PTMVision
Web application for the interactive visualization and exploration of post-translational modifications of proteins from open and closed search software.
Install / Use
/learn @Integrative-Transcriptomics/PTMVisionREADME
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.
<p align="center"> <img width="900px" height="250px" src="https://raw.githubusercontent.com/Integrative-Transcriptomics/PTMVision/refs/heads/main/app/ptmvision/static/resources/abstract.png"> </p>🔗 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 Localizationfield. 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.
🐳 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?
- 📖 Read the Usage Guide
- 🐛 Found an issue or missing format? Open a GitHub issue
✏️ Citation
If you use this software, please cite it as below:
PTMVision: An Interactive Visualization Webserver for Post-translational Modifications of Proteins
Simon Hackl, Caroline Jachmann, Mathias Witte Paz, Theresa Anisja Harbig, Lennart Martens, and Kay Nieselt
Journal of Proteome Research 2025 24 (2), 919-928
DOI: 10.1021/acs.jproteome.4c00679
