Protocol for mapping murine transcription factor interactomes and composite motifs combining affinity purification mass spectrometry and ChIP-seq.

Mass spectrometry (MS)-based approaches have significantly advanced our ability to study protein interaction networks in an unbiased manner. Here, we present a protocol that uses affinity purification (AP)-MS to identify interaction partners of a biotinylated transcription factor of interest, isolated from primary murine T cells. The resulting interactome data are integrated with motif analyses from chromatin immunoprecipitation sequencing (ChIP-seq) experiments. This combined approach facilitates the concurrent identification of protein interactors and composite DNA motifs, with each dataset corroborating the findings of the other. For complete details on the use and execution of this protocol, please refer to Gabele et al.1.