Photo-cross-linking mass spectrometry for single amino acid assignment of RNA-binding sites in RNA-binding proteins

Mass spectrometry data of peptide–RNA cross-links derived from complex biological systems. Yeast (pre-)mRNPs were isolated by TAP tag purification of Cbp20; human protein–RNA complexes were assembled on an aptamer tagged pre-mRNA. Isolated complexes were UV irradiated. For each of the aforementioned experiments, a non-irradiated control was prepared. Yeast RBPs cross-linked in vivo after labeling with 4-thio-uridine (4SU) were isolated with oligo d(T). All samples were enriched for cross-linked heteroconjugates prior to LC-MS analysis.