PhosphoPep—a database of protein phosphorylation—provides a comprehensive resource for the analysis and quantification of protein phosphorylation. This database enables researchers to identify and quantify phosphorylation sites across the proteome, facilitating the understanding of protein function and regulation. By leveraging advanced computational tools and machine learning algorithms, PhosphoPep offers a robust platform for the analysis of large-scale phosphoproteomic data, empowering researchers to uncover novel insights into biological processes and disease mechanisms.