Fig. 1: Establishing the SEE-CITE interaction site mapping platform using scout SEE-CITE probes.
From: Small-molecule binding-site discovery using silyl ether-enabled chemoproteomics
a, Overview of the SEE-CITE chemoproteomics workflow. b, Structures of minimalist compound 1 and first-generation scout probes 2a–2d. c, Gel-based AfBPP analysis of K562 cells treated with the indicated probes (20 μM, 1 h). Representative data are presented for n = 2 independent experiments. d, Coverage comparison of SEE-CITE-modified PSMs identified for K562 cells labelled with 2a (20 μM, 1 h) versus 2b (20 μM, 1 h) (from left to right, P = 0.003476, 0.039729 and 0.000908). Data are the mean ± standard deviation (s.d.) calculated from n = 3 biological replicates. Statistical significance was calculated with a two-tailed unpaired Student’s t-test with *P < 0.05, **P < 0.01,***P < 0.001, and NS (not significant) P > 0.05. e, Distribution of identified M2-modified amino acids for 2a-labelled samples from d (140-min gradient). Data are presented as mean values ± s.d. f, Protein-directed AfBPP analysis of K562 cells treated with 2a (20 μM, 1 h) in a UV-dependent manner. The volcano plot displays a comparison between enriched proteins for ±UV-treated groups (n = 3 biological replicates for each group). Significant proteins were defined as log2(fold change) >1.0 and P < 0.05, determined from two-tailed unpaired Student’s t-tests. g, Overlapping SEE-CITE-labelled peptides by 2a from d (140-min gradient) with protein-directed AfBPP from f. h,i, Protein classes of the enriched (h) versus non-enriched (i) proteins in ‘F’ with or without SEE-CITE-labelled peptides from d. All MS data can be found in Supplementary Table 2.
