Fig. 6

Assessment of protein normalization across plexes. A Each boxplot represents the distribution of Z-score normalized expression intensity for all proteins in a sample (see “Methods” for details on how abundances were normalized across plexes). The normalization shows some sample-to-sample variability but produces consistent distributions across all samples across all four plexes, showing no obvious plex bias. B In addition to the bridge-channel pool aliquot, each of the four plexes in experiment 2 contained an aliquot of the pooled control samples (pool 1) from experiment 1 as a technical replicate. The pairwise scatter plots of normalized protein intensity across pool 1 aliquots and their corresponding Spearman correlations show excellent correlation across plexes