Brownovo Client

A desktop application for proteomics analysis, built with Electron and Node.js.

Features

1. Recover

• Process MGF (Mascot Generic Format) files
• Filter spectra based on emergence and minimum UPN
• Apply minimum intensity filtering (mean or median)

2. De Novo Sequencing

• Support for two prediction methods:
  • Novor: Traditional de novo sequencing
  • Powernovo: GPU-accelerated prediction with configurable resources
• Filtering options:
  • Minimum global score
  • Minimum residue score
  • Minimum peptide length
• Automatic subsequence extraction for high-confidence regions

3. MS-BLAST

• Protein database searching using MS-BLAST algorithm
• Interactive protein visualization:
  • Search proteins by accession
  • Adjustable similarity filters
  • Visual sequence coverage with peptide mapping
  • Color-coded peptide sequences showing:
    • Full sequence regions
    • Filtered sequence regions
    • Matched regions (aligned)
    • Mismatches in alignments
  • Click-to-expand peptide details with de novo scores

Requirements

• Node.js 16+
• Electron 33+
• Python Flask server (for backend processing)

Installation

# Install dependencies
npm install

# Start the application in development mode
npm start

Building Executables

# Package the application
npm run package

# Create distributables
npm run make

This will create platform-specific executables in the out/ directory.

Project Structure

Brownovo-client/
├── client/           # Frontend JavaScript modules
│   ├── app.js
│   ├── denovo.js
│   ├── fileDisplay.js
│   ├── jobManager.js
│   ├── msblast.js
│   ├── recover.js
│   ├── renderer.js
│   └── templateLoader.js
├── css/              # Stylesheets
│   └── styles.css
├── img/              # Application icons and images
├── server/           # Electron main process
│   ├── config.js
│   ├── main.js
│   └── preload.js
├── templates/        # HTML templates for results
│   ├── denovo-result.html
│   ├── msblast-result.html
│   └── recover-result.html
├── index.html        # Main application window
└── package.json      # Project configuration

Architecture

The application follows a modular architecture:

1. Main Process (server/main.js): Handles IPC communication, file operations, and Flask server requests
2. Renderer Process (client/): Manages UI, user interactions, and result visualization
3. Template System: Dynamic HTML templates for displaying processing results
4. Job Manager: Tracks and displays ongoing operations

Development

Flask Server Integration

The application communicates with a Python Flask server for heavy computations:

• Recover processing
• De novo prediction (Novor/Powernovo)
• MS-BLAST searches
• Protein index generation

Server configuration is managed in server/config.js.

File Handling

The application supports:

• Local file loading
• Automatic file upload to Flask server when needed
• Server-side file caching
• Download of generated results

License

ISC

Authors

LSMBO (Laboratoire de Spectrométrie de Masse Bio-Organique)