TOPPView-Lite

A lightweight web-based viewer for mass spectrometry data.

Features

• Peak Map: Interactive 2D heatmap with zoom-based resolution
• Spectrum View: Click to view individual mass spectra
• Data Tables: Browse spectra and peaks with sorting/filtering
• Identification Support: Load idXML files for peptide sequence visualization
• Ion Mobility: FAIMS/TIMS data support
• Fast Loading: Preprocessed parquet caching for instant visualization

Run Locally

1. Clone the repository

   git clone https://github.com/t0mdavid-m/TOPPView-Lite.git
   cd TOPPView-Lite

2. Create environment and install dependencies

   conda create -n toppview-lite python=3.10 -y
   conda activate toppview-lite
   pip install -r requirements.txt

3. Launch the app

   streamlit run app.py

Docker Deployment

# Build and run with docker-compose
docker-compose up -d --build

# Or build manually
docker build -t toppview-lite:latest .
docker run -p 8501:8501 toppview-lite:latest

Windows Installer

Windows MSI installers are automatically built via GitHub Actions on each release. Download from the Releases page.

Supported File Formats

• mzML: Mass spectrometry data (MS1 and MS2)
• idXML: Peptide identifications (optional, for sequence visualization)

Citation

Please cite:

Müller, T. D., Siraj, A., et al. OpenMS WebApps: Building User-Friendly Solutions for MS Analysis. Journal of Proteome Research (2025). https://doi.org/10.1021/acs.jproteome.4c00872

References

• Pfeuffer, J., Bielow, C., Wein, S. et al. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nat Methods 21, 365–367 (2024). https://doi.org/10.1038/s41592-024-02197-7

• Röst HL, Schmitt U, Aebersold R, Malmström L. pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library. Proteomics. 2014 Jan;14(1):74-7. https://doi.org/10.1002/pmic.201300246