Emerging evidence has shown that RNA-binding proteins (RBPs) dynamically regulate all aspects of RNA in cells and involve in major biological processes of RNA, including splicing, modification, transport, transcription and degradation. RBPs, as powerful and versatile regulatory molecule, are essential to maintain cellular homeostasis. Perturbation of RNA-pro- tein interactions and aberration of RBPs function is associated with diverse diseases, such as cancer, autoimmune disease, and neurological disorders. Therefore, it is crucial to systematically investigate the RNA-binding proteome for understanding inter- actions of RNA with proteins. Thanks to the development of the mass spectrometry, a variety of proteome-wide methods have been explored to define comprehensively RNA-protein interactions in recent years and thereby contributed to speeding up the study of RNA biology. In this review, we systematically described these methods and summarized the advantages and disadvan- tages of each method.