Fig. 3

Reproducibility of SWATH-MS measurements. a The CVs of peak areas for each of the 30 SIS peptides for S4 sample, depicted on the y-axis using logarithmic scaling, were determined at the intra-day level within the site (light blue—without normalization, dark blue with normalization), inter-day level within site (light green—without normalization, dark green with normalization), and inter-site level (i.e., over all S4 samples in the study; light gray—without normalization, dark gray—with normalization). The orange line indicates 20% CV for visual reference. b Similarly, the CV of protein abundances for the 4077 proteins that were detected in >80% all samples were computed at the intra-day level within the site, inter-day with site, and inter-site (i.e., all 229 samples in the study). c The inter-site CVs were binned based on log2 protein abundance to visualize the dependence of CV on protein abundance