Table 2. Total Number of Scans, Number of MS1 and MS2 Scans, and MS2 Efficiency (Eff) for the Two Experiment Iterations (Iter)^a.

		beer (4592 peaks)				serum (3032 peaks)
Iter	method	total	MS1	MS2	Eff	total	MS1	MS2	Eff
	TopN	6404	583	5821	0.18	6317	575	5742	0.11
1	WeightedDEW	6282	572	5710	0.33	6235	567	5668	0.19
	SmartROI	4948	1050	3898	0.43	4271	1268	3003	0.33
	SmartROI (shift = 1)	5247	1056	4191	0.44	4299	1309	2990	0.37
	SmartROI (shift = 2)	5361	1054	4307	0.43	4353	1315	3038	0.34
2	WeightedDEW	6294	573	5721	0.31	6205	566	5639	0.22
	SmartROI	5078	1032	4046	0.38	4572	1237	3335	0.30
	SmartROI (shift = 1)	5395	1027	4368	0.40	4376	1329	3047	0.39
	SmartROI (shift = 2)	5413	1063	4350	0.40	4085	1414	2671	0.44

^aEfficiency is the number of picked peaks that are fragmented divided by the number of MS2 scans.