PlantPTM Accurate prediction of diverse PTM sites in plant with multi-view deep learning and protein language models

This dataset contains integrated mass spectrometry-based profiling of N-glycosylation, lysine acetylation, and lysine ubiquitylation in rice samples. N-glycosylated peptides were enriched using lectin affinity enrichment followed by PNGase F deglycosylation in H2(18)O and analyzed using timsTOF Pro in PASEF mode. Acetylated and ubiquitinated peptides were enriched using PTM-specific antibody affinity enrichment and analyzed using Orbitrap Astral in DIA mode. The dataset was generated to support PTM characterization and PlantPTM-related analyses in plants.