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ProbMetab: an R package for Bayesian probabilistic annotation of LC–MS-based metabolomics

Summary: We present ProbMetab, an R package that promotes substantial improvement in automatic probabilistic liquid chromatography–mass spectrometry-based metabolome annotation. The inference engine core is based on a Bayesian model implemented to (i) allow diverse source of experimental data and me...

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Autores principales: Silva, Ricardo R., Jourdan, Fabien, Salvanha, Diego M., Letisse, Fabien, Jamin, Emilien L., Guidetti-Gonzalez, Simone, Labate, Carlos A., Vêncio, Ricardo Z. N.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998140/
https://www.ncbi.nlm.nih.gov/pubmed/24443383
http://dx.doi.org/10.1093/bioinformatics/btu019
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author Silva, Ricardo R.
Jourdan, Fabien
Salvanha, Diego M.
Letisse, Fabien
Jamin, Emilien L.
Guidetti-Gonzalez, Simone
Labate, Carlos A.
Vêncio, Ricardo Z. N.
author_facet Silva, Ricardo R.
Jourdan, Fabien
Salvanha, Diego M.
Letisse, Fabien
Jamin, Emilien L.
Guidetti-Gonzalez, Simone
Labate, Carlos A.
Vêncio, Ricardo Z. N.
author_sort Silva, Ricardo R.
collection PubMed
description Summary: We present ProbMetab, an R package that promotes substantial improvement in automatic probabilistic liquid chromatography–mass spectrometry-based metabolome annotation. The inference engine core is based on a Bayesian model implemented to (i) allow diverse source of experimental data and metadata to be systematically incorporated into the model with alternative ways to calculate the likelihood function and (ii) allow sensitive selection of biologically meaningful biochemical reaction databases as Dirichlet-categorical prior distribution. Additionally, to ensure result interpretation by system biologists, we display the annotation in a network where observed mass peaks are connected if their candidate metabolites are substrate/product of known biochemical reactions. This graph can be overlaid with other graph-based analysis, such as partial correlation networks, in a visualization scheme exported to Cytoscape, with web and stand-alone versions. Availability and implementation: ProbMetab was implemented in a modular manner to fit together with established upstream (xcms, CAMERA, AStream, mzMatch.R, etc) and downstream R package tools (GeneNet, RCytoscape, DiffCorr, etc). ProbMetab, along with extensive documentation and case studies, is freely available under GNU license at: http://labpib.fmrp.usp.br/methods/probmetab/. Contact: rvencio@usp.br Supplementary information: Supplementary data are available at Bioinformatics online.
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spelling pubmed-39981402014-04-24 ProbMetab: an R package for Bayesian probabilistic annotation of LC–MS-based metabolomics Silva, Ricardo R. Jourdan, Fabien Salvanha, Diego M. Letisse, Fabien Jamin, Emilien L. Guidetti-Gonzalez, Simone Labate, Carlos A. Vêncio, Ricardo Z. N. Bioinformatics Applications Notes Summary: We present ProbMetab, an R package that promotes substantial improvement in automatic probabilistic liquid chromatography–mass spectrometry-based metabolome annotation. The inference engine core is based on a Bayesian model implemented to (i) allow diverse source of experimental data and metadata to be systematically incorporated into the model with alternative ways to calculate the likelihood function and (ii) allow sensitive selection of biologically meaningful biochemical reaction databases as Dirichlet-categorical prior distribution. Additionally, to ensure result interpretation by system biologists, we display the annotation in a network where observed mass peaks are connected if their candidate metabolites are substrate/product of known biochemical reactions. This graph can be overlaid with other graph-based analysis, such as partial correlation networks, in a visualization scheme exported to Cytoscape, with web and stand-alone versions. Availability and implementation: ProbMetab was implemented in a modular manner to fit together with established upstream (xcms, CAMERA, AStream, mzMatch.R, etc) and downstream R package tools (GeneNet, RCytoscape, DiffCorr, etc). ProbMetab, along with extensive documentation and case studies, is freely available under GNU license at: http://labpib.fmrp.usp.br/methods/probmetab/. Contact: rvencio@usp.br Supplementary information: Supplementary data are available at Bioinformatics online. Oxford University Press 2014-05-01 2014-01-17 /pmc/articles/PMC3998140/ /pubmed/24443383 http://dx.doi.org/10.1093/bioinformatics/btu019 Text en © The Author 2014. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Silva, Ricardo R.
Jourdan, Fabien
Salvanha, Diego M.
Letisse, Fabien
Jamin, Emilien L.
Guidetti-Gonzalez, Simone
Labate, Carlos A.
Vêncio, Ricardo Z. N.
ProbMetab: an R package for Bayesian probabilistic annotation of LC–MS-based metabolomics
title ProbMetab: an R package for Bayesian probabilistic annotation of LC–MS-based metabolomics
title_full ProbMetab: an R package for Bayesian probabilistic annotation of LC–MS-based metabolomics
title_fullStr ProbMetab: an R package for Bayesian probabilistic annotation of LC–MS-based metabolomics
title_full_unstemmed ProbMetab: an R package for Bayesian probabilistic annotation of LC–MS-based metabolomics
title_short ProbMetab: an R package for Bayesian probabilistic annotation of LC–MS-based metabolomics
title_sort probmetab: an r package for bayesian probabilistic annotation of lc–ms-based metabolomics
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998140/
https://www.ncbi.nlm.nih.gov/pubmed/24443383
http://dx.doi.org/10.1093/bioinformatics/btu019
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