Fig. 4: Correlation of surface with total abundance during differentiation.

a Comparison of the surface pool against the total protein pool. Peptides analyzed by autoCSC (blue) are surface exposed and thus specifically report on the acute surface pool. Tryptic peptides from the same samples (orange) report the total protein abundance including both intracellular and surface-localized proteins. b Correlation of surface and total abundance protein pools. Spearman’s rho of surface and total abundance time series, median indicated with dashed line. c Boxplots of distribution of Spearman’s rho for log2 fold-changes between indicated time intervals for surface and total protein. Boxes indicate median and percentiles (25th and 75th). d Bar chart of counts of overlapping significantly different proteins (fold-change > 1.5 and p < 0.05) for comparisons between surface and total pools with respect to interval times. e–i Impulse model fit for data for e Sv2a, f Sv2b, g Slc6a17, h GGt7, and i Nptxr. Crosses indicate the normalized median abundance values of three replicates for each time point for surface (blue) and total (red) pools. Lines indicate impulse model fits; gray lines are fits to combined data from surface and total pool analyses. Source data are provided as a Source Data file.