Extended Data Fig. 4: Integrated protein- and cysteine-directed.
From: Multi-tiered chemical proteomic maps of tryptoline acrylamide–protein interactions in cancer cells
a, Workflow for cysteine-directed ABPP experiments where stereoprobe reactivity with cysteines is determined by multiplexed (tandem mass tagging, TMT10plex) MS-based proteomics, as described previously22. The workflow was created with BioRender.com. b, Number of proteins stereoselectively liganded by one (single; black) versus multiple (red) stereoprobe core configurations. c, Proportion of stereoselectively liganded proteins showing essentiality in the Cancer Dependency Map. d, Heatmap of quantified cysteines in PRKDC showing two cysteines (C1229 and C1499/C1507) displaying distinct stereoselective liganding profiles in cysteine-directed ABPP experiments in Ramos cells. e, Protein-directed ABPP data showing lack of enantioselective enrichment for PRKDC. f, Protein-directed ABPP data showing stereoselective enrichment of PIKFYVE by alkyne WX-03-338 in 22Rv1 cells and blockade of this enrichment by WX-03-57. g, Violin plot showing native-vs-denatured reactivity ratios for cysteine-containing tryptic peptides from stereoselectively liganded proteins with good predicted proteotypicity (DeepMS probability > 0.5) that were either quantified or not quantified in cysteine-directed ABPP experiments performed in native cell proteomes. n = 3 biological replicate/cell line; unpaired two-tailed t-test, ****P < 0.0001. h, Protein-directed ABPP data showing stereoselective enrichment of FXR1 by WX-03-346 without blockade of this enrichment by WX-03-57. i, Cysteine-directed ABPP data showing greater stereoselective liganding of FXR1_C157 by WX-03-346 (left) versus WX-03-57 (right). j, Pie chart showing fraction of proteins liganded in a stereoselective (blue) or non-stereoselective (green) manner in protein-directed ABPP experiments. For e, f, h, and i, data represent mean values ± s.d. of n = 4 biological replicates.
