Peptidoform analysis of IP-MS data allows detection of differentially present bait proteoforms

While it is recognised that protein functions are determined by their proteoform state, such as mutations and post-translational modifications, methods to determine their differential abundance between conditions are limited. Here, we present a novel workflow for classical immunoprecipitation coupled to mass spectrometry (IP-MS) data that focuses on identifying differential peptidoforms of the bait protein between conditions, providing additional information about protein function.