publication . Article . Other literature type . 2018

DExSI: a new tool for the rapid quantitation of 13C-labelled metabolites detected by GC-MS.

Dagley, Michael J; McConville, Malcolm J;
Open Access
  • Published: 18 Jan 2018
  • Publisher: Oxford University Press (OUP)
Abstract
Abstract Summary Stable isotope directed metabolomics is increasingly being used to measure metabolic fluxes in microbial, plant and animal cells. Incorporation of 13C/15N isotopes into a wide range of metabolites is typically determined using gas chromatography-mass spectrometry (GC/MS) or other hyphenated mass spectrometry approaches. The DExSI (Data Extraction for Stable Isotope-labelled metabolites) pipeline is an interactive graphical software package which can be used to rapidly quantitate isotopologues for a wide variety of metabolites detected by GC/MS. DExSI performs automated metabolite annotation, mass and positional isotopomer abundance determination...
Subjects
free text keywords: Statistics and Probability, Computational Theory and Mathematics, Biochemistry, Molecular Biology, Computational Mathematics, Computer Science Applications, Applications Notes, Systems Biology
Related Organizations
Funded by
NHMRC| Targeting carbohydrate metabolism in Leishmania
Project
  • Funder: National Health and Medical Research Council (NHMRC) (NHMRC)
  • Project Code: 1100000
  • Funding stream: Project Grants
16 references, page 1 of 2

Biller J.E., Biemann K. (1974) Reconstructed mass spectra, a novel approach for the utilization of gas chromatograph—mass spectrometer data. Anal. Lett., 7, 515–528.

Buescher J.M.et al (2015) A roadmap for interpreting (13)C metabolite labeling patterns from cells. Curr. Opin. Biotechnol., 34, 189–201.25731751 [OpenAIRE] [PubMed]

Eylert E.et al (2008) Carbon metabolism of Listeria monocytogenes growing inside macrophages. Mol. Microbiol., 69, 1008–1017.18627458 [PubMed]

Hartel T.et al (2012) Characterization of central carbon metabolism of Streptococcus pneumoniae by isotopologue profiling. J. Biol. Chem., 287, 4260–4274.22167202 [OpenAIRE] [PubMed]

Junker B.H.et al (2006) VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics, 7, 109.16519817 [OpenAIRE] [PubMed]

Kloehn J.et al (2015) Characterization of metabolically quiescent Leishmania parasites in murine les ions using heavy water labeling. PLoS Pathog., 11, e1004683.25714830 [OpenAIRE] [PubMed]

Lange E.et al (2005) OPENMS; a generic open source framework for chromatography/MS-based proteomics. Mol. Cell Proteomics, 4, S25–S25.

MacRae J.I.et al (2012) Mitochondrial metabolism of glucose and glutamine is required for intracellular growth of Toxoplasma gondii. Cell Host Microbe, 12, 682–692.23159057 [OpenAIRE] [PubMed]

Nanchen A.et al (2007) Determination of metabolic flux ratios from 13C-experiments and gas chromatography-mass spectrometry data: protocol and principles. Methods Mol. Biol., 358, 177–197.17035687 [OpenAIRE] [PubMed]

O’Callaghan S.et al (2012) PyMS: a Python toolkit for processing of gas chromatography-mass spectrometry (GC-MS) data. Application and comparative study of selected tools. BMC Bioinformatics, 13, 115.22647087 [OpenAIRE] [PubMed]

Obata T.et al (2013) Gas-chromatography mass-spectrometry (GC-MS) based metabolite profiling reveals mannitol as a major storage carbohydrate in the coccolithophorid alga Emiliania huxleyi. Metabolites, 3, 168–184.24957896 [OpenAIRE] [PubMed]

Perez de Souza L.et al (2017) From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics. Gigascience, 6, 1–20. [OpenAIRE]

Saunders E.C.et al (2015) Use of (13)C stable isotope labelling for pathway and metabolic flux analysis in Leishmania parasites. Methods Mol. Biol., 1201, 281–296.25388122 [PubMed]

Savitzky A., Golay M.J.E. (1964) Smoothing and differentiation of data by simplified least squares procedures. Anal. Chem., 36, 1627–1639. [OpenAIRE]

van der Walt S.et al (2014) scikit-image: image processing in Python. PeerJ, 2, e453.25024921 [OpenAIRE] [PubMed]

16 references, page 1 of 2
Abstract
Abstract Summary Stable isotope directed metabolomics is increasingly being used to measure metabolic fluxes in microbial, plant and animal cells. Incorporation of 13C/15N isotopes into a wide range of metabolites is typically determined using gas chromatography-mass spectrometry (GC/MS) or other hyphenated mass spectrometry approaches. The DExSI (Data Extraction for Stable Isotope-labelled metabolites) pipeline is an interactive graphical software package which can be used to rapidly quantitate isotopologues for a wide variety of metabolites detected by GC/MS. DExSI performs automated metabolite annotation, mass and positional isotopomer abundance determination...
Subjects
free text keywords: Statistics and Probability, Computational Theory and Mathematics, Biochemistry, Molecular Biology, Computational Mathematics, Computer Science Applications, Applications Notes, Systems Biology
Related Organizations
Funded by
NHMRC| Targeting carbohydrate metabolism in Leishmania
Project
  • Funder: National Health and Medical Research Council (NHMRC) (NHMRC)
  • Project Code: 1100000
  • Funding stream: Project Grants
16 references, page 1 of 2

Biller J.E., Biemann K. (1974) Reconstructed mass spectra, a novel approach for the utilization of gas chromatograph—mass spectrometer data. Anal. Lett., 7, 515–528.

Buescher J.M.et al (2015) A roadmap for interpreting (13)C metabolite labeling patterns from cells. Curr. Opin. Biotechnol., 34, 189–201.25731751 [OpenAIRE] [PubMed]

Eylert E.et al (2008) Carbon metabolism of Listeria monocytogenes growing inside macrophages. Mol. Microbiol., 69, 1008–1017.18627458 [PubMed]

Hartel T.et al (2012) Characterization of central carbon metabolism of Streptococcus pneumoniae by isotopologue profiling. J. Biol. Chem., 287, 4260–4274.22167202 [OpenAIRE] [PubMed]

Junker B.H.et al (2006) VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics, 7, 109.16519817 [OpenAIRE] [PubMed]

Kloehn J.et al (2015) Characterization of metabolically quiescent Leishmania parasites in murine les ions using heavy water labeling. PLoS Pathog., 11, e1004683.25714830 [OpenAIRE] [PubMed]

Lange E.et al (2005) OPENMS; a generic open source framework for chromatography/MS-based proteomics. Mol. Cell Proteomics, 4, S25–S25.

MacRae J.I.et al (2012) Mitochondrial metabolism of glucose and glutamine is required for intracellular growth of Toxoplasma gondii. Cell Host Microbe, 12, 682–692.23159057 [OpenAIRE] [PubMed]

Nanchen A.et al (2007) Determination of metabolic flux ratios from 13C-experiments and gas chromatography-mass spectrometry data: protocol and principles. Methods Mol. Biol., 358, 177–197.17035687 [OpenAIRE] [PubMed]

O’Callaghan S.et al (2012) PyMS: a Python toolkit for processing of gas chromatography-mass spectrometry (GC-MS) data. Application and comparative study of selected tools. BMC Bioinformatics, 13, 115.22647087 [OpenAIRE] [PubMed]

Obata T.et al (2013) Gas-chromatography mass-spectrometry (GC-MS) based metabolite profiling reveals mannitol as a major storage carbohydrate in the coccolithophorid alga Emiliania huxleyi. Metabolites, 3, 168–184.24957896 [OpenAIRE] [PubMed]

Perez de Souza L.et al (2017) From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics. Gigascience, 6, 1–20. [OpenAIRE]

Saunders E.C.et al (2015) Use of (13)C stable isotope labelling for pathway and metabolic flux analysis in Leishmania parasites. Methods Mol. Biol., 1201, 281–296.25388122 [PubMed]

Savitzky A., Golay M.J.E. (1964) Smoothing and differentiation of data by simplified least squares procedures. Anal. Chem., 36, 1627–1639. [OpenAIRE]

van der Walt S.et al (2014) scikit-image: image processing in Python. PeerJ, 2, e453.25024921 [OpenAIRE] [PubMed]

16 references, page 1 of 2
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