Vacuoles were isolated from wild-type and vps35Δ S. cerevisiae cells grown to stationary phase. Peptides were digested using Preomics iST kit, analyzed by Bruker timsTOF Pro in DDA-PASEF mode. Data were searched against UniProt yeast database using PEAKS Studio X (1% FDR). This dataset was used to identify retromer cargoes accumulating in vps35Δ vacuoles.