Extended Data Fig. 8: Characterization of TME binders in the PD and healthy control lymphoblast datasets.

a, TME binders in Fig. 4a and 4b were not heavily enriched in functional cysteines, indicating TME displayed a completely distinct reactivity towards cellular cysteines compared to the IA alkyne probe. On top of each bar shows the fold enrichment, followed by the significance level. b, TME binders in Fig. 4a and b were enriched in intracellular proteins (for example, nucleus, cytoplasm, ER). On top of each bar shows the fold enrichment, followed by the significance level. P value was calculated by Fisher’s Exact Test; ‘ns’, no significance; *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001. c-d, Enrichment analysis of TME binders in Fig. 4a (c) and 4b (d). “Healthy binders” refer to TME binders in the healthy control group and “PD binders” refer to TME binders in the PD group. P value was calculated by Fisher’s Exact Test, and further adjusted by Benjamini-Hochberg procedure as the multi-test adjustment method. e-g, IUPred2, ANCHOR2, degree and betweenness value of TME binders in Fig. 4a and b were significantly higher than the proteome average. Data show n = 20383 for Proteome, 438 for Healthy, and 464 for PD; P value was calculated using the unpaired two-sample two-sided Wilcoxon test; ‘ns’, no significance; ****, P < 0.0001. The boxplot displays five key elements: the median, shown as the white circle at the center; the upper hinge, representing the third quartile (75th percentile); and the lower hinge, representing the first quartile (25th percentile). The upper whisker extends to the largest value within 1.5 * IQR (interquartile range) from the upper hinge, while the lower whisker extends to the smallest value within 1.5 * IQR from the lower hinge. h, Parallel comparison of scree plots of lysate profiling using cell lysate (left) and protein disorder profiling using RUBICON (right).