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. We here employed auxin-inducible degradation of S. cerevisiae PP2A regulatory subunit Cdc55 in combination with quantitative phosphoproteomics. A prevalence of hyperphosphorylated phosphopeptides and enrichment of proteins containing the PP2A consensus sequence indicates that the approach successfully identified direct PP2A-Cdc55 targets. PRM follow up of DDA-results confirmed that vacuolar amino acid transporters are among the proteins most strongly affected by Cdc55 depletion.