Fig. 2.

Processing times for different methods and sample sizes. directLFQ scales (sub-) linearly for (A) data-dependent acquisition (DDA) data and (B) data-independent acquisition (DIA) data, resulting in more than 1000-fold faster execution times than MaxLFQ. X in the plot marks instances with prohibitive calculation times. ∗Extrapolated times, as the templates for the 100,000 sample set had to be shortened to adhere to 128 GB memory. See Experimental procedures and discussion section for details.