LC‐Inspector ‐ README - MateuszFido/LCMSpector GitHub Wiki

License: MIT DOI Tests

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Table of Contents

1. Description
2. Features
3. Usage
User-interface
Running from source
4. Installation
5. Contributing
6. Licensing

🔍 Description

LC-Inspector is an open-source application for analyzing targeted mass spectrometry data.

It allows you to process raw mass spectrometry and/or chromatography files and look for a set of compounds or peaks, trace their intensities, graph and export them (also the raw data), check with databases via MS/MS, and quantify using calibration standards.

✨ Features

  • Trace compounds in raw mass spec data
  • Analyze and process LC/GC spectra
  • View the underlying MS spectra, scan by scan
  • Graph and export your data in SVG, TIFF, PNG, JPG or CSV formats
  • Calculate concentrations using in-built calibration features
  • Compare with integrated MS/MS libraries
  • Vendor-agnostic, accepts any .mzML and .txt files
  • Process everything on your machine without registration/uploading to external websites or servers
  • Easy UI, works on Windows and macOS >

LC-Inspector-demo

⛯ Usage

User-interface

LC-Inspector simplifies the MS analysis process to only a few steps:

  1. Drag and drop your mass spectrometry files into the main window
  2. Choose a list of metabolites to look for in the MS data or define your own
  3. Click Process
  4. View the results:
  • raw data, scan by scan;
  • extracted ion chromatograms (XICs) of your compounds;
  • total ion current (TIC);
  • chromatograms labelled with your compounds' retention times;
  • (optional) ion mobility data
  1. Verify the structure of your compounds with MS/MS database matching
  2. Quantify based on MS and/or chromatography data

The user can upload and process the data entirely locally on their machine. No need to register an account anywhere or upload to external websites or web servers.

Running from source

  1. Clone the repository or download the compressed version and unpack
  2. Install Python 3.12 or later
  3. Navigate to the folder containing main.py in the terminal
  4. Install dependencies listed in requirements.txt using pip3 install -r requirements.txt
  5. Prepare the input data
  6. Run the script via main.py using python3 main.py

💽 Installation

Binaries are distributed for Windows and macOS, published under Releases.

  • On Windows, if you encounter a warning, go to Windows Defender -> Protection history -> LC-Inspector, find the LC-Inspector entry, and click Restore. If the warning "Windows protected your PC" appears, click More info and Run anyway.
  • On MacOS, you can remove the app from quarantine by running the following command: xattr -d com.apple.quarantine /path/to/app.app

🙋 Contributing

If you have an idea to improve LC-Inspector, don't hesitate to let me know -- any and all contributions are very welcome!

There are two main ways to contribute:

  • opening an issue: describe feature(s) you would like to see or any bugs or problems you encountered: please enclose your exact system configuration and attach the log file (app.log)
  • opening a pull request with your suggested code changes

📋 Licensing

LC-Inspector is distributed under the MIT license and available free of charge.

LC-Inspector makes use of the MoNA database libraries for MS/MS spectra comparison, which are distributed under the CC BY 4.0 License https://creativecommons.org/licenses/by/4.0/. No changes are made to the content of the libraries.