Installation Guide

This guide will help you install the MSCI package and its dependencies.

Installing MSCI via pip

You can install MSCI directly using pip, which will also handle the necessary dependencies.

pip install MSCI==0.2.3

If you’re working in a Jupyter notebook or a Colab environment, you may need to adjust the Python path to include the MSCI module:

import sys
sys.path.append('/path/to/MSCI')

Note: If you already have matchms installed and your environment prompts you to restart the session, select ‘Cancel’ to avoid any disruptions.

Clone the Repository

If you prefer to work with the latest functions directly from the repository, you can clone it using the following command:

git clone https://github.com/proteomicsunitcrg/MSCI.git

After cloning the repository, navigate to the MSCI directory:

cd MSCI

This step ensures that you are in the correct directory before running any scripts or modules from the MSCI package.

Conclusion

Once installed, you can start using the MSCI package to process mass spectrometry data, perform peptide grouping, and calculate similarity scores.