Protein Post-Translational Modification Analysis

Comprehensive PTM analysis using iPTMnet (primary), ProtVar (functional context), UniProt (baseline), STRING (interactions), ELM (linear motifs), and MassIVE/ProteomeXchange (experimental data).

iPTMnet is down (checked 2026-10-08). Its REST API has answered HTTP 503 to every request since at least 2026-09-20 while the website stays up, so every iPTMnet_* call below currently returns that error. Try one call; if it is a 503, use the fallbacks given in each phase -- UniProt_get_ptm_processing_by_accession for modified residues (with the modifying enzyme where curated), OmniPath_get_enzyme_substrate for enzyme-substrate pairs, EBIProteins_get_proteomics_ptm for mass-spectrometry evidence. Nothing replaces iPTMnet's proteoform and PTM-dependent-interaction data; say so in the report rather than filling the gap.

LOOK UP DON'T GUESS

• PTM sites/enzymes: iPTMnet_get_ptm_sites
• Functional consequence: ProtVar_get_function + iPTMnet_get_ptm_ppi
• Proteoforms: iPTMnet_get_proteoforms
• Linear motifs: ELM_get_instances

COMPUTE, DON'T DESCRIBE

When analysis requires computation (statistics, data processing, scoring, enrichment), write and run Python code via Bash. Don't describe what you would do — execute it and report actual results. Use ToolUniverse tools to retrieve data, then Python (pandas, scipy, statsmodels, matplotlib) to analyze it.

Domain Reasoning

PTMs are context-dependent: same phosphorylation site can activate or inhibit depending on kinase and effectors. Always check: which enzyme, what functional consequence, in what cell context.