<img src="https://github.com/matchms/matchmsextras/blob/main/images/matchmsextras_logo.png" width="600">
[](https://pypi.org/project/matchmsextras/)
# matchmsextras
Additional functionalities to be used with [matchms](https://github.com/matchms/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](https://doi.org/10.1371/journal.pcbi.1008724) 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.
## Installation
```
pip install matchmsextras
```
## Citing us
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!
## Tutorial on matchms and Spec2Vec
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](https://blog.esciencecenter.nl/build-your-own-mass-spectrometry-analysis-pipeline-in-python-using-matchms-part-i-d96c718c68ee)
+ [Part II - Compute spectral similarity using Spec2Vec](https://blog.esciencecenter.nl/build-a-mass-spectrometry-analysis-pipeline-in-python-using-matchms-part-ii-spec2vec-8aa639571018)
+ [Part III - Create molecular networks from Spec2Vec similarities](https://blog.esciencecenter.nl/build-a-mass-spectrometry-analysis-pipeline-in-python-using-matchms-part-iii-molecular-91891248ee34)
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