Saliva has emerged as a promising diagnostic resource due to its accessibility, non-invasiveness, and repeatability, enabling early disease detection and timely intervention. However, current studies often overlook the distinction between whole saliva (WS) and cell-free saliva (CFS). This study aims to compare the proteomic profiles of WS and CFS, both with and without low-abundance proteins enrichment using nanoparticles, employing DIA-MS technology.