Ratio lists for two representative phosphopeptides from the ratio matrix.

Phosphorylation level of each phosphopeptide is represented in a list of ratios. We used the peptide ratios provided by the MaxQuant output, which have been normalized for each LC-MS/MS run [30]. The significance B values provided by MaxQuant are not shown here. For the cluster analysis, if a phosphopeptide is detected multiple times under the same KD-versus-WT condition, the median of all its ratios are taken. S(ph) or T(ph) indicates that the specific amino acid, serine or threonine, is phosphorylated, respectively.