Fig. 4: Interactome analysis of asciminib using protein-directed AfBPP.

a, Workflow for protein-level directed AfBPP. b–d, Probe–probe AfBPP comparison of K562 cells treated for 1 h with 4b (10 μM) versus 5b (10 μM) (b), 4b (10 μM) versus 5c (100 μM) (c) and 5b (10 μM) versus 5c (100 μM) (d). The 5c probe was screened at a higher concentration to match general protein labelling. Volcano plots display comparisons between enriched proteins from three groups with red representing 4b-labelled proteins, darker blue representing 5b-labelled proteins and lighter blue representing 5c-labelled proteins (n = 3 biological replicates for each group per experiment). Black coloured dots represent labelled kinases. e, Kinome tree annotation⁷⁸ for data in b. f, Heatmaps of high-value targets in b and in K562 cells labelled with 5b (10 μM), 5c (1, 10 and 20 μM), or 3 (4 μM) in a UV-dependent manner (1 h) or in a competitive manner with asciminib pretreatment (50 μM, 0.5 h) followed by 0.5-h-probe treatment. g, Overlap of proteins significantly enriched in a UV-dependent manner for 5b (10 μM) and 5c (100 μM) in K562 cells. h, Heatmap of BCR and ABL1 in KCL-22 cells labelled with 4b (100 μM, 1 h) and 5b (10 μM, 1 h) in a UV-dependent or in competitive manner with asciminib pretreatment (50 μM, 0.5 h). i,j, GO Cellular Component analysis for enriched proteins in b captured by 4b (i) and 5b in (j). Significance was calculated with Fisher’s exact test, and adjusted P values were derived using the Benjamini–Hochberg method. For probe–probe analyses in b–d and f and the UV-dependent labelling experiment in f, significant proteins were defined as log₂(FC) >1.0 and P < 0.05 determined from two-tailed unpaired Student’s t-tests. For competitive analysis in f, significant proteins were defined as log₂(FC) >0.5 and P < 0.05. Comp., competition; NS, not significant; ND, not detected; FC, fold change. All MS data can be found in Supplementary Table 6.