Natural products have historically been regarded as a significant reservoir of lead compounds pertinent to the advancement of pharmacological development. Unlike traditional medicine, which employs whole plant extracts during therapeutic interventions, contemporary scientific approaches necessitate the isolation and purification of individual compounds from these extracts, followed by their assessment as potential pharmacological agents, hence frequently rendering the drug discovery process protracted and financially burdensome. An integration of pioneering drug design methodologies and the application of cutting-edge technologies, including artificial intelligence, is imperative for the formulation of novel pharmaceuticals essential for addressing both current and forthcoming global health dilemmas. Analytical methodologies such as mass spectrometry and nuclear magnetic resonance are employed to meticulously characterize the constituents of natural products, serving purposes that encompass screening, drug discovery, and quality control, particularly pertinent to nature-derived medicines. In selecting the most suitable analytical technique for a given research endeavor, investigators must contend with a multitude of critical considerations. These considerations encompass but are not limited to, the specific nature of the research inquiry, the characteristics of the sample, the anticipated outcomes, the sensitivity of the analytical technique, the throughput capabilities, and the accessibility of data analysis tools. To ensure the attainment of optimal results, the aforementioned factors must be duly considered during the selection process of an analytical technique. This chapter delineates the contemporary advancements in the quantification of natural indole alkaloids, alongside foundational principles of the respective analytical techniques, aimed at facilitating their successful application in the domain of natural product drug discovery.