Chromascope

A lightweight GUI for reading and visualizing mzML mass spectrometry data

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Why Chromascope?

mzML is an open, XML-based format widely used for storing and processing mass spectrometry data. While vendor-specific tools handle proprietary formats well, finding a truly lightweight GUI that works seamlessly with mzML files remains surprisingly difficult.

Chromascope fills that gap by offering instant, no-setup inspection of your mass spectrometry data. The compiled binary is incredibly small (less than 5 MB on Windows), making it highly portable, fast, and perfect for smaller machines or low-resource environments.

Features & Interactive Controls

Chromascope is designed to be highly interactive and easy to use. Here is what you can do and how to do it:

• Native mzML & Multi-file support: Load and compare multiple .mzML files simultaneously. Simply use the File menu to load them in parallel.
• View Mass Spectra: Double-click anywhere on a chromatogram to extract and display the mass spectrum for that specific retention time.
• Peak integration: Right-click and drag across a peak on the chromatogram to perform a trapezoidal area integration.
• Trace Extraction (TIC, BPC, XIC): Switch between Total Ion Chromatogram, Base Peak Chromatogram, and Extracted Ion Chromatogram modes. Right-click the chromatogram to open Plot Properties and select your desired trace.
• Advanced filtering: Filter your mass spectrometry data by MS level (e.g., MS1 vs MS2), polarity, precursor m/z, and specific m/z ranges directly from the Plot Properties menu.
• Customizable display: Personalize how your data is presented by adjusting line color, style, smoothing, and line width via the Display menu.
• Cross-platform: Runs as a standalone executable on Windows, macOS, and Linux without needing an installer.

Usage

1. Launch Chromascope:

   • Run the application by executing the binary or running cargo run from the project directory.

2. Open mzML Files:

   • Use the File menu to load one or more mzML files into Chromascope.

3. Explore Data:

   • Switch between TIC, BPC, and XIC modes using the Plot Properties. Use the interactive controls (double-click, right-click drag) to extract a corresponding mass spectrum or integrate a peak area.

4. Customizing Views:

   • Adjust the display settings via the Display menu to customize how your data is presented.

Installation

Downloading pre-built binaries

You can download pre-built binaries for your operating system from the Releases page.

Building from source

To build Chromascope from source, follow these steps:

1. Clone the Repository:

   git clone https://github.com/adamcseresznye/chromascope.git
   cd chromascope

2. Build the Application:

   cargo build --release

3. Run the Application:

   ./target/release/chromascope

Contributing

We welcome contributions to Chromascope! If you have suggestions for new features, bug reports, or would like to contribute code, please open an issue or submit a pull request. For the contribution guidelines see here.

License

Chromascope is licensed under the GPL-3.0 License. See the LICENSE file for more details.

Acknowledgements

The project would not have been possible without these excellent libraries:

• egui library
• mzdata