Fig. 4
Total proteins confidently identified and quantified within a single TMT plex. A An upset plot shows that most detected proteins were assigned abundances in all samples in experiment 1. The lower-left plot shows the number of proteins measured for each sample (row); excepting sample PPV210, all samples quantified abundance for 989 proteins. The center matrix and upper bar plot show how different samples measured the different sets of proteins. Each row represents a sample, and each column represents a set of one or more measured proteins; at the row-column coordinate, a gray node indicates this protein-set was not measured by this sample and a black node indicates this protein-set was measured; black nodes are vertically connected by intersection lines. The first column shows that 988 proteins abundances were assigned across all samples; likewise, 163 proteins were detected but were not assigned an abundance, and one protein was detected in only 9 samples (excluding PPV210). B Pairwise scatter plots of normalized protein abundance across pool 1 aliquots run in the same TMT batch in experiment 1 show samples listed in blue down the diagonal and Spearman correlations in black along the upper triangle. The axes show the normalized protein abundance; all axes are identically scaled. C Protein abundance as above, but across individual biological replicates. Plots in panels B and C show nearly perfect Spearman correlation between technical replicates and very strong correlation between biological replicates