Phosphoproteomic Effects of Acute Depletion of PP2A Regulatory Subunit Cdc55

Protein phosphatase regulatory subunits are increasingly recognized as promising drug targets. In the absence of an existing drug, inducible degradation provides a means of predicting candidate targets. Here auxin-inducible degradation of Saccharomyces cerevisiae PP2A regulatory subunit Cdc55 in combination with quantitative phosphoproteomics is employed. A prevalence of hyperphosphorylated phosphopeptides indicates that the approach successfully identified direct PP2A^Cdc55 targets. PRM follow up of data-dependent acquisition results confirmed that vacuolar amino acid transporters are among the proteins most strongly affected by Cdc55 depletion.