In the last thirty years, ion/ion reactions have been developed and applied to answer increasingly difficult analytical problems across a variety of industries. This requires the constant development of instrumentation that can enable work with the analyte modalities of highest impact. Such analytes have become increasingly high in molecular weight precluding many analysis techniques, such as mass spectrometry. In this work, a commercial quadrupole time-of-flight mass spectrometer was modified and adapted to support the analysis of high-mass bio-ions using ion/ion reactions. Using a highly modified instrument, novel capabilities and theory were developed around the analysis and detection of ions with m/z ratios as high as 400,000 m/z and 2.2 mDa. These capabilities enabled and benefitted the analysis of polymers, peptides, and proteins and in this work was demonstrated as an effective instrument a variety of applications. By using data generated on this apparatus, the rapid characterization of PS 80 samples using MATLAB programs to aide in peak identification, native ion parking, and novel ETD reagents were completed. Given the expanding role of biological systems in all areas of science, the development, characterization, and utilization of a highly versatile mass spectrometer is described herein.