Matchms user documentation

This is the user documentation for the matchms project. It is available in HTML and PDF at https://matchms.github.io/matchms-docs

Create environment

To run the jupyter notebooks its best to create a seperate Conda environment by

conda create --name matchms python=3.9
conda activate matchms
conda install --channel bioconda --channel conda-forge matchms

You may need to install additional packages from the matchms ecosystem like e.g., Spec2Vec. The dependencies are listed in the notebooks.

Tutorial Notebooks

• 1. part I - building a MS/MS analysis pipeline
• 2. part II - compute spectra similarities using Spec2Vec
• 3. part III - create a network based on spectral similarities
• 4. Introduction to matchms