Raw MS files were analyzed by MaxQuant software version 1.5.3.33 or 1.6.0.17 (TMT 11-plex phosphoproteomics) using the Andromeda search engine (77, 78) by which the precursor MS signal intensities were determined and SILAC triplets were automatically quantified. Proteins were identified by searching the higher-energy collisional dissociation (HCD)–MS/MS peak lists against a target/decoy version of the human UniProt protein database (release 2015_03 or release April 2017 for TMT 11-plex phosphoproteomics) using default settings. TMT correction factors were edited for the TMT labels, and the reporter ion mass accuracy was set to 0.002 Da. Carbamidomethylation of cysteine was specified as fixed modification, and protein N-terminal acetylation, oxidation of methionine, pyro-glutamate formation from glutamine, and phosphorylation of serine, threonine, and tyrosine residues were considered as variable modifications. The “maximum peptide mass” was set to 7500 Da, and the “modified peptide minimum score” and “modified maximum peptide score” were set to 25. Everything else was set to default values.

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