Fig. 3

Differential proteome as a reliability indicator. A Venn diagram of proteins identified in the Quartet samples. B Heatmap of differentially expressed proteins. Cluster analysis was performed using Z-score-transformed protein intensities for the proteins with expression level fold-change > 2. Red indicates a high expression level and blue indicates a low expression level. C Occurrence frequency of differentially expressed proteins (DEPs), according to the pairwise comparisons between samples of the Quartet, over 24 experiments with three technical replicates each using a single-shot strategy. Left panel: number of DEPs in different partition intervals for each pairwise comparison. Red and blue indicate upregulation and downregulation directions of DEPs within a comparison, respectively, such as D5 versus D6, with D6 as the reference group. Right panel: numeric table corresponding to the distribution map in the left panel. IDF: identification frequency. D Heatmap of 15 DEPs with a consistent upregulation/downregulation trend across all 24 experiments. E Proteins with highly sample-specific expression in the Quartet