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Liquid chromatography tandem mass spectrometry (LC-MS/MS) is an essential tool for drug discovery that enables simple and rapid identification and quantification of chemical substances. A combination of a mobile phase and column makes it possible to analyze a wide range of target substances from low-molecular weight high-polar substances, such as amino acids and peptides, to low-polar substances such as lipids, and even macromolecular substances such as proteins. In this paper, we describe the results of applying LC-MS/MS to the analysis of phospholipids and related substances in biological samples and the analysis of photoproducts of pharmaceuticals. First, MS conditions were optimization using several standards, and a system that enables measurement of a vast number of molecular species with different carbon chain lengths and degrees of unsaturation. Its application to the lipid profiling of influenza A virus-infected cells suggested that viral infection triggered the increase of intracellular levels of diacylglycerols and ceramides at the later stages of infection concomitant with viral replication. In addition, the analysis of lysophospholipids in several cell lines revealed partial functions of several types of glycerophosphodiester phosphodiesterase, which metabolize lysophospholipids. Next, the chemical structures of several photoproducts of pharmaceuticals were elucidated. Novel photoproducts of photo-exposed pharmaceuticals were identified, and the photodegradation pathways were suggested. Based on the photodegradation mechanism, the photodegradability of naproxen was regulated by the addition of several additives such as polyphenols.