Extended Data Fig. 9: CsoDIAq results as a function of the chosen library.

(A-B) Peptide length distributions for (A) the original DI-SPA library and (B) a library generated using the original DI-SPA library targets and decoys generated by CHIMERYS. (C) Boxplot visualizing the number of peptide groups identified by CsoDIAq at 1% run-specific FDR in each sample using different libraries (individual boxplots), including the ones shown in (A) and (B) (first and last, respectively, see also Supplementary Methods). The bottom (lower hinge), center and top of the box (upper hinge) are the first, second (median) and third quartile of the data points. The upper whisker extends from the hinge to the largest value no further than 1.5 * IQR from the hinge (IQR is the inter-quartile range, that is the distance between the first and third quartiles). The lower whisker extends from the hinge to the smallest value at most 1.5 * IQR of the hinge. All individual data points are shown (n = 88 raw files).