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matchms - processing and similarity evaluation of mass spectrometry data

Florian Huber, Stefan Verhoeven, Christiaan Meijer, Hanno Spreeuw, Efraín Castilla, Cunliang Geng, Justin van der Hooft, Simon Rogers, Adam Belloum, Faruk Diblen, Jurriaan Spaaks
2020 Journal of Open Source Software  
Summary Mass spectrometry data is at the heart of numerous applications in the biomedical and life sciences.  ...  ., 2020) serve as an open-access hub for sharing of raw, processed, or annotated fragmentation mass spectrometry data.  ... 
doi:10.21105/joss.02411 fatcat:bqnyr4u6lrcchgjsxelljbf5iu

matchms - processing and similarity evaluation of mass spectrometry data [article]

Florian Huber, Stefan Verhoeven, Christiaan Meijer, Hanno Spreeuw, Efrain Manuel Villanueva Castilla, Cunliang Geng, Justin JJ van der Hooft, Simon Rogers, Adam Belloum, Faruk Diblen, Jurriaan H Spaaks
2020 biorxiv/medrxiv   pre-print
Matchms is an open-access Python package to import, process, clean, and compare mass spectrometry data (MS/MS).  ...  Mass spectrometry data is at the heart of numerable applications in the biomedical and life sciences.  ...  Summary Mass spectrometry data is at the heart of numerous applications in the biomedical and life sciences.  ... 
doi:10.1101/2020.08.06.239244 fatcat:folnxbg2t5aqhf32pcf3mln5b4

Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships

Florian Huber, Lars Ridder, Stefan Verhoeven, Jurriaan H Spaaks, Faruk Diblen, Simon Rogers, Justin J J van der Hooft
2021 PLoS Computational Biology  
Spectral similarity is used as a proxy for structural similarity in many tandem mass spectrometry (MS/MS) based metabolomics analyses such as library matching and molecular networking.  ...  Spec2Vec learns fragmental relationships within a large set of spectral data to derive abstract spectral embeddings that can be used to assess spectral similarities.  ...  Acknowledgments We want to thank Marnix Medema and Michelle Schorn for many helpful discussions. We thank Mingxun Wang for creating the first GNPS-Spec2Vec implementation. Author Contributions  ... 
doi:10.1371/journal.pcbi.1008724 pmid:33591968 pmcid:PMC7909622 fatcat:4iugdivf3vgi3o6vcjpz5tatca

Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships [article]

Florian Huber, Lars Ridder, Simon Rogers, Justin JJ van der Hooft
2020 biorxiv/medrxiv   pre-print
Spectral similarity is used as a proxy for structural similarity in many tandem mass spectrometry (MS/MS) based metabolomics analyses, such as library matching and molecular networking.  ...  The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.  ...  Acknowledgments We want to thank Marnix Medema and Michelle Schorn for many helpful discussions. We thank Mingxun Wang for creating the first GNPS-Spec2Vec implementation. Author Contributions  ... 
doi:10.1101/2020.08.11.245928 fatcat:4kyhntm7fnhcdjcx7fecyqjwvm

MS2DeepScore - a novel deep learning similarity measure for mass fragmentation spectrum comparisons [article]

Florian Huber, Sven van der Burg, Justin J.J. van der Hooft, Lars Ridder
2021 bioRxiv   pre-print
Mass spectrometry data is one of the key sources of information in many workflows in medicine and across the life sciences.  ...  Added to the recently introduced unsupervised Spec2Vec metric, we believe that machine learning-supported mass spectral similarity metrics have great potential for a range of metabolomics data processing  ...  Acknowledgements This work was carried out on the Dutch national e-infrastructure with the support of SURF Cooperative.  ... 
doi:10.1101/2021.04.18.440324 fatcat:ig4rj63lvrefbhbs4267m55z4e

MS2DeepScore: a novel deep learning similarity measure to compare tandem mass spectra

Florian Huber, Sven van der Burg, Justin J. J. van der Hooft, Lars Ridder
2021 Journal of Cheminformatics  
AbstractMass spectrometry data is one of the key sources of information in many workflows in medicine and across the life sciences.  ...  Added to the recently introduced unsupervised Spec2Vec metric, we believe that machine learning-supported mass spectral similarity measures have great potential for a range of metabolomics data processing  ...  Acknowledgements This work was carried out on the Dutch national e-infrastructure with the support of SURF Cooperative.  ... 
doi:10.1186/s13321-021-00558-4 pmid:34715914 fatcat:n2vvvvmmirhydgmcplrd36w6lu

MEMO: Mass Spectrometry-based Sample Vectorization to Explore Chemodiverse Datasets [article]

Arnaud Gaudry, Florian Huber, Louis-Felix Nothias, Sylvian Cretton, Marcel Kaiser, Jean-Luc Wolfender, Pierre-Marie Allard
2021 bioRxiv   pre-print
MEMO thus allows the comparison of vast ensembles of samples, even when analyzed over long periods of time, and on different chromatographic or mass spectrometry platforms.  ...  Samples are usually analyzed by liquid chromatography coupled with fragmentation mass spectrometry to acquire informative mass spectral ensembles.  ...  The authors are grateful to the authors of the Qemistree article for making their valuable evaluation dataset available to the community, allowing for optimal data reuse.  ... 
doi:10.1101/2021.12.24.474089 fatcat:nmo7rvnxorgatcrtvagyssshhy

SIMILE enables alignment of fragmentation mass spectra with statistical significance [article]

Daniel GC Treen, Trent R Northen, Ben Bowen
2021 bioRxiv   pre-print
Interrelating compounds according to their aligned fragmentation spectra is central to tandem mass spectrometry-based metabolomics.  ...  We found SIMILE yields 550% more pairs of structurally similar compounds than commonly used cosine-based scoring algorithms, and anticipate SIMILE will fill an important role by also providing p-values  ...  Sharing and community curation of mass spectrometry data with Global Natural Products 302 Social Molecular Networking. Nat. Biotechnol. 34, 828-837 (2016). 303 4. Dührkop, K. et al.  ... 
doi:10.1101/2021.02.24.432767 fatcat:c2xrfueryfh65hhev4gepo2i6e

Global network alignment using multiscale spectral signatures

R. Patro, C. Kingsford
2012 Bioinformatics  
Motivation: Protein interaction networks provide an important system-level view of biological processes.  ...  evolutionary divergence between the two species and the evolution of complexes and pathways.  ...  Furthermore, at a similar level of topological quality, GHOST produces alignments that have far more biological relevance than those produced by MI-GRAAL.  ... 
doi:10.1093/bioinformatics/bts592 pmid:23047556 pmcid:PMC3509496 fatcat:m47ufwb4x5h3lcx3drq5myxo54