Mass spectrometric identification of RNA binding proteins from dried EMSA gels

Electrophoretic mobility shift assays (EMSA) are commonly employed for the analysis of nucleic acid/ protein interactions with a native gel system. Here, we report a method to identify RNA binding proteins from a dried EMSA gel by mass spectrometry following autoradiography. Compared to wet gel exposure, our approach resulted in an improved protein identification sensitivity and RNA/protein complex isolation accuracy. The method described here is useful for the large scale characterization of RNA- or DNA-protein complexes.