biostudies-literature00460Scheibe MNCI NIH HHS9897-902https://www.ebi.ac.uk/biostudies/studies/S-EPMC3479200biostudies-literatureUnknown40(19)Systematic analysis of the RNA-protein interactome requires robust and scalable methods. We here show the combination of two completely orthogonal, generic techniques to identify RNA-protein interactions: PAR-CLIP reveals a collection of RNAs bound to a protein whereas SILAC-based RNA pull-downs identify a group of proteins bound to an RNA. We investigated binding sites for five different proteins (IGF2BP1-3, QKI and PUM2) exhibiting different binding patterns. We report near perfect agreement between the two approaches. Nevertheless, they are non-redundant, and ideally complement each other to map the RNA-protein interaction network.Nucleic acids researchQuantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions.PMC34792001RC1CA145442Tuschl THafner MScheibe MButter FMann M46falseQuantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions.Systematic analysis of the RNA-protein interactome requires robust and scalable methods. We here show the combination of two completely orthogonal, generic techniques to identify RNA-protein interactions: PAR-CLIP reveals a collection of RNAs bound to a protein whereas SILAC-based RNA pull-downs identify a group of proteins bound to an RNA. We investigated binding sites for five different proteins (IGF2BP1-3, QKI and PUM2) exhibiting different binding patterns. We report near perfect agreement between the two approaches. Nevertheless, they are non-redundant, and ideally complement each other to map the RNA-protein interaction network.2012-01-01T00:00:00Z2012 Oct2024-11-07T14:18:08.026Z2019-03-27T00:59:25ZS-EPMC34792002288530410.1093/nar/gks746