In recent years, liquid chromatography with tandem mass spectrometry (LC-MS/MS) has become a fundamental technology in clinical practice. In Japan, the LC-MS/MS system is used in many large hospitals. It has become popular among pharmacists and laboratory technicians. LC-MS/MS has some advantages in terms of accuracy, speed, and comprehensiveness compared to conventional automated chemical testing equipment. However, LC-MS/MS is by no means a universal method, and it is necessary to understand its characteristics before using it. In the field of therapeutic drug monitoring (TDM), there is an issue with linearity in comprehensive measurement; however, ion-abundance adjustment methods, such as in-source collision-induced dissociation, have been proposed as a solution to this problem. The development of a biomarker analysis includes search, identification, and quantification, and it is necessary to select an appropriate mass spectrometric method for each step. In this paper, we review cutting-edge technologies that can expand the performance of LC-MS/MS in the clinical field and consider current issues and future prospects.