Interactive mass spectrometry data analysis dashboard for Thermo Scientific instruments. Built with FastAPI, React, and Bokeh.

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Spectrum Explorer	Heatmap View

Precursor S/N Analysis	Bulk S/N Analysis

See all releases: Releases

• Upload & Convert: Upload Thermo .raw files (automatically converted to mzML) or .mzML files directly
• Drag & Drop: Simple drag-and-drop file upload interface
• File Browser: Quick switching between multiple loaded files

• File Statistics: Total scans, MS1/MS2 scan counts, retention time range, m/z range, polarity
• TIC Plot: Total Ion Chromatogram with interactive zoom and pan
• BPC Plot: Base Peak Chromatogram visualization
• Quick Stats: Maximum and mean TIC values at a glance

• Interactive Chromatogram: Click anywhere on TIC/BPC to select a retention time
• RT Slider: Fine-tune retention time selection with precision slider
• Mass Spectrum View: Full mass spectrum at selected retention time with zoom capabilities
• 2D Heatmap: m/z vs retention time intensity visualization
• Intensity Range Control: Adjustable min/max intensity thresholds for heatmap

• Precursor SNR: Calculate Signal-to-Noise Ratio for any m/z at a given retention time
• PPM Tolerance: Configurable mass tolerance (default ±5 ppm for Orbitrap)
• RT Window: Adjustable retention time search window for peak detection
• Peak Apex Detection: Automatic detection of chromatographic peak apex
• XIC Visualization: Extracted Ion Chromatogram for the target m/z
• Apex Spectrum: Mass spectrum at the detected peak apex

• Batch Processing: Analyze multiple compounds in a single operation
• CSV Import: Upload compound lists (name, m/z, RT) from CSV files
• Paste Support: Directly paste tab or comma-separated compound data
• Results Table: Sortable results with SNR, signal, noise, apex RT, and actual m/z
• CSV Export: Download results as CSV for further analysis
• Top Peaks: View highest intensity peaks with their SNR values

• Thermo Noise Data: Uses actual instrument noise data when available (mzML converted with -N flag)
• Binary Caching: Parsed files are cached for instant subsequent access
• Native Desktop App: Standalone executable with native window (no browser required)
• Cross-Platform: Available for macOS (Apple Silicon), Windows (x64), and Linux (x64)
• Dark/Light Theme: Automatic theme detection with manual override

The easiest way to run locally for development:

git clone https://github.com/RusEu/thermo-raw.git
cd thermo-charts
docker-compose up

• Frontend: http://localhost:5173
• Backend API: http://localhost:8000

Docker handles all dependencies including ThermoRawFileParser for .raw file conversion.

thermo-charts/
├── apps/
│   ├── backend/          # FastAPI + Bokeh backend
│   │   ├── src/thermo_raw/
│   │   │   ├── main.py           # FastAPI app entry point
│   │   │   ├── api/              # API routes
│   │   │   └── services/         # Data processing services
│   │   └── pyproject.toml
│   └── frontend/         # React + Vite frontend
│       ├── src/
│       └── package.json
├── scripts/              # Build scripts
└── docker-compose.yml    # Docker development setup

Requires:

• Python 3.12+
• Node.js 20+
• uv (Python package manager)
• Mono (for .raw file conversion on macOS/Linux)

# Clone the repository
git clone https://github.com/RusEu/thermo-raw.git
cd thermo-charts

# Backend
cd apps/backend
uv sync
uv run python -m thermo_raw.main

# Frontend (in another terminal)
cd apps/frontend
npm install
npm run dev

# macOS/Linux
./scripts/build-standalone.sh

# Windows
scripts\build-standalone.bat

The executable will be in apps/backend/dist/.

For .raw file conversion, download ThermoRawFileParser from compomics/ThermoRawFileParser and place it in:

• apps/backend/vendor/macos/ThermoRawFileParser (macOS)
• apps/backend/vendor/windows/ThermoRawFileParser.exe (Windows)
• apps/backend/vendor/linux/ThermoRawFileParser (Linux)

Or set the THERMO_RAW_FILE_PARSER environment variable to the executable path.

MIT