MIAMI––a tool for non-targeted detection of metabolic flux changes for mode of action identification

SUMMARY: Mass isotopolome analysis for mode of action identification (MIAMI) combines the strengths of targeted and non-targeted approaches to detect metabolic flux changes in gas chromatography/mass spectrometry datasets. Based on stable isotope labeling experiments, MIAMI determines a mass isotopo...

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Detalles Bibliográficos
Autores principales: Dudek, Christian-Alexander, Reuse, Carsten, Fuchs, Regine, Hendriks, Janneke, Starck, Veronique, Hiller, Karsten
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7320603/
https://www.ncbi.nlm.nih.gov/pubmed/32324861
http://dx.doi.org/10.1093/bioinformatics/btaa251
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author Dudek, Christian-Alexander
Reuse, Carsten
Fuchs, Regine
Hendriks, Janneke
Starck, Veronique
Hiller, Karsten
author_facet Dudek, Christian-Alexander
Reuse, Carsten
Fuchs, Regine
Hendriks, Janneke
Starck, Veronique
Hiller, Karsten
author_sort Dudek, Christian-Alexander
collection PubMed
description SUMMARY: Mass isotopolome analysis for mode of action identification (MIAMI) combines the strengths of targeted and non-targeted approaches to detect metabolic flux changes in gas chromatography/mass spectrometry datasets. Based on stable isotope labeling experiments, MIAMI determines a mass isotopomer distribution-based (MID) similarity network and incorporates the data into metabolic reference networks. By identifying MID variations of all labeled compounds between different conditions, targets of metabolic changes can be detected. AVAILABILITY AND IMPLEMENTATION: We implemented the data processing in C++17 with Qt5 back-end using MetaboliteDetector and NTFD libraries. The data visualization is implemented as web application. Executable binaries and visualization are freely available for Linux operating systems, the source code is licensed under General Public License version 3.
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spelling pubmed-73206032020-07-01 MIAMI––a tool for non-targeted detection of metabolic flux changes for mode of action identification Dudek, Christian-Alexander Reuse, Carsten Fuchs, Regine Hendriks, Janneke Starck, Veronique Hiller, Karsten Bioinformatics Applications Notes SUMMARY: Mass isotopolome analysis for mode of action identification (MIAMI) combines the strengths of targeted and non-targeted approaches to detect metabolic flux changes in gas chromatography/mass spectrometry datasets. Based on stable isotope labeling experiments, MIAMI determines a mass isotopomer distribution-based (MID) similarity network and incorporates the data into metabolic reference networks. By identifying MID variations of all labeled compounds between different conditions, targets of metabolic changes can be detected. AVAILABILITY AND IMPLEMENTATION: We implemented the data processing in C++17 with Qt5 back-end using MetaboliteDetector and NTFD libraries. The data visualization is implemented as web application. Executable binaries and visualization are freely available for Linux operating systems, the source code is licensed under General Public License version 3. Oxford University Press 2020-06-15 2020-04-23 /pmc/articles/PMC7320603/ /pubmed/32324861 http://dx.doi.org/10.1093/bioinformatics/btaa251 Text en © The Author(s) 2020. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Dudek, Christian-Alexander
Reuse, Carsten
Fuchs, Regine
Hendriks, Janneke
Starck, Veronique
Hiller, Karsten
MIAMI––a tool for non-targeted detection of metabolic flux changes for mode of action identification
title MIAMI––a tool for non-targeted detection of metabolic flux changes for mode of action identification
title_full MIAMI––a tool for non-targeted detection of metabolic flux changes for mode of action identification
title_fullStr MIAMI––a tool for non-targeted detection of metabolic flux changes for mode of action identification
title_full_unstemmed MIAMI––a tool for non-targeted detection of metabolic flux changes for mode of action identification
title_short MIAMI––a tool for non-targeted detection of metabolic flux changes for mode of action identification
title_sort miami––a tool for non-targeted detection of metabolic flux changes for mode of action identification
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7320603/
https://www.ncbi.nlm.nih.gov/pubmed/32324861
http://dx.doi.org/10.1093/bioinformatics/btaa251
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