a, KU86 IP-MS and U3 ChIRP-MS overlap. Zhou et al.33 (n = 2 independent MS assays; for each assay, n = 2 technical replicates) identified 292 proteins enriched with KU86 protein. U3 ChIRP-MS identified 483 proteins enriched more than twofold with the U3 snoRNA (Supplementary Table 1). These identified factors were intersected, resulting in 153 proteins in common between the two affinity purification strategies, which is highly significant (hypergeometric P < 6.650 × 10−166). To understand what types of protein were enriched only with KU86, only with U3, or together with both factors, we isolated the enrichment values (−log 10 (Benjamini)) for GO biological process terms for each of these sets and compared them. Factors commonly bound were biased for rRNA processing, ribosomal terms and SSU biogenesis. U3-specific factors had additional enrichment in these categories and KU86 had a set of unique terms that were not well represented in U3. b, Independent repeat of northern blot analyses of 18S rRNA maturation in v-ABL kinase-transformed B cells from noted genotypes. The probe covers the sequence just after the 18S rRNA (red line). This experiment was repeated independently four times. Another repeat is shown in Fig. 3c. c, d, MS characterization of commercial DNA-PK holoenzyme (Promega) used in EMSA and kinase reactions. A detailed description of proteins and their quality in this mixture has not been published. We subjected the DNA-PK enzyme mix as provided to SDS–PAGE separation followed by LC–MS identification of proteins from mass ranges between 65 and 600 kDa. KU70 and KU86 were clearly present in the gel and via MS. For masses above 130 kDa, DNA-PKcs was the major protein identified. For each of the five slices analysed (coloured regions) we tabulated the starting positions of peptides matching the DNA-PKcs polypeptide and mapped them to the position within DNA-PKcs. As expected, in the highest-molecular-weight slices, we identified peptides across the majority of the length of DNA-PKcs. DNA-PKcs peptides were present in lower slices, but poorer overall coverage was evident, suggesting that these are degradation products. As this was a confirmatory experiment of a validated and commercially available product (see Methods), it was conducted only once.