1,080	414	93	321	769	107	662	585	118	467
	3	598	117	481	1,112	113	999	360	86	274	716	105	611	581	117	464
	4	612	118	494	1,080	116	964	368	87	281	689	112	577	553	114	439
	UKP		138			135			100			137			128
480 amol	1	668	101	567	1,237	108	1,129	450	83	367	778	87	691	630	100	530
	2	622	94	528	1,191	97	1,094	431	81	350	768	89	679	592	94	498
	3	608	100	508	1,094	103	991	388	76	312	731	99	632	569	90	479
	4	593	93	500	1,063	93	970	358	71	287	688	94	594	498	93	405
	UKP		115			123			88			118			104
96 amol	1	688	97	591	1,488	102	1,386	433	76	357	730	83	647	673	89	584
	2	636	88	548	1,311	92	1,219	408	71	337	717	83	634	658	87	571
	3	583	92	491	1,103	89	1,014	379	68	311	703	84	619	584	77	507
	4	553	88	465	1,060	87	973	316	64	252	697	85	612	489	76	413
	UKP		106			110			79			110			94

Values in individual rows for each concentration represent the individual number of known peptides of BSA and the four other standard proteins from 4 replicates. Values in UKP rows represent the total numbers of unique known peptides identified from 4 replicates. TP and FP represent true positive and false positive, respectively.

ISSN: 1471-2105