Fig. 2.

A, In black, number of proteins quantified from 500 ng of peptide in 21 min in a DIA experiment without FAIMS and with FAIMS using different compensation voltages. In blue, number of peptides quantified in the same experiments. The plotted values are the average of at least two technical replicates. B, Visualization of peptide identification across the gradient length for DIA run with CV of −45 V with FAIMS and 500 ng load. C, Cumulative protein identifications across the gradient for DIA runs without (light blue) and with CV of −45 V with FAIMS (dark blue). D, Bar chart of all protein identifications (dark gray), proteins with coefficient of variation below 20% (gray) and below 10% (light gray) for DIA with and without CV of −45 V with FAIMS. E, Histogram of the protein abundance distribution represented as copy number in log10 scale of a deep HeLa proteome (gray), and in a single shot analysis of 21 min using DDA and optimal CV of −75 V with FAIMS (dark green) or using DIA and optimal CV of −45 V with FAIMS (blue).