MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data

BACKGROUND: Microbiomes are now recognized as the main drivers of ecosystem function ranging from the oceans and soils to humans and bioreactors. However, a grand challenge in microbiome science is to characterize and quantify the chemical currencies of organic matter (i.e., metabolites) that microb...

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Autores principales: Ayala-Ortiz, Christian, Graf-Grachet, Nathalia, Freire-Zapata, Viviana, Fudyma, Jane, Hildebrand, Gina, AminiTabrizi, Roya, Howard-Varona, Cristina, Corilo, Yuri E., Hess, Nancy, Duhaime, Melissa B., Sullivan, Matthew B., Tfaily, Malak M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9936664/
https://www.ncbi.nlm.nih.gov/pubmed/36803638
http://dx.doi.org/10.1186/s40168-023-01476-3
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author Ayala-Ortiz, Christian
Graf-Grachet, Nathalia
Freire-Zapata, Viviana
Fudyma, Jane
Hildebrand, Gina
AminiTabrizi, Roya
Howard-Varona, Cristina
Corilo, Yuri E.
Hess, Nancy
Duhaime, Melissa B.
Sullivan, Matthew B.
Tfaily, Malak M.
author_facet Ayala-Ortiz, Christian
Graf-Grachet, Nathalia
Freire-Zapata, Viviana
Fudyma, Jane
Hildebrand, Gina
AminiTabrizi, Roya
Howard-Varona, Cristina
Corilo, Yuri E.
Hess, Nancy
Duhaime, Melissa B.
Sullivan, Matthew B.
Tfaily, Malak M.
author_sort Ayala-Ortiz, Christian
collection PubMed
description BACKGROUND: Microbiomes are now recognized as the main drivers of ecosystem function ranging from the oceans and soils to humans and bioreactors. However, a grand challenge in microbiome science is to characterize and quantify the chemical currencies of organic matter (i.e., metabolites) that microbes respond to and alter. Critical to this has been the development of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), which has drastically increased molecular characterization of complex organic matter samples, but challenges users with hundreds of millions of data points where readily available, user-friendly, and customizable software tools are lacking. RESULTS: Here, we build on years of analytical experience with diverse sample types to develop MetaboDirect, an open-source, command-line-based pipeline for the analysis (e.g., chemodiversity analysis, multivariate statistics), visualization (e.g., Van Krevelen diagrams, elemental and molecular class composition plots), and presentation of direct injection high-resolution FT-ICR MS data sets after molecular formula assignment has been performed. When compared to other available FT-ICR MS software, MetaboDirect is superior in that it requires a single line of code to launch a fully automated framework for the generation and visualization of a wide range of plots, with minimal coding experience required. Among the tools evaluated, MetaboDirect is also uniquely able to automatically generate biochemical transformation networks (ab initio) based on mass differences (mass difference network-based approach) that provide an experimental assessment of metabolite connections within a given sample or a complex metabolic system, thereby providing important information about the nature of the samples and the set of microbial reactions or pathways that gave rise to them. Finally, for more experienced users, MetaboDirect allows users to customize plots, outputs, and analyses. CONCLUSION: Application of MetaboDirect to FT-ICR MS-based metabolomic data sets from a marine phage-bacterial infection experiment and a Sphagnum leachate microbiome incubation experiment showcase the exploration capabilities of the pipeline that will enable the research community to evaluate and interpret their data in greater depth and in less time. It will further advance our knowledge of how microbial communities influence and are influenced by the chemical makeup of the surrounding system. The source code and User’s guide of MetaboDirect are freely available through (https://github.com/Coayala/MetaboDirect) and (https://metabodirect.readthedocs.io/en/latest/), respectively. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40168-023-01476-3.
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spelling pubmed-99366642023-02-18 MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data Ayala-Ortiz, Christian Graf-Grachet, Nathalia Freire-Zapata, Viviana Fudyma, Jane Hildebrand, Gina AminiTabrizi, Roya Howard-Varona, Cristina Corilo, Yuri E. Hess, Nancy Duhaime, Melissa B. Sullivan, Matthew B. Tfaily, Malak M. Microbiome Software BACKGROUND: Microbiomes are now recognized as the main drivers of ecosystem function ranging from the oceans and soils to humans and bioreactors. However, a grand challenge in microbiome science is to characterize and quantify the chemical currencies of organic matter (i.e., metabolites) that microbes respond to and alter. Critical to this has been the development of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), which has drastically increased molecular characterization of complex organic matter samples, but challenges users with hundreds of millions of data points where readily available, user-friendly, and customizable software tools are lacking. RESULTS: Here, we build on years of analytical experience with diverse sample types to develop MetaboDirect, an open-source, command-line-based pipeline for the analysis (e.g., chemodiversity analysis, multivariate statistics), visualization (e.g., Van Krevelen diagrams, elemental and molecular class composition plots), and presentation of direct injection high-resolution FT-ICR MS data sets after molecular formula assignment has been performed. When compared to other available FT-ICR MS software, MetaboDirect is superior in that it requires a single line of code to launch a fully automated framework for the generation and visualization of a wide range of plots, with minimal coding experience required. Among the tools evaluated, MetaboDirect is also uniquely able to automatically generate biochemical transformation networks (ab initio) based on mass differences (mass difference network-based approach) that provide an experimental assessment of metabolite connections within a given sample or a complex metabolic system, thereby providing important information about the nature of the samples and the set of microbial reactions or pathways that gave rise to them. Finally, for more experienced users, MetaboDirect allows users to customize plots, outputs, and analyses. CONCLUSION: Application of MetaboDirect to FT-ICR MS-based metabolomic data sets from a marine phage-bacterial infection experiment and a Sphagnum leachate microbiome incubation experiment showcase the exploration capabilities of the pipeline that will enable the research community to evaluate and interpret their data in greater depth and in less time. It will further advance our knowledge of how microbial communities influence and are influenced by the chemical makeup of the surrounding system. The source code and User’s guide of MetaboDirect are freely available through (https://github.com/Coayala/MetaboDirect) and (https://metabodirect.readthedocs.io/en/latest/), respectively. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40168-023-01476-3. BioMed Central 2023-02-17 /pmc/articles/PMC9936664/ /pubmed/36803638 http://dx.doi.org/10.1186/s40168-023-01476-3 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Software
Ayala-Ortiz, Christian
Graf-Grachet, Nathalia
Freire-Zapata, Viviana
Fudyma, Jane
Hildebrand, Gina
AminiTabrizi, Roya
Howard-Varona, Cristina
Corilo, Yuri E.
Hess, Nancy
Duhaime, Melissa B.
Sullivan, Matthew B.
Tfaily, Malak M.
MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data
title MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data
title_full MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data
title_fullStr MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data
title_full_unstemmed MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data
title_short MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data
title_sort metabodirect: an analytical pipeline for the processing of ft-icr ms-based metabolomic data
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9936664/
https://www.ncbi.nlm.nih.gov/pubmed/36803638
http://dx.doi.org/10.1186/s40168-023-01476-3
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