Table 4.

Number of proteins with nonzero intensities from MaxQuant (MQ) and IonQuant (IQ)

Data type	MQ MBR−	MQ MBR+	IQ MBR−	IQ MBR+, 1% FDR	IQ MBR+, 2% FDR	IQ MBR+, 5% FDR
Blank	79 (152)	492 (887)	97 (195)	153 (314)	252 (548)	482 (954)
Single-cell HeLa	557 (853)	1230 (1902)	756 (1024)	1156 (1638)	1481 (2093)	2046 (2591)

The total nonredundant protein count in parentheses, and average proteins per run are outside parentheses.

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