Fig. 3: Performance evaluation.

Twenty-seven technical replicates of HepG2 cell lysate were analyzed on an Orbitrap mass spectrometer (Methods). a, Number of identified protein groups with 1% FDR on protein and peptide level and number of peptides at 1% library-to-DIA-sample FDR obtained with MaxDIA, Spectronaut 13 and Spectronaut 14. b, Histograms of peptide lengths identified with MaxDIA (blue) and Spectronaut 13 (red). c, Number of proteins with, at most, x out of 27 valid values for Spectronaut 13 (red), Spectronaut 14 (magenta) and MaxDIA with MaxLFQ minimum ratio count = 1 (blue, dashed) and = 2 (blue, solid). Multiple curves for the two MaxQuant series of curves correspond to seven different choices for the transfer q value (0.01, 0.03, 0.05, 0.1, 0.3, 0.5 and 1). d, Histograms of coefficients of variation for analyses with default settings in MaxDIA (solid blue) and in Spectronaut 13 and Spectronaut 14 (open). e, log–log scatter plot of LFQ intensities between two representative replicates obtained with MaxQuant. The two replicates were chosen to have the median Pearson correlation of all pairwise replicate comparisons. f, Same as in e for Spectronaut intensities. Similarly, the two replicates were chosen to represent the median Pearson correlation coefficient of all pairwise comparisons. g, Heat map with all pairwise Pearson correlations among the 27 replicates for MaxDIA (upper triangle) and Spectronaut (lower traingle). The two values corresponding to the comparisons in e and f are marked with red squares. h, log–log scatterplot of iBAQ protein intensities from MaxDIA against Spectronaut protein intsnsities. i, log–log scatterplot of MaxDIA iBAQ values averaged over the replicates against RPKM values from RNA-seq data. j, Same as i with protein intensities from Spectronaut.