mzML Analyzer

A Shiny application for analyzing mass spectrometry data in mzML format.

Features

• Interactive Total Ion Chromatogram (TIC) visualization
• Automated peak detection and analysis
• Peak capacity calculation
• MS1 and MS2 spectra analysis
• Downloadable results in CSV format
• User-friendly web interface

Requirements

• R version 4.0.0 or higher
• Required R packages:

  install.packages(c("shiny", "shinydashboard", "DT", "plotly"))
  
  if (!requireNamespace("BiocManager", quietly = TRUE))
      install.packages("BiocManager")
  BiocManager::install(c("MSnbase", "xcms", "mzR"))

Installation

1. Clone this repository:

git clone https://github.com/youngbee12/mzML-Analyzer.git
cd mzml-analyzer

2. Install required packages (see Requirements section)

3. Run the application:

shiny::runApp("src")

Project Structure

mzml-analyzer/
├── src/
│   ├── app.R           # Main Shiny application
│   ├── mzml_analyzer.R # Core analysis functions
│   └── help.md         # Help documentation
├── example/            # Example data files
└── README.md          # This file

Usage

1. Launch the application
2. Upload your mzML file
3. Set analysis parameters:
   • Gradient Time (minutes)
   • Mass Accuracy (ppm)
   • Peak Width Range (seconds)
4. Click "Analyze" to start processing
5. View results and download data

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

License

This project is licensed under the MIT License - see the LICENSE file for details.

Authors

• Zhicheng Yang
• yangzhicheng@simm.ac.cn

Acknowledgments

• The R community
• Bioconductor project
• Contributors to the MSnbase and xcms packages