Fig. 1. Introducing prioritization to MaxQuant.Live increases identification consistency and protein coverage.

a, Shotgun topN analysis selects the n most abundant precursors for isolation and fragmentation (shown in blue). Among the many detected precursors, prioritized analysis first selects the ones with highest priority (shown in solid red) and then from lower-priority tiers (shown with decreasingly saturated red tones). Prioritization can also selectively allocate increased fill times to high-priority peptides of low abundance, as shown in the second cycle of MS² scans. b, Prioritized analysis increases the consistency of peptide identification over default MaxQuant.Live operation for high-priority peptides while also increasing protein coverage per run. The box plots showing proteins identified per experiment contain six points per analysis method, one for each experiment. c, Rates of MS¹ detection and MS² analysis for prioritized precursors from all tiers of the benchmarking experiments displayed in b. These box plots contain six points per analysis method, one for each experiment. The fourth panel displays peptides used for retention time (RT) alignment only and not intended for MS² scans. For all box plots, whiskers display the minimum and maximum values within 1.5 times the interquartile range of the 25th and 75th percentiles, respectively; the 25th percentile, median and 75th percentile are also featured.