Resulting RAW files were analyzed in Proteome Discover™ 2.4 (Thermo Fisher Scientific, RRID: SCR_014477) with a mus musculus UniProt FASTA plus common contaminants. Quantification methods utilized isotopic impurity levels available from Thermo Fisher Scientific. SEQUEST HT searches were conducted with a maximum number of 3 missed cleavages; precursor mass tolerance of 10 ppm; and a fragment mass tolerance of 0.02 Da. Static modifications used for the search were, 1) carbamidomethylation on cysteine (C) residues; 2) TMTpro label on lysine (K) residues and the N-termini of peptides. Dynamic modifications used for the search were oxidation of methionines and acetylation of N-termini. Percolator False Discovery Rate was set to a strict setting of 0.01 and a relaxed setting of 0.05. IMP-ptm-RS node was used for all modification site localization scores. For SPS-MS3 quantification, SEQUEST HT searches were conducted with a maximum number of 3 missed cleavages; precursor mass tolerance of 10 ppm; and a fragment mass tolerance of 0.5 Da, and MS3 FTMS reporter ion tolerance of 20 ppm. Values from both unique and razor peptides were used for quantification. In the
