Fig. 4.

Peptides and proteins from MaxQuant and IonQuant analysis of the single-cell dataset. “MBR+” and “MBR−” indicate that the analysis was performed with and without match-between-runs, respectively.A, numbers of proteins with nonzero intensities from samples with 0 cells (blank runs), one cell, three cells, and ten cells, respectively. Two ion-level MBR false discovery rate (FDR) thresholds (1% and 5%) were applied. Black dots indicate the numbers from individual runs. B, peptides/proteins quantified in at least two runs and median protein quantification coefficient of variation (CV) from 11 replicates of one cell samples, as a function of FDR threshold. “MQ” indicates MaxQuant and “IQ” indicates IonQuant. Black curves and dots indicate the median of CV of the corresponding tool.