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We introduce serial ultrafiltration combined with limited proteolysis-coupled mass spectrometry (FLiP\u2013MS), a structural proteomics workflow that generates a library of peptide markers specific to changes in PPIs by probing differences in protease susceptibility between complex-bound and monomeric forms of proteins. The library includes markers mapping to protein-binding interfaces and markers reporting on structural changes that accompany PPI changes. Integrating the marker library with LiP\u2013MS data allows for global profiling of protein\u2013protein interactions (PPIs) from unfractionated lysates. We apply FLiP\u2013MS to <jats:italic>Saccharomyces cerevisiae<\/jats:italic> and probe changes in protein complex dynamics after DNA replication stress, identifying links between Spt-Ada-Gcn5 acetyltransferase activity and the assembly state of several complexes. 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