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?

📖 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

Integrative-Transcriptomics/PTMVision