Highly parallel quantification and compartment localization of transcription factors and nuclear proteins

Transcription factors and other chromatin-associated proteins are difficult to quantify comprehensively. Here we combine facile nuclear sub-fractionation with data-independent acquisition mass spectrometry to achieve rapid, sensitive, and highly-parallel quantification of the nuclear proteome in human cells. We apply this approach to quantify the response to acute degradation of BET bromodomains, revealing unexpected chromatin regulatory dynamics. The method is simple and enables systems-level study of previously inaccessible chromatin and genome regulators. Overall design: Epigenomic characterization of K562 BET domains by CUT&RUN