Hence, focusing only on the mononucleotide species in the spectra of Figure , revealed that crosslinking in the FOXRBE involved almost uniquely U1, G2 and G6 (Fig. ). The numbers of cross-links were in a similar range for the three nucleotides, although numbers of cross-links cannot be confidently compared between different experiments using the current CLIR-MS protocols. Analysis of cross-link products comprising the oligonucleotides in light of the data of the mononucleotides, revealed that the olgonucleotide species shown in Figure with few exceptions derived from crosslinking with only one of these three nucleotides (to U1, G2 or G6). For example, when A4 is labeled, no mononucleotide are detected but small amounts of the tetranucleotides U1G2C3A4 and A4U5G6U7 are found cross-linked to F126 and F160, respectively (Fig. ). This results from U1/G2 and G6 crosslinking to F126 and F160, respectively. The cross-linking of G2 and G6 was consistent with published CLIP data (Fig. ). Although cross-linking from U1 was detected in the CLIR-MS experiments, cross-linking was hardly observed to U5 (vide infra) or U7, consistent with the hypothesis that strict structural parameters govern the photo-induced reactions between FOXRRM and FOXRBE. Very small numbers of isolated cross-links were also observed in some of the spectra of Figure . Although low numbers of cross-links must be considered with caution, their locations suggested that in several cases they were not artifacts. In particular, the cross-links at F160 seen with *UGCAUGU and U*GCAUGU (Fig. Sites of cross-linking at the protein appear clearly centred at two phenylalanines (F126 and F160), with a distribution of 1-3 amino acids flanking these sites (Götze et al. submitted). This was confirmed from study of the MS2 spectra in which fragment ions present localise the RNA adducts unambiguously on the peptide backbone (Fig. ). Exchange of G2 or G6 for A2 or A6 greatly reduced overall cross linking of the mutated sites to the amino-acid clusters 126 and 160, respectively (Fig. ). The cross-links of U1, G2 and G6 aligned well with the NMR structure of FOXRRM bound to FOXRBE (Fig. ) (PDB ID: 2ERR). The largest number of spectra corresponded to U1 reacting with P125 and F126 and to a lesser extent with I124 and R127 (Fig. ). Similarly, G2 cross-linked to P125, I124, F126 and R127. U1 and G2 each stack on one face of F126. Hydrogen-bonds also occur between the bases of U1 and G2, and between R127 and I124, respectively. G6 reacted with F160, to which it also stacks, as well as with neighbouring amino acids at positions 158-164. F158 contacts the ribose of G6. Notably, several close RNA-protein contacts visible in the NMR structure, such as C3 interacting with F126 (but not stacking), G6 stacking with R194 and U5 stacking to H120 , did not produce extensive cross-linking.