Protocol to study direct (de)phosphorylation events on a proteome-wide scale using on-bead in vitro enzyme assays

Protein phosphorylation regulates essential cellular processes, yet probing kinase and phosphatase activities in native contexts remains challenging. Here, we present a protocol to study direct (de)phosphorylation events on a proteome-wide scale using on-bead in vitro kinase and phosphatase assays (OBIKA/OBIPhA). We describe steps for employing active enzyme complexes and identifying direct substrates and regulated phosphosites using mass spectrometry. Compared to traditional in vitro approaches, this protocol operates under native conditions to preserve protein interactions and modifications in eukaryotic cell systems. For complete details on the use and execution of this protocol, please refer to Brunner et al.¹ and Hu et al.².