Enrichment strategies such as affinity purification can be coupled to qualitative and quantitative mass spectrometry workflows to examine a subset of proteins in complex samples. Affinity enrichment makes use of specific binding interactions between molecules to isolate proteins of interest. In this approach, affinity purification mass spectrometry can be used to examine specific protein-protein interactions within protein complexes or to look at protein complexes more globally at the interactome level using the proximity biotinylation approach. By coupling affinity purification to quantitative MS, interactions can be studied under different conditions thereby providing much more dynamic view of protein-protein interactions. Furthermore, this workflow is amenable for PTM analysis which makes it possible to examine the role post-translational modifications (PTMs) play in facilitating protein-protein interactions.