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NTFD—a stand-alone application for the non-targeted detection of stable isotope-labeled compounds in GC/MS data
Summary: Most current stable isotope-based methodologies are targeted and focus only on the well-described aspects of metabolic networks. Here, we present NTFD (non-targeted tracer fate detection), a software for the non-targeted analysis of all detectable compounds derived from a stable isotope-lab...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3634188/ https://www.ncbi.nlm.nih.gov/pubmed/23479350 http://dx.doi.org/10.1093/bioinformatics/btt119 |
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author | Hiller, Karsten Wegner, André Weindl, Daniel Cordes, Thekla Metallo, Christian M. Kelleher, Joanne K. Stephanopoulos, Gregory |
author_facet | Hiller, Karsten Wegner, André Weindl, Daniel Cordes, Thekla Metallo, Christian M. Kelleher, Joanne K. Stephanopoulos, Gregory |
author_sort | Hiller, Karsten |
collection | PubMed |
description | Summary: Most current stable isotope-based methodologies are targeted and focus only on the well-described aspects of metabolic networks. Here, we present NTFD (non-targeted tracer fate detection), a software for the non-targeted analysis of all detectable compounds derived from a stable isotope-labeled tracer present in a GC/MS dataset. In contrast to traditional metabolic flux analysis approaches, NTFD does not depend on any a priori knowledge or library information. To obtain dynamic information on metabolic pathway activity, NTFD determines mass isotopomer distributions for all detected and labeled compounds. These data provide information on relative fluxes in a metabolic network. The graphical user interface allows users to import GC/MS data in netCDF format and export all information into a tab-separated format. Availability: NTFD is C++- and Qt4-based, and it is freely available under an open-source license. Pre-compiled packages for the installation on Debian- and Redhat-based Linux distributions, as well as Windows operating systems, along with example data, are provided for download at http://ntfd.mit.edu/. Contact: gregstep@mit.edu |
format | Online Article Text |
id | pubmed-3634188 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-36341882013-04-24 NTFD—a stand-alone application for the non-targeted detection of stable isotope-labeled compounds in GC/MS data Hiller, Karsten Wegner, André Weindl, Daniel Cordes, Thekla Metallo, Christian M. Kelleher, Joanne K. Stephanopoulos, Gregory Bioinformatics Applications Notes Summary: Most current stable isotope-based methodologies are targeted and focus only on the well-described aspects of metabolic networks. Here, we present NTFD (non-targeted tracer fate detection), a software for the non-targeted analysis of all detectable compounds derived from a stable isotope-labeled tracer present in a GC/MS dataset. In contrast to traditional metabolic flux analysis approaches, NTFD does not depend on any a priori knowledge or library information. To obtain dynamic information on metabolic pathway activity, NTFD determines mass isotopomer distributions for all detected and labeled compounds. These data provide information on relative fluxes in a metabolic network. The graphical user interface allows users to import GC/MS data in netCDF format and export all information into a tab-separated format. Availability: NTFD is C++- and Qt4-based, and it is freely available under an open-source license. Pre-compiled packages for the installation on Debian- and Redhat-based Linux distributions, as well as Windows operating systems, along with example data, are provided for download at http://ntfd.mit.edu/. Contact: gregstep@mit.edu Oxford University Press 2013-05-01 2013-03-11 /pmc/articles/PMC3634188/ /pubmed/23479350 http://dx.doi.org/10.1093/bioinformatics/btt119 Text en © The Author 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Applications Notes Hiller, Karsten Wegner, André Weindl, Daniel Cordes, Thekla Metallo, Christian M. Kelleher, Joanne K. Stephanopoulos, Gregory NTFD—a stand-alone application for the non-targeted detection of stable isotope-labeled compounds in GC/MS data |
title | NTFD—a stand-alone application for the non-targeted detection of stable isotope-labeled compounds in GC/MS data |
title_full | NTFD—a stand-alone application for the non-targeted detection of stable isotope-labeled compounds in GC/MS data |
title_fullStr | NTFD—a stand-alone application for the non-targeted detection of stable isotope-labeled compounds in GC/MS data |
title_full_unstemmed | NTFD—a stand-alone application for the non-targeted detection of stable isotope-labeled compounds in GC/MS data |
title_short | NTFD—a stand-alone application for the non-targeted detection of stable isotope-labeled compounds in GC/MS data |
title_sort | ntfd—a stand-alone application for the non-targeted detection of stable isotope-labeled compounds in gc/ms data |
topic | Applications Notes |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3634188/ https://www.ncbi.nlm.nih.gov/pubmed/23479350 http://dx.doi.org/10.1093/bioinformatics/btt119 |
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