Photodynamic therapy (PDT), a noninvasive cancer treatment, relies on three components: light source, oxygen, and photosensitizer (PS). When PS is excited by a specific wavelength of light in the presence of oxygen, it leads to the generation of reactive oxygen species (ROS), which results in targeted destruction of cancer cells. The success of PDT mainly depends on the properties of the chosen PS, emphasizing selectivity, high absorbance, drug conjugation, controlled biodistribution, and low toxicity. Nanomaterials not only play an important role in photochemical activity by maximizing the absorption of photons from the light source but can also adjust the pharmacokinetics and tumor selectivity of photoactive molecules. Therefore, they can be used as a PS on their own and conjugated with other PS molecules. When combined with selectivity, high targeting capacity, and finally, light of the appropriate wavelength, the scenario results in localized ROS formation and cell death. However, the signaling pathways of PDT-induced cell death may differ depending on the cell type or nanomaterial properties. For this reason, omics analyses are needed to clarify the mechanisms underlying photodynamic reactions. Proteomics, crucial in molecular sciences, sheds light on cancer mechanisms, identifying biomarkers and therapeutic targets. Examining nanoparticle-based PDT in cancer cell lines in vitro, this chapter aims to molecularly evaluate efficacy, utilizing proteomic analysis to understand the underlying mechanisms.