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.