. Author manuscript; available in PMC: 2012 Nov 29.

Published in final edited form as: Nat Methods. 2012 Apr 27;9(5):455–456. doi: 10.1038/nmeth.1983

Table 1.

Reanalysis of the Colaert et al data set with correct parameters for Census. Results for the other software tools are from Colaert et al.

	Forward labeling				Reverse labeling
Software	Census	MsQuant	MaxQuant	Mascot distiller	Census	MsQuant	MaxQuant	Mascot distiller
Quantified proteins	4,752(RD) 4,431(NR) 2,555(UN)	2,066	1,452	2,092	4,694(RD) 4,371(NR) 2,516(UN)	2,425	1,689	2,135
validated proteins with up regulated ratio¹	57	38	45	35	93	94	55	71
validated proteins with down regulated ratio¹	127	5	29	37	138	1	59	63

Colaert et al provided biological validation for proteins present in the sample.