MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

Pluskal, Tomáš; Castillo, Sandra; Villar-Briones, Alejandro; Orešič, Matej

doi:10.1186/1471-2105-11-395

Table 3 Performance comparison of MZmine 2 alignment methods (right side of the table) to previously published results (left side of the table) obtained using several different software packages [11].

From: MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

	Results published by Lange et al. (2008), avaiable at the time of writing at http://msbi.ipb-halle.de/msbi/caap							MZmine 2 results
	msInspect	MZmine (version 0.6)	OpenMS	SpecArray	XAlign	XCMS
						without RT correction	With correction	Join aligner	RANSAC aligner
*Proteomics data set P1*
fraction 00
Recall	0.52	0.81	0.86	0.61	0.82	0.72	0.62	0.80	0.86
Precision	0.38	0.81	0.86	0.61	0.82	0.54	0.58	0.80	0.86
fraction 20
Recall	0.56	0.90	0.92	0.62	0.85	0.88	0.81	0.90	0.93
Precision	0.45	0.90	0.92	0.62	0.85	0.84	0.80	0.90	0.93
fraction 40
Recall	0.63	0.90	0.94	0.75	0.87	0.92	0.81	0.87	0.94
Precision	0.48	0.90	0.94	0.75	0.87	0.85	0.80	0.87	0.94
fraction 60
Recall	0.73	0.84	0.96	0.71	0.87	0.91	0.78	0.89	0.97
Precision	0.54	0.84	0.96	0.71	0.87	0.80	0.75	0.89	0.97
fraction 80
Recall	0.70	0.94	0.96	0.74	0.90	0.94	0.89	0.94	0.97
Precision	0.57	0.94	0.96	0.74	0.90	0.88	0.88	0.94	0.97
fraction 100
Recall	0.82	0.94	0.94	0.77	0.96	0.95	0.96	0.95	0.96
Precision	0.56	0.94	0.94	0.77	0.96	0.89	0.96	0.95	0.96
*Proteomics data set P2*
fraction 00
Recall	0.23	0.62	0.77	0.07	0.65	0.70	0.58	0.63	0.56
Precision	0.07	0.49	0.65	0.05	0.49	0.31	0.44	0.53	0.49
fraction 20
Recall	0.67	0.87	0.92	0.57	0.84	0.89	0.86	0.81	0.93
Precision	0.24	0.71	0.77	0.42	0.70	0.55	0.66	0.69	0.78
fraction 40
Recall	0.44	0.79	0.76	0.60	0.71	0.72	0.72	0.74	0.78
Precision	0.26	0.76	0.74	0.41	0.69	0.56	0.69	0.73	0.77
fraction 80
Recall	0.73	0.60	0.80	0.65	0.58	0.64	0.49	0.61	0.61
Precision	0.34	0.56	0.70	0.44	0.56	0.50	0.45	0.58	0.61
fraction 100
Recall	0.82	0.80	0.90	0.63	0.85	0.95	0.85	0.85	0.88
Precision	0.39	0.64	0.75	0.44	0.69	0.65	0.69	0.71	0.75
*Metabolomics data sets*
M1
Recall	0.27	0.92	0.87	-	0.88	0.98	0.94	0.90	0.91
Precision	0.46	0.73	0.69	-	0.70	0.60	0.70	0.74	0.74
M2
Recall	0.23	0.98	0.93	-	0.93	0.97	0.98	0.98	0.98
Precision	0.47	0.84	0.79	-	0.79	0.58	0.78	0.83	0.83

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ISSN: 1471-2105

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