LC-MS/MS technology is the method of choice for pharmaceutical bioanalysis for its superior quantitative analytical performance. However, true high-throughput screening of candidate compounds during drug discovery has been hindered by the limitations in speed and complexity of method development in traditional liquid chromatography. Here we present Acoustic Ejection Mass Spectrometry (AEMS), which allows sample analyses at speeds up to 50 times faster than conventional LC-MS/MS, enabling HTS screens of complex biology with unequivocal endpoint(s) to reduce ambiguity and enable better decision-making on progression of therapeutic along the development pipeline.