Proteomic data from different mouse models were performed using MaxQuant v1.6. with the Andromeda search algorithm embedded. Default settings were used such that proteins detected with only one peptide and as a posttranslational modification (site) only were excluded. Peptide spectrum match, protein, and peptide false discovery rate (FDR) were adjusted to <0.01, and a target decoy approach was used against the rat UniProt database (reference proteome) downloaded in January 2017. Match between run option was enabled. Intensity-based quantification (iBAQ) was performed as previously described (15). Protein intensities concatenated by the MaxQuant algorithm were quantitatively analyzed using the MaxLFQ algorithm, an algorithm aligning peaks and performing accurate quantification. Phosphopeptide site localization probability was set to be larger than 0.8. Phosphorylation motifs were annotated on the basis of the phosphosite plus (40) dataset downloaded in January 2018, and Fisher’s exact test was performed for enrichment (FDR value cutoff was smaller than 0.01). Motifs were generated using the iceLogo (41) algorithm using rat UniProt database as a reference set.

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