As the field of mass spectrometry has progressed throughout history, new technologies have enabled the interrogation of new analytes and scientific questions. Especially since the advent of soft ionization techniques in the 1980s and 1990s, which allowed for the ionization of large nonvolatile macromolecules, mass spectrometry can now be used routinely to study many large, macromolecular systems. Every mass spectrometry experiment can be reduced to three simple features: (i) ionization, (ii) mass analysis, and (iii) detection. Significant efforts in the field have led to drastic advances in both ionization and mass analysis over time; however, less attention has been given towards advancing ion detection. The theme of this dissertation covers the incorporation of a type of nontraditional, cryogenic detector into mass spectrometry detection schemes. Throughout my research, superconducting tunnel junctions (STJs) have been employed for ion/neutral particle detection. At the core of the research presented in this dissertation is the development of advanced mass spectrometry instrumentation. Chapters 2, 3, and 11 discuss the development of new STJ cryodetection technologies used for heavy ion mass spectrometry. STJs have two key advantages in mass spectrometry experiments: (i) theoretically mass independent detection bias and (ii) energy-sensitive detection. The application of these two advantages are described in detail throughout the chapters of this dissertation. In this dissertation, STJ cryodetection mass spectrometry has been applied to the study of ultra-high mass macromolecules such as virus particles, protein complexes, synthetic nanoparticles, and polymers. In many cases, these experiments provide the first intact measurement of such large macromolecules and from which information about their size and composition was garnered. In Chapters 4-6, STJ cryodetection mass spectrometry was utilized for applications related to biology. In Chapters 7-9, applications related to nanotechnology were addressed by STJ cryodetection mass spectrometry. In the experiments performed in Chapters 7-10, energy measurements afforded through STJ cryodetection provided information related to metastable fragmentation. These results are some of the first of their kind, and have been used to provide fundamental insights into ion stability, structure, and ionization mechanism. Ion energy measurements afforded by STJ cryodetection have provided results which suggest that additional analytical information may be gained from a single STJ mass spectrometry experiment. These results serve as motivation for the community to further explore the utilization of this STJ cryodetection mass spectrometry technology to investigate complex scientific problems.