Protein modifications regroup a repertoire of functional groups that are reversibly conjugated to a wide range of substrates under different environmental cues, and impact almost all aspects of cell homeostasis and pathogenesis. The development of affinity methods that facilitate the enrichment of modified residues has been essential to determine how protein modifications are affected upon cell perturbation. When combined with quantitative proteomics, affinity chromatography enables the temporal profiling of protein modifications and can be used to determine crosstalk taking place between modifications. For example, important interplay exists between ubiquitin-like modifiers (ULMs) such as the SUMOylation of proteasome subunits that is required for the recruitment to PML nuclear bodies and the co-regulation of SUMOylation and ubiquitylation that modulate deubiquitinase activities. Here, we present different strategies to profile protein modifications such as acetylation, phosphorylation and ULMs and highlight their analytical merits in the context of protein degradation and cell senescence.