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 system-level study of previously inaccessible chromatin and genome regulators. [Display omitted] •Quantification of global protein levels across different chromatin compartments•Protein levels correspond to functional differences in euchromatin versus heterochromatin•Method used to interrogate system-wide effects of BET degradation compounds Proteins that bind DNA and regulate the expression of genes are difficult to measure accurately. In this study, we present a method that quantifies these proteins with high coverage and in high throughput, providing a system-wide view of protein dynamics on chromatin.