matchms - processing and similarity evaluation of mass spectrometry data

Florian Huber; Stefan Verhoeven; Christiaan Meijer; Hanno Spreeuw; Efraín Manuel Villanueva Castilla; Cunliang Geng; J.J.J. van der Hooft; Simon Rogers; Adam Belloum; Faruk Diblen; Jurriaan H. Spaaks

doi:10.5281/zenodo.4001990

matchms - processing and similarity evaluation of mass spectrometry data

Florian Huber, Stefan Verhoeven, Christiaan Meijer, Hanno Spreeuw, Efraín Manuel Villanueva Castilla, Cunliang Geng, J.J.J. van der Hooft, Simon Rogers, Adam Belloum, Faruk Diblen, Jurriaan H. Spaaks

Bioinformatics

Research output: Non-textual form › Software

Abstract

Matchms is an open-source Python package to import, process, clean, and compare mass spectrometry data (MS/MS). It allows to implement and run an easy-to-follow, easy-to-reproduce workflow from raw mass spectra to pre- and post-processed spectral data. Spectral data can be imported from common formats such mzML, mzXML, msp, metabolomics-USI, MGF, or json (e.g. GNPS-syle json files). Matchms then provides filters for metadata cleaning and checking, as well as for basic peak filtering. Finally, matchms was build to import and apply different similarity measures to compare large amounts of spectra. This includes common Cosine scores, but can also easily be extended by custom measures.

Original language	English
Publisher	Zenodo
Media of output	Online
DOIs	https://doi.org/10.5281/zenodo.4001990
Publication status	Published - 26 Aug 2020

Keywords

Python
mass spectrometry
similarity scores

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10.5281/zenodo.4001990Licence: CC BY

1 Article

matchms - processing and similarity evaluation of mass spectrometry data
Huber, F., Verhoeven, S., Meijer, C., Spreeuw, H., Villanueva Castilla, E. M., Geng, C., van der Hooft, J. J. J., Rogers, S., Belloum, A., Diblen, F. & spaaks, J. H., 31 Aug 2020, In: The Journal of Open Source Software. 5, 52, 6 p., 2411.
Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Cite this

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title = "matchms - processing and similarity evaluation of mass spectrometry data",

abstract = "Matchms is an open-source Python package to import, process, clean, and compare mass spectrometry data (MS/MS). It allows to implement and run an easy-to-follow, easy-to-reproduce workflow from raw mass spectra to pre- and post-processed spectral data. Spectral data can be imported from common formats such mzML, mzXML, msp, metabolomics-USI, MGF, or json (e.g. GNPS-syle json files). Matchms then provides filters for metadata cleaning and checking, as well as for basic peak filtering. Finally, matchms was build to import and apply different similarity measures to compare large amounts of spectra. This includes common Cosine scores, but can also easily be extended by custom measures.",

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AU - Huber, Florian

AU - Verhoeven, Stefan

AU - Meijer, Christiaan

AU - Spreeuw, Hanno

AU - Villanueva Castilla, Efraín Manuel

AU - Geng, Cunliang

AU - van der Hooft, J.J.J.

AU - Rogers, Simon

AU - Belloum, Adam

AU - Diblen, Faruk

AU - Spaaks, Jurriaan H.

PY - 2020/8/26

Y1 - 2020/8/26

N2 - Matchms is an open-source Python package to import, process, clean, and compare mass spectrometry data (MS/MS). It allows to implement and run an easy-to-follow, easy-to-reproduce workflow from raw mass spectra to pre- and post-processed spectral data. Spectral data can be imported from common formats such mzML, mzXML, msp, metabolomics-USI, MGF, or json (e.g. GNPS-syle json files). Matchms then provides filters for metadata cleaning and checking, as well as for basic peak filtering. Finally, matchms was build to import and apply different similarity measures to compare large amounts of spectra. This includes common Cosine scores, but can also easily be extended by custom measures.

AB - Matchms is an open-source Python package to import, process, clean, and compare mass spectrometry data (MS/MS). It allows to implement and run an easy-to-follow, easy-to-reproduce workflow from raw mass spectra to pre- and post-processed spectral data. Spectral data can be imported from common formats such mzML, mzXML, msp, metabolomics-USI, MGF, or json (e.g. GNPS-syle json files). Matchms then provides filters for metadata cleaning and checking, as well as for basic peak filtering. Finally, matchms was build to import and apply different similarity measures to compare large amounts of spectra. This includes common Cosine scores, but can also easily be extended by custom measures.

KW - Python

KW - mass spectrometry

KW - similarity scores

U2 - 10.5281/zenodo.4001990

DO - 10.5281/zenodo.4001990

M3 - Software

PB - Zenodo

ER -

matchms - processing and similarity evaluation of mass spectrometry data

Abstract

Keywords

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matchms - processing and similarity evaluation of mass spectrometry data

Cite this