HeLa cells were incubated with affinity-based probes, synthetic analogs of endogenous metabolites: putrescine, spermidine, and spermine. Cells were photoirradiated briefly and proteins were extracted, digested with trypsin, and the resulting peptides were labeled with TMT. Proteins were quantified across conditions to assess the effect of polyamine analogs on total protein levels in cells. This dataset is related to dataset PXD058706 (HeLa cell protein interactome of polyamine affinity-based probes).