Table 3.

Proteins quantified in at least two runs and median coefficient of variation (CV) from four HeLa cell lysate replicates

Tool			Proteins quantified	Median CV
MaxQuant	MBR−	min 1 peptide	5406	5.3%
		min 2 peptides	4186	4.3%
	MBR+	min 1 peptide	5950	5.3%
		min 2 peptides	5073	4.7%
IonQuant	MBR−	min 1 ion	5971	4.0%
		min 2 ions	5061	3.5%
	MBR+	min 1 ion	6346	4.0%
		min 2 ions	5527	3.6%

“MBR+” and “MBR−” indicate that the analysis was performed with and without match-between-runs (MBR), respectively.