Interactive proteoform-centric visualization for top-down proteomics
Live demo → https://laurapiro17-proteoclinview-app-tv7oqq.streamlit.app/
GSoC 2026 proposal prototype · Organization: OpenMS · Project C1
ProteoClinView bridges the gap between computational proteomics and clinical research. Visualise intact proteoforms, annotate fragment ions, and validate top-down MS/MS results — designed to be readable by wet-lab scientists and clinical researchers, not just bioinformaticians.
| Module | Status | Description |
|---|---|---|
| 🧬 Sequence Viewer | ✅ Live | OpenMS-Insight SequenceView + LinePlot + StateManager cross-linking |
| 📊 Mirror Plot | ✅ Live | Experimental vs theoretical spectrum comparison with Δppm per peak |
| 🔍 FLASHTnT Search | 🔜 Planned | On-demand targeted search via pyOpenMS |
| 🗺️ Feature Map | 🔜 Planned | m/z vs RT proteoform feature visualization |
Built on the OpenMS-WebApps framework (same stack as TOPPView-Lite and FLASHApp):
- Frontend: Streamlit + OpenMS-Insight components (
SequenceView,LinePlot,StateManager) - Fragment matching: OpenMS-Insight Vue-side annotation engine
- Data layer: Polars LazyFrames; parquet caching for fast reload
- Computation: Monoisotopic fragment ion calculation (c, z, b, y ions; multi-charge)
- Export: CSV download of matched ions and fragment tables
| Protein | Length | Clinical relevance |
|---|---|---|
| Human Insulin B chain | 30 AA | Diabetes research; neonatal diabetes mutations |
| Human Ubiquitin | 76 AA | Neurodegeneration; cancer (ubiquitin pathway) |
| Hemoglobin α N-terminal | 30 AA | Sickle cell disease (E6V variant); thalassemia |
git clone https://github.com/laurapiro17/ProteoClinView.git
cd ProteoClinView
python -m venv .venv && source .venv/bin/activate
pip install -r requirements.txt
streamlit run app.pyLaura Piñero Roig · 3rd year Medicine, Universitat de Barcelona GitHub: @laurapiro17 GSoC 2026 proposal: OpenMS Project C1 — Interactive Proteoform-Centric Visualization