Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements

BMC Bioinformatics

Table 4 Alignment recall and precision results for the proteomics data set P2.

	msInspect	MZmine	OpenMS	SpecArray	XAlign	XCMS
						without retention time	with correction
fraction 00
Recall_Align	0.23	0.77	0.77	0.07	0.65	0.70	0.58
Precision_Align	0.07	0.6	0.65	0.05	0.49	0.31	0.44
fraction 20
Recall_Align	0.67	0.87	0.92	0.57	0.84	0.89	0.86
Precision_Align	0.24	0.71	0.77	0.42	0.70	0.55	0.66
fraction 40
Recall_Align	0.44	0.79	0.76	0.60	0.71	0.72	0.72
Precision_Align	0.26	0.76	0.74	0.41	0.69	0.56	0.69
fraction 80
Recall_Align	0.73	0.61	0.80	0.65	0.58	0.64	0.49
Precision_Align	0.34	0.56	0.70	0.44	0.56	0.50	0.45
fraction 100
Recall_Align	0.82	0.80	0.90	0.63	0.85	0.95	0.85
Precision_Align	0.39	0.65	0.75	0.44	0.69	0.65	0.69

ISSN: 1471-2105