pChem: a modification-centric assessment tool for the performance of chemoproteomic probes

We report a modification-centric, blind-search tool termed pChem to provide a streamlined pipeline for unbiased assessing of the performance of chemoproteomic probes. The pipeline starts with an experimental setting for isotopically coding probe-derived modifications that can be automatically recognized, accurately calculated and precisely localized by pChem with neither prior knowledge nor manual inspection. Further, pChem exports on-demand reports by scoring the profiling efficiency, modification-homogeneity and proteome-wide residue selectivity of a tested probe. The performance and robustness of pChem were benchmarked by applying it to various bioorthogonal probes, including 15 activity-based protein profiling (ABPP) probes and 3 metabolic labeling probes. Together, pChem is a user-friendly computational tool for probe developers, even those with no experience in informatics, and aims to facilitate the development and optimization of probes for the ever-growing field of chemoproteomics.