Cancer is a leading cause of death worldwide, with rising mortality rates. Chemotherapy, essential for over half of diagnosed cases, often causes side effects. To enhance efficacy and reduce side effects, drug carriers such as liposomes are used. These biocompatible carriers selectively deliver drugs to cancer cells. Existing techniques for studying liposome systems have limitations, such as observing only one chemical element at a time. To overcome these, a novel method capillary electrophoresis with inductively coupled plasma tandem mass spectrometry (CE-ICP-MS/MS) was proposed. This technique enables both quantitative and qualitative analysis, assessing drug encapsulation efficiency, carrier polydispersity, and stability. The study examined how lipid composition and drug concentration affect encapsulation efficiency and analyzed post-processing modifications to optimize liposome properties. Tandem mass spectrometry enables precise phosphorus, platinum, and sulfur quantification while minimizing interference. A key advantage of this technique is its ability to study liposome–protein interactions. After producing liposome–drug systems, they are incubated with human serum proteins like albumin and transferrin to simulate in vivo conditions and by CE-ICP-MS/MS technique it can be determined whether proteins interact with liposomes, indicating protein corona formation.