This dissertation describes methodologies designed to take advantage of innovations in mass spectrometry and accessory devices. These methodologies are primarily geared toward enhancing throughput and sensitivity—two important attributes that enable the application of mass spectrometry to problems in the continually-evolving biomedical health landscape. Specifically, I outline mass spectrometry-based methods for analyzing whole proteomes, sub-proteomic samples, and single proteins over condensed timescales. Further, I discuss the enabling technological advances for these methods as well as strategies for data interpretation.