DeepMVP: deep learning models trained on high-quality data accurately predict PTM sites and variant-induced alterations

Abstract

Post-translational modifications (PTMs) are critical regulators of protein function, and their disruption is a key mechanism by which missense variants contribute to disease. Accurate PTM site prediction using deep learning can help identify PTM-altering variants, but progress has been limited by the lack of large, high-quality training datasets. Here, we introduce PTMAtlas, a curated compendium of 397,524 PTM sites generated through systematic reprocessing of 241 public mass-spectrometry datasets, and DeepMVP, a deep learning framework trained on PTMAtlas to predict PTM sites for phosphorylation, acetylation, methylation, sumoylation, ubiquitination and N-glycosylation. DeepMVP substantially outperforms existing tools across all six PTM types. Its application to predicting PTM-altering missense variants shows strong concordance with experimental results, validated using literature-curated variants and cancer proteogenomic datasets. Together, PTMAtlas and DeepMVP provide a robust platform for PTM research and a scalable framework for assessing the functional consequences of coding variants through the lens of PTMs.