Phosphorylation is a key post-translational modification that regulates cellular signaling and function, making phosphoproteomics essential for understanding biological processes in health and disease. While mass spectrometry has advanced significantly, the complexity and volume of phosphoproteomics data pose analytical challenges. Extracting meaningful biological insights requires specialized computational tools. Phosphomatics is a free, web-based platform that integrates statistical analysis, data visualization, and biological interpretation to facilitate phosphoproteomics research. In this update, we introduce new features that improve missing data imputation, enable upstream kinase prediction from protein sequences, and expand visualization options, offering researchers a more flexible and comprehensive analytical framework.
Phosphomatics now includes an improved kinase prediction module that utilizes the recently published Kinase Library, enabling upstream kinase identification and hyperactivation analysis based on primary protein sequences. This advancement addresses the challenge of unannotated phosphorylation sites by enabling upstream kinase inference, allowing researchers to explore signaling pathways more comprehensively. The platform also introduces robust methods for handling missing data, including visualization tools to assess missingness patterns and new imputation algorithms for more accurate quantitative analyses. Additionally, enhanced visualization capabilities provide users with greater flexibility in customizing plots and highlighting key findings. Researchers can now dynamically emphasize phosphorylation sites known to be substrates of specific kinases, facilitating clearer and more effective data interpretation.
Phosphomatics has gained global adoption, evidenced by 44,070 page views and 4,946 active sessions from 45 countries. The number of active monthly users has increased from 47 in 2021 to 122 in 2023 and has reached 381 in 2025 (year-to-date), reflecting its expanding impact in the phosphoproteomics community. These advancements establish Phosphomatics as an essential tool for phosphoproteomics researchers, enabling deeper biological insights from complex datasets.