Additional functionalities to be used with matchms.

Usually this is stuff which either in scope and/or in code quality and/or in degree of unit testing does not match the criteria we have for matchms. For producing the results shown in our Spec2Vec article, PLoS Computational Biology, 2021 we used code from matchmsextras 0.1.0. To fully reproduce those results you can install this via pip install matchmsextras==0.1.0. For all other purposes we recommend using the latest release.

pip install matchmsextras

If you use matchmsextras for your research, please cite the following references:

Huber F, Ridder L, Verhoeven S, Spaaks JH, Diblen F, Rogers S, van der Hooft JJJ, (2021) "Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships". PLoS Comput Biol 17(2): e1008724. https://doi.org/10.1371/journal.pcbi.1008724

F. Huber, S. Verhoeven, C. Meijer, H. Spreeuw, E. M. Villanueva Castilla, C. Geng, J.J.J. van der Hooft, S. Rogers, A. Belloum, F. Diblen, J.H. Spaaks, (2020). "matchms - processing and similarity evaluation of mass spectrometry data". Journal of Open Source Software, 5(52), 2411, https://doi.org/10.21105/joss.02411

Many extra thanks!

Possibly the easiest way to learn how to run matchmsextras is to follow our tutorial on matchms.

• Part I - Import and process MS/MS data using matchms
• Part II - Compute spectral similarity using Spec2Vec
• Part III - Create molecular networks from Spec2Vec similarities