All mass spectra were analyzed with MaxQuant software version 1.3.0 (ref. 20 (link)). using a human UniProt database. MS/MS searches for the proteome data sets were performed with the following parameters: Oxidation of methionine and protein N-terminal acetylation as variable modifications; carbamidomethylation as fixed modification. For PTM data sets additional variable modifications were searched: Phosphorylation of serine, threonine and tyrosine residues for IMAC enriched samples; diglycine modification of lysine residues for K(GG) enriched samples; and epsilon-acetylated lysine for K(Ac) enriched samples. To study co-occurrence of different PTMs on the same peptides, phosphorylation, di-glycine modification and acetylation were searched simultaneously in a separate MS/MS search. Trypsin/P was selected as the digestion enzyme, and a maximum of 3 labeled amino acids and 2 missed cleavages per peptide were allowed. The mass tolerance for precursor ions was set to 20 p.p.m. for the first search (used for nonlinear mass re-calibration) and 6 p.p.m. for the main search. Fragment ion mass tolerance was set to 20 p.p.m. For identification we applied a maximum FDR of 1% separately on protein, peptide and PTM-site level. We required 2 or more unique/razor peptides for protein identification and a ratio count of 2 or more for protein quantification per replicate measurement. PTM-sites were considered to be fully localized when they were measured with a localization probability >0.75 in each of the three replicates. To assign regulated proteins and PTM-sites we used the Limma package in the R environment to calculate moderated t-test P values corrected by the Benjamini Hochberg method, as described previously14 (link).