The advent of electrospray ionization enabled the study of intact protein complexes via MS. For example, in the mid-1990s, the observation that viruses can survive after entering the gas-phase and still retain activity was shown. Advances in sample preparation methodologies, mainly native MS, allowed for the preservation of large non-covalently bound complexes, which led to structural characterization studies that were previously unachievable. However, native MS suffers from complications arising from inherent heterogeneity and severe salt adduction. Consequently, the spectra can consist of broad and overlapping peaks that may even preclude the ability to obtain a mass measurement. This dissertation will focus on a gas-phase technique to address highly complex native MS scenarios that give rise to poorly resolved signals using the E. coli ribosome as one model system. Moreover, brief discussion of improvements made on our QToF platform (SCIEX 5600) will be compared with other state-of-the-art instruments. Lastly, other applications to our ion/ion reaction workflow will be explored.