Analysis of Protein Cysteine Acylation Using a Modified Suspension Trap (Acyl-Trap)

Proteins undergo reversible S -acylation via a thioester linkage in vivo. S -palmitoylation, modification by C16:0 fatty acid, is a common S -acylation that mediates critical protein-membrane and protein-protein interactions. The most widely used S -acylation assays, including acyl-biotin exchange and acyl resin-assisted capture, utilize blocking of free Cys thiols, hydroxylamine-dependent cleavage of the thioester and subsequent labeling of nascent thiol. These assays generally require >500 micrograms of protein input material per sample and numerous reagent removal and washing steps, making them laborious and ill-suited for high throughput and low input applications. To overcome these limitations, we devised Acyl-Trap, a suspension trap-based assay that utilizes a thiol-reactive quartz to enable buffer exchange and hydroxylamine-mediated S -acyl enrichment. We show that the method is compatible with protein-level detection of S -acylated proteins (e.g. H-Ras) as well as S -acyl site identification and quantification using on-trap isobaric labeling and LC-MS/MS from as little as 20 micrograms of protein input. In mouse brain, Acyl-Trap identified 279 reported sites of S -acylation and 1298 previously unreported putative sites. Also described are conditions for long-term hydroxylamine storage, which streamlines the assay. More generally, Acyl-Trap serves as a proof-of-concept for PTM-tailored suspension traps suitable for both traditional protein detection and chemoproteomic workflows.