Unbiased characterization and systematic profiling of metabolically labeled RNA-binding sites

Here we introduce pRBS-ID, an amenable platform that enables robust profiling of PAR-crosslinked RBSs. Using tandem mass spectrometry (MS/MS) approaches, we unbiasedly characterize the PAR adducts on peptides, to develop an optimal MS/MS search pipeline that enables robust identification and quantification. Using pRBS-ID, we systematically profile RBSs crosslinked to U or G in PAR-labeled mRNA, which can serve as a rich resource for studying RNA-protein interactions. Especially, pRBS-ID is widely applicable to studies on time-course RNP remodelling, host-virus interactions, and RNP structure prediction.