Mass spectrometry is often used to identify protein-protein interaction partner. This technique is named affinity-purification mass spectrometry, or AP-MS. To be successful, this technique requires that the bait is isolated from the sample by affinity purification, either by pulldown or immunoprecipitation. After a stringent wash, the interacting proteins are digested with the bait and identified by MS. This technique can easily be combined with the SWATHTM acquisition mode to get quantitative information on the proteins.
This technique can also be used to study post-tranlational modifications or anything that can be isolated by affinity purification. Fields like glycoproteomics, phosphoproteomics, methylomics and so on are perfect candidates for AP-MS studies.