We synthesized the seven C-labelled isotopic versions of FOXRBE and confirmed the correct incorporation of the label by liquid-chromatography mass spectrometry (LC-MS) (Fig. ). We incubated each version of FOXRBE with FOXRRM and performed the CLIR-MS protocol. Mass analysis identified short oligonucleotide fragments cross-linked to peptides in clusters close to F126 and F160 (Fig. ).Each oligonucleotide signal in the spectrum of Figure was detected because it contained a C-labelled ribose. However, other than for mononucleotides, the actual site of cross-linking in the fragment could not be called; for example, the tetranucleotide fragment containing A, C, G and U might have cross-linked at any of the four bases (A, G, C, U). We noted that all (>99%) of the fragments contained at least one uridine or guanosine, consistent with literature reports that uracil and guanine mainly participate in cross-linking. Here, the use of alkaline hydrolysis for RNA digestion proved advantageous, since it caused a larger fraction of the RNA to be fully fragmented to mononucleotides (Fig. ), thereby facilitating unambiguous assignment of cross-linking sites.