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PTMVision

PTMVision is an interactive web-based platform for the visual exploration of post-translational modifications (PTMs) identified in mass spectrometry-based proteomics data. It enables researchers to interpret the complex PTM landscape, supporting insights into molecular mechanisms of biological processes and disease.

🔗 Web server: https://ptmvision-tuevis.cs.uni-tuebingen.de

✨ Features

  • Rich interactive visualizations for sample-level and protein-level PTM data
  • Linked plots for seamless navigation and exploration
  • 3D structure integration and contact map analysis for structural context
  • Highlights residue-residue PTM interactions in close spatial proximity
  • Annotation integration from UniProt and UniMod for interpretability
  • Support for multiple search engine output formats and a custom CSV format
  • Session export/import for reproducibility and collaboration
  • Intuitive UI accessible to users without programming expertise

📁 Supported Input Formats

PTMVision accepts output from several widely-used search engines:

Search Engine Tested Versions Key Columns Processing Steps
ionbot v0.10.0, v0.11.0 uniprot_id, unexpected_modification, position Direct parsing of modification information
MSFragger (via FragPipe + PTMShepherd) MSFragger v4.0, PTMShepherd v2.0.6 Modified Peptide, Assigned Modifications, Localization, Protein ID, Protein Start Filtering ambiguous or multi-localized sites; mass shift mapping to UniMod; UniProt sequence alignment; UniMod classification
Sage v0.13.1 See psm-utils FDR filtering; decoy removal; UniMod mapping; PTM localization from variable mods only
MaxQuant v2.4.13.0 Search result columns used for mapping Mapping MaxQuant-specific names to UniMod; resolving multi-mapping peptides; UniProt mapping
Spectronaut (PTM Site Report) v9 PTM.ProteinId, PTM.SiteLocation, PTM.ModificationTitle, PTM.SiteAA Infers mass shifts and UniMod classifications from reported data and UniProt sequence

Note: For FragPipe-derived data, localization confidence is inferred from the MSFragger Localization field. Use caution until future versions provide dedicated localization scores.

📄 Custom Plain CSV Format

Users can submit manually compiled PTM data using a structured CSV format when other formats are unavailable.

Required Columns

Column Name Description
uniprot_id UniProt accession of the protein
position 1-based index of the modified residue
modification_unimod_name Name of the UniMod modification
modification_unimod_id UniMod ID
mass_shift (optional) Monoisotopic mass shift in Daltons (inferred from UniMod ID if omitted)
classification (optional) UniMod classification (inferred from ID and sequence context if omitted)

Example entry:

P04075,5,carbamidomethyl,4,57.021464,Artefact

⚠ Note: Classification relies on up-to-date UniProt sequences. Sequence version mismatches may lead to misaligned positions.

📄 Download CSV template

🐳 Running Locally via Docker

To deploy PTMVision locally:

# Clone repository
git clone https://github.com/Integrative-Transcriptomics/PTMVision.git
cd PTMVision

# Build Docker image
docker build --tag ptmvision app

# Run locally
docker run -dp 127.0.0.1:5001:5001 ptmvision

Note: Prebuilt Docker images are not currently provided.

🙋 Need Help?