HeLa cells were grown in media containing either regular (light) Lys and Arg or 13C6-labelled (heavy) Lys and Arg. Light cells were transfected with miRNA, and heavy cells were mock-transfected. After 24 h some cells were harvested for mRNA expression profiling. After 48 h the remaining cells were harvested, and equal numbers from both populations were mixed and enriched for soluble nuclear proteins. Neutrophil culture was as outlined in Fig. 2a. Protein mixtures were separated by SDS-PAGE, and fractions were digested with trypsin. Peptides were analysed by liquid chromatography-tandem mass spectrometry (LC-MS/MS), which identified peptides and quantified the relative amounts of isotopic pairs of the same peptide. To prevent double-counting of any targeting interactions, peptides were mapped to a non-redundant complementary DNA data set (Supplementary Data 5), and targeting analyses were as performed previously on mRNA destabilization data7 . To compare to target-prediction algorithms, predictions by TargetScan (release 4.1)2 ,7 , PicTar (human, chimp, mouse, rat, dog)4 ,25 , miRanda (January 2008 release)23 ,24 , miRBase Targets (version 5)22 , RNA22 (ref. 28 ) and PITA26 were obtained from their respective websites, using the most recent predictions publicly available as of March 2008.