A composition of proteasome complexes in WT yeast, and the changes these complexes undergo upon the deletion of Pre9 (Δα3) or of Sem1 (ΔSem1) based on whole-cell proteomic analysis and to activity-guided proteasome profiling of indicates that the amounts of proteasomal proteins and proteasome interacting proteins in the assembled active proteasomes differ significantly from their total amounts in the cell as a whole. This data set is of the activity-guided profiling of the proteasome LFQ analysis.