Dynamically interacting proteins associate and dissociate with their binding partners at high on/off rates. Although their identification is of great significance to proteomics research, lack of an efficient strategy to distinguish stable and dynamic interactors has hampered the efforts toward this goal. In this work, we developed a new method, MAP (mixing after purification)-SILAC (stable isotope labeling of amino acids in cell culture), to quantitatively investigate the interactions of protein complexes by mass spectrometry. In combination with the original SILAC approach, stable and dynamic components were effectively distinguished by the differences in their relative abundance ratio changes. We applied the newly developed strategies to decipher the dynamics of the human 26 S proteasomeinteracting proteins. A total of 67 putative human proteasome-interacting proteins were identified by the MAP-SILAC method among which 14 proteins would have been misidentified as background proteins due to low relative abundance ratios in standard SILAC experiments and 57 proteins have not been reported previously. In addition, 35 of the 67 proteins were classified as stable interactors of the proteasome complex, whereas 16 of them were identified as dynamic interactors. The methods reported here provide a valuable expansion of proteomics technologies for identification of important but previously unidentifiable interacting proteins. Molecular & Cellular Proteomics 7:46 -57, 2008.Protein-protein interactions are one of the major mechanisms for controlling protein functions in various cellular processes. To fully understand these functions, global mapping of protein-protein interactions has become a major goal in current proteomics research. MS in combination with affinity purification in particular has evolved as a powerful tool for deciphering protein interaction networks at the proteome level (1-6). Although conventional affinity purification can preserve stable interactions under native conditions, we have shown recently that affinity purification coupled with in vivo crosslinking can extend identification of interacting proteins by capturing weak affinity or transient interactors (7). In contrast to stably interacting proteins, dynamically interacting proteins associate and dissociate with their binding partners at high on/off rates and are likely to be more susceptible to rapid regulation in response to cellular cues. Their identification is of great significance to proteomics research but is considerably challenging as efficient strategies to distinguish between stable and dynamic components of protein complexes are currently lacking. A new development that adds the ability to describe protein complex dynamics is thus needed for the advancement of interactive proteomics.Identification of specific protein interactions has been successfully achieved by quantitative MS using stable isotope labeling such as the stable isotope labeling of amino acids in cell culture (SILAC) 1 strategy, which allows effective discrimination ag...