Fig. 2: ProtacID tool development.

a ProtacID treatment timeline. See “Methods” for details. Created in BioRender. Duan, S. (2025) https://BioRender.com/8lrbx5r. b Schematic diagrams of the canonical (cBAF), polybromo-associated (PBAF), and non-canonical (ncBAF) BAF complex variants. Components specific to each BAF variant are color-coded as in panel d. Created in BioRender. Duan, S. (2025) https://BioRender.com/7p89ex4. c FmT-VHL proteins form a ternary complex with ACBI1 and SMARCA4. MLN4924 and increasing doses of ACBI1 (0, 10, 100, 1000 nM) were applied to 293 Flp-In cells expressing the indicated FmT-tagged VHL proteins. After biotin treatment, cells were lysed, and biotinylated proteins were isolated using streptavidin-sepharose. Isolated proteins (PD, pulldown) or whole cell lysates (input) were subjected to western blotting with the indicated antibodies. IB immunoblot. n = 3 biological replicates. d FmT-VHL tool testing. ProtacID was conducted on 293 Flp-In cells expressing the indicated FmT-tagged VHL protein variants, and treated with either DMSO (−) or 200 nM ACBI1 (+). The Dot Plot depicts proteins identified by ProtacID, where dot size indicates relative peptide abundance across experiments, dot shade indicates average peptide counts, and dot border indicates protein identification confidence level. Standard BioID (right) was also conducted in 293 Flp-In cells expressing FmT-SMARCA2 or FmT-SMARCA4. PROTAC neo-substrates are indicated by arrowheads (right). Proteins grouped according to the BAF variant. See “Methods” for a description of SAINTexpress statistical analysis, which provides a Bayesian false discovery rate (BFDR) for all mass spectrometry data. Source data are provided as a Source data file.