MIAMI--a tool for non-targeted detection of metabolic flux changes for mode of action identification.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
01 06 2020
01 06 2020
Historique:
received:
13
09
2019
revised:
13
02
2020
accepted:
16
04
2020
pubmed:
24
4
2020
medline:
29
12
2020
entrez:
24
4
2020
Statut:
ppublish
Résumé
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. 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.
Identifiants
pubmed: 32324861
pii: 5824294
doi: 10.1093/bioinformatics/btaa251
pmc: PMC7320603
doi:
Substances chimiques
Carbon Isotopes
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
3925-3926Informations de copyright
© The Author(s) 2020. Published by Oxford University Press.
Références
Anal Chem. 2010 Aug 1;82(15):6621-8
pubmed: 20608743
Bioinformatics. 2013 May 1;29(9):1226-8
pubmed: 23479350
Curr Pharm Biotechnol. 2011 Jul;12(7):1075-86
pubmed: 21466455
Anal Chem. 2012 Oct 16;84(20):8442-7
pubmed: 22946681
Trends Biotechnol. 2005 Jan;23(1):28-33
pubmed: 15629855
IEEE Trans Vis Comput Graph. 2011 Dec;17(12):2301-9
pubmed: 22034350
Anal Chem. 2017 Sep 5;89(17):9518-9526
pubmed: 28787149
Bioinformatics. 2016 Sep 15;32(18):2875-6
pubmed: 27273671
J Am Soc Mass Spectrom. 2016 Dec;27(12):1897-1905
pubmed: 27624161
Electrophoresis. 2018 Apr;39(7):909-923
pubmed: 29292835
Anal Chem. 2009 May 1;81(9):3429-39
pubmed: 19358599
Cancer Metab. 2016 Apr 23;4:10
pubmed: 27110360
Curr Opin Biotechnol. 2015 Aug;34:189-201
pubmed: 25731751
Metab Eng. 2007 Jan;9(1):68-86
pubmed: 17088092