Quantitative Chemical Proteomics Approach To Identify Post- translational Modification-Mediated Protein−Protein Interactions

ABSTRACT: Post-translational modifications (PTMs) (e.g., acetylation, methylation, and phosphorylation) play crucial roles in regulating the diverse protein−protein interactions involved in essentially every cellular process. While significant progress has been made to detect PTMs, profiling protein−protein interactions mediated by these PTMs remains a challenge. Here, we report a method that combines a photo-cross-linking strategy with stable isotope labeling in cell culture (SILAC)-based quantitative mass spectrometry to identify PTM-dependent protein−protein interactions. To develop and apply this approach, we focused on trimethylated lysine-4 at the histone H3 N-terminus (H3K4Me3), a PTM linked to actively tran-scribed gene promoters. Our approach identified proteins previously known to recognize this modification an