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

BMC Bioinformatics

Table 2 Summary of the numbers of peaks generated by AB3D, MZmine 2, MSight, SuperHirn and OpenMS for the real biological data (data set 2)

Fraction.	N	AB3D			MZmine2			MSight			SuperHirn			OpenMS
Fraction.	N	Total	TP	FP	Total	TP	FP	Total	TP	FP	Total	TP	FP	Total	TP	FP
FK1	1	496	197	299	529	155	374	328	147	181	760	105	655	500	195	305
	2	498	193	305	469	148	321	365	172	193	739	112	627	447	190	257
	3	490	211	279	503	150	353	379	178	201	808	127	681	484	205	279
	UKP		279			231			234			209			258
FK2	1	1,049	426	623	1,117	344	773	779	392	387	1,416	254	1,162	917	390	527
	2	1,074	433	641	1,087	337	750	743	386	357	1,517	248	1,269	813	352	461
	3	1,416	515	901	1,454	404	1,050	767	429	338	2,036	333	1,703	1,284	440	844
	UKP		651			547			547			496			551
FK3	1	613	330	283	651	275	376	686	323	363	763	184	579	528	310	218
	2	725	344	381	757	280	477	675	310	365	975	194	781	636	349	287
	3	657	372	285	897	373	524	754	298	456	1,064	236	828	604	344	260
	UKP		489			468			481			366			453
FK4	2	1,476	446	1,030	1,465	335	1,130	1,317	430	887	1,969	266	1,703	1,064	355	709
	3	1,452	576	876	1,705	509	1,196	1,574	533	1,041	2,064	361	1,703	1,213	506	707
	UKP		681			597			650			474			566
FK5	1	1,709	423	1,286	1,674	329	1,345	526	251	275	2,128	237	1,891	643	229	414
	2	2,038	425	1,613	2,231	349	1,882	721	305	416	2,988	259	2,729	834	274	560
	3	2,031	572	1,459	2,432	509	1,923	1,696	489	1,207	3,126	340	2,786	1,186	401	785
	UKP		768			687			636			553			516

Values in individual rows for each fraction represent the individual numbers of identified peptides from 3 replicates. In fraction 4, results for two replicates were presented because there was one missing replicate. Values in UKP rows represent the total numbers of unique known peptides identified from 2-3 replicates. TP and FP represent true positive and false positive, respectively.

ISSN: 1471-2105