a-b Heat map of Pearson correlation coefficients showing reproducibility between phosphoproteomes of mouse livers stimulated with insulin or PBS (‘Fasted’) for a four ‘early’ and b seven ‘intermediate’ time points. c-d PCA of insulin stimulated mouse liver. e Summary of quantified unique phosphoproteins, phosphopeptides and phosphorylation sites (Class 1) from the complete liver insulin time-series study. f Overlap between the phosphorylation sites quantified in this study, and the combined data from 9 mouse tissues from a large tissue-specific phosphorylation atlas (Huttlin et al., 2010). Data were kindly provided by the authors, and analyzed using MaxQuant using identical settings to enable likewise comparison. g Quantification coverage of unique phosphopeptide species (singly, doubly or greater phosphopeptides) containing only localized (Class 1) phosphosites. Inner circle denotes phosphopeptides quantified in ≥ 3 biological replicates across all insulin stimulated time points for the respective study, and average quantification coverage is shown for this core phosphoproteome (77% and 85% respectively). h Distribution of phosphosite localization probabilities for all phosphosites in the liver time series study, and for Class 1 sites the proportion of phosphoserine (pS), phosphothreonine (pT) and phosphotyrosine (pY) sites. i Dynamic range of MS-signals of phosphopeptides from the liver insulin time-series study span 7 orders of magnitude. Enrichment of protein GO terms (biological process and cellular component) in each intensity abundance range was assessed by Fisher’s exact test (Benjamini-Hochberg FDR < 0.02). The position of GO terms along the horizontal axis represents enrichment of these terms within the respective abundance quartile.