Depending on the mode of normalization, RIC captures different aspects of the protein–RNA interaction landscape. Normalization to a non-crosslinked control yields a quantitative snapshot of the partial proteome that an average RNA molecule interacts with (left). Here, enrichment values represent occupancy of a given RBP on RNA. In contrast, normalization to protein abundances will yield the relative enrichment of RBPs in the interactome compared to statistical expectation, thus providing an estimate of the fraction of an RBP that is associated with poly(A)+ RNA (right). Here, enrichment values represent in vivo poly(A)+ RNA-binding activity of a given RBP. The numbers represent an idealized case for the purpose of illustration.
