PhosPhAt

PhosPhAt catalogs phosphorylation sites in Arabidopsis thaliana identified by mass spectrometry to support analysis and prediction of protein phosphorylation dynamics.

Key Features:

• Comprehensive Data Collection: Contains over 1,187 unique tryptic peptide sequences mapping to 1,053 Arabidopsis thaliana proteins identified by mass spectrometry.
• Advanced Search and Spectral Annotation: Supports combinatorial searches using Boolean terms and provides annotated fragmentation spectra exportable as text files.
• External Data Integration: Integrates dynamic links to external web resources to enrich protein- and site-level information.
• Time-Resolved Diagrams: Displays time-resolved diagrams for experimental phosphorylation sites showing dynamic responses to external stimuli.
• Predictive Capabilities: Provides predictions for phosphothreonine (pT), phosphotyrosine (pY), and updated phosphoserine (pS) sites and performs on-the-fly predictions for uploaded protein sequences.
• Protein Domain Mapping: Maps Pfam domain structures onto protein sequence displays adjacent to experimental and predicted phosphorylation sites.
• Functional Annotation: Employs MAPMAN ontology for functional annotation of proteins.
• Serine Phosphorylation Prediction: Uses a prediction method based on 802 experimentally validated serine phosphorylation sites to predict 27,782 phosphoserine sites across 17,035 proteins, with results summarized graphically alongside experimental data.

Scientific Applications:

• Phosphorylation site identification and analysis: Support identification and analysis of phosphorylation events from mass spectrometry data in Arabidopsis thaliana.
• Protein function and regulation inference: Aid interpretation of phosphorylation in relation to protein function and regulation via Pfam mapping and MAPMAN annotations.
• Temporal dynamics analysis: Enable analysis of phosphorylation dynamics in response to external stimuli using time-resolved diagrams.
• Prediction and hypothesis generation: Provide pS/pT/pY predictions and on-the-fly sequence predictions to generate hypotheses and inform experimental design.
• Cross-domain utility: Offer dataset and prediction outputs applicable beyond plant sciences for studies of protein phosphorylation.

Methodology:

Phosphorylation sites originate from mass spectrometry-based large-scale experiments; serine phosphorylation prediction was developed from 802 experimentally validated serine sites; Pfam domain mapping and MAPMAN ontology are used for domain and functional annotation; predictions for pS, pT, and pY and combinatorial Boolean search and annotated fragmentation spectra export are implemented as described.