Individual skill
tooluniverse-protein-modification-analysis
Post-translational modification (PTM) analysis — phosphorylation, ubiquitination, acetylation, glycosylation, methylation. Uses iPTMnet (sites + enzymes), ProtVar (functional consequences), UniProt (baseline), STRING, ELM (linear motifs), MassIVE/ProteomeXchange (experimental), and the EBI Proteins API (mutagenesis, MS-proteomics/HPP peptide evidence, antigenic regions, genomic coordinates, protein-level variant lookup by accession/dbSNP/HGVS) as a cross-validation source. Use for PTM site annotation, kinase-substrate identification, and PTM-disease associations.
skills/tooluniverse-protein-modification-analysis/SKILL.md
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# 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