The application of mass spectrometry for the analysis of protein complexes can be used in parallel with chromatin immunoprecipitation–sequencing experiments to provide information on both the cistrome and interactome for a given protein. Hisham Mohammed and colleagues developed the Rapid Immunoprecipitation Mass spectrometry of Endogenous protein (RIME) approach, a rapid and robust method to study chromatin and transcription factor complexes. The method relies on the stabilization of protein complexes by formaldehyde fixation and the preparation of the chromatin samples using the Bioruptor®. The method can be used for the affinity purification of endogenous protein complexes and is enough sensitive for identifying the high affinity and transient interactions of complexes composed of low-abundance proteins.
Method published in Nature protocol