Fig. 5

Distribution of identified proteins across all samples and plexes. These two upset plots show that in experiment 2, 1157 distinct proteins were assigned an abundance, but not all proteins were measured in all samples. The two plots represent the same data from different perspectives: the upper plot orders samples by plex, and the lower plot by phenotype. (See Fig. 3 for more details on interpreting the upset figure.) The first column (purple) of the top-most bar plot shows that 727 proteins were measured consistently across all samples. The next 14 columns (black) illustrate inter-plex dropout, where a protein was consistently measured for all samples within one or more plexes but was wholly absent in other plexes. Inter-plex dropout accounted for 390 proteins overall. The remaining 40 columns show intra-plex dropout (gray diamonds), where a protein is not consistently measured within a single plex. In this dataset, intra-plex dropout accounts for 40 proteins. As depicted in the left plot, the number of measured proteins for a given sample correlated strongly with the TMT plex; on average each sample measured 946 proteins, with individual counts ranging from 886 to 984. The horizontal green bands in the upper intersection matrix mark the divisions between plexes. The vertical cyan lines highlight 151 proteins measured by a single plex. In the bottom matrix, the cyan horizontal band across the intersection matrix marks the divide between pooled and individual samples. The intersection lines connecting the nodes indicate the majority of proteins measured in the individual samples were also measured in the pool aliquots and also that all proteins measured by at least one control sample were also measured by at least one PDR sample