Peptides from all samples were eluted from C18 StageTips using 40% ACN and 0.5% acetic acid. Peptides were analyzed using online nanoflow LC-MS/MS on a Q Exactive Plus (interactome and phosphoproteome), a Q Exactive HF (phosphotyrosine interactome and proteome), or a Q Exactive HF-X (TMT 11-plex phosphoproteomics) mass spectrometer (Thermo Fisher Scientific), which was interfaced with an EASY-nLC system (Proxeon, Odense, Denmark) equipped with a nanoelectrospray ion source essentially as described (76).

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