End-to-end Throughput Chemical Proteomics for Photoaffinity Labeling Target Engagement and Deconvolution

Photoaffinity labeling (PAL) methodologies have proven to be a critical tool for the unbiased deconvolution of protein-ligand binding events in complex biological systems. However, like other chemical proteomic workflows, it is limited by time-intensive sample manipulations and data acquisition techniques. Here, we describe an approach to address this challenge through the innovation of a carboxylate bead-based protein cleanup procedure to isolate protein and coupling it to plate-based, proteomic sample processing as a semi-automated solution. Combining this with label-free, data-independent acquisition (DIA) sample analysis led to improvements on a workflow time per sample basis over current standard practices. This unified strategy for processing and analyzing these complex samples could greatly facilitate drug discovery efforts and open new opportunities in chemical proteomics.