The integration of advanced mass spectrometry (MS) techniques with quantitative modeling has revolutionized the field of drug analysis, offering unprecedented accuracy, sensitivity, and specificity in the detection and quantification of pharmaceutical compounds and their metabolites. High-Resolution Mass Spectrometry (HRMS) and Tandem Mass Spectrometry (MS/MS) have emerged as pivotal tools, capable of distinguishing isobaric species and providing detailed structural information, respectively. Ambient ionization techniques such as Desorption Electrospray Ionization (DESI) and Direct Analysis in Real Time (DART) have further simplified sample preparation, enabling rapid, direct analyses under ambient conditions. This review discusses the significant strides made in enhancing drug analysis through these innovations, alongside the application of calibration curves and mathematical models for quantitation and pharmacokinetic modeling. Additionally, it addresses the challenges inherent in quantitative MS, including matrix effects, analyte stability, and the need for improved sensitivity and specificity. Through a comprehensive overview, this article underscores the transformative impact of these advancements on drug analysis, paving the way for more accurate and efficient pharmaceutical research and diagnostics.