Integrated omics analysis for small molecule-mediated host-microbiome interactions
Advancing our understanding of molecular mechanisms of health and disease
matchms
Python library for fuzzy comparison of mass spectrum data and other Python objects
13
mentions
14
contributors
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What matchms can do for you
- import mass spectrometry data
- process mass spectrometry data
- compute mass spectra similarities
- perform queries on spectrometry data
Matchms is an open-access 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.
Tags
Programming Language
- Python
License
- Apache-2.0
Source code
Participating organizations
Mentions
Build a mass spectrometry analysis pipeline in Python using matchms — part III: molecular…
August 18, 2021
Read the blog
Build a mass spectrometry analysis pipeline in Python using matchms — part II: Spec2Vec
February 17, 2021
Read the blog
Build your own mass spectrometry analysis pipeline in Python using matchms — part I
January 11, 2021
Read the blog
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matchms - processing and similarity evaluation of mass spectrometry dataAugust 06, 2020
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matchms - processing and similarity evaluation of mass spectrometry data.August 31, 2020
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Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationshipsSeptember 25, 2020
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Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationshipsFebruary 16, 2021
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SIMILE enables alignment of fragmentation mass spectra with statistical significanceFebruary 25, 2021
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MS2DeepScore - a novel deep learning similarity measure for mass fragmentation spectrum comparisonsApril 20, 2021
Projects with matchms
Contributors
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Florian HuberNetherlands eScience Center
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Justin J. J. van der HooftUniversity of Glasgow
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Jurriaan H. SpaaksNetherlands eScience Center
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Faruk DiblenNetherlands eScience Center
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Stefan VerhoevenNetherlands eScience Center
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Cunliang GengNetherlands eScience Center
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Christiaan MeijerNetherlands eScience Center
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Simon RogersNetherlands eScience Center
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Adam BelloumNetherlands eScience Center
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Hanno SpreeuwNetherlands eScience Center
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Efrain M. Villanueva CastillaUniversity of Glasgow
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Kianoosh Ashouritaklimi
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Niek de JongeNetherlands eScience Center
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Helge Hecht
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