We performed immunoprecipitation followed by LC-MS/MS (IP-MS) in mouse embryonic stem cells in which endogenous RLF, ZFP292 or ZFP654 was tagged with FLAG. This approach enabled the identification of proteins associated with RLF/ZFP292/ZFP654. The dataset provides a resource to investigate the composition of RLF/ZFP292.ZFP654-associated chromatin regulatory complexes.