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IQMNMR: Open source software using time-domain NMR data for automated identification and quantification of metabolites in batches
BACKGROUND: One of the most promising aspects of metabolomics is metabolic modeling and simulation. Central to such applications is automated high-throughput identification and quantification of metabolites. NMR spectroscopy is a reproducible, nondestructive, and nonselective method that has served...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3169537/ https://www.ncbi.nlm.nih.gov/pubmed/21838867 http://dx.doi.org/10.1186/1471-2105-12-337 |
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author | Song, Xu Zhang, Bo-Li Liu, Hong-Min Yu, Bo-Yang Gao, Xiu-Mei Kang, Li-Yuan |
author_facet | Song, Xu Zhang, Bo-Li Liu, Hong-Min Yu, Bo-Yang Gao, Xiu-Mei Kang, Li-Yuan |
author_sort | Song, Xu |
collection | PubMed |
description | BACKGROUND: One of the most promising aspects of metabolomics is metabolic modeling and simulation. Central to such applications is automated high-throughput identification and quantification of metabolites. NMR spectroscopy is a reproducible, nondestructive, and nonselective method that has served as the foundation of metabolomics studies. However, the automated high-throughput identification and quantification of metabolites in NMR spectroscopy is limited by severe spectral overlap. Although numerous software programs have been developed for resolving overlapping resonances, as well as for identifying and quantifying metabolites, most of these programs are frequency-domain methods, considerably influenced by phase shifts and baseline distortions, and effective only in small-scale studies. Almost all these programs require multiple spectra for each application, and do not automatically identify and quantify metabolites in batches. RESULTS: We created IQMNMR, an R package that integrates a relaxation algorithm, digital filter, and similarity search algorithm. It differs from existing software in that it is a time-domain method; it uses not only frequency to resolve overlapping resonances but also relaxation time constants; it requires only one NMR spectrum per application; is uninfluenced by phase shifts and baseline distortions; and most important, yields a batch of quantified metabolites. CONCLUSIONS: IQMNMR provides a solution that can automatically identify and quantify metabolites by one-dimensional proton NMR spectroscopy. Its time-domain nature, stability against phase shifts and baseline distortions, requirement for only one NMR spectrum, and capability to output a batch of quantified metabolites are of considerable significance to metabolic modeling and simulation. IQMNMR is available at http://cran.r-project.org/web/packages/IQMNMR/. |
format | Online Article Text |
id | pubmed-3169537 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-31695372011-09-09 IQMNMR: Open source software using time-domain NMR data for automated identification and quantification of metabolites in batches Song, Xu Zhang, Bo-Li Liu, Hong-Min Yu, Bo-Yang Gao, Xiu-Mei Kang, Li-Yuan BMC Bioinformatics Software BACKGROUND: One of the most promising aspects of metabolomics is metabolic modeling and simulation. Central to such applications is automated high-throughput identification and quantification of metabolites. NMR spectroscopy is a reproducible, nondestructive, and nonselective method that has served as the foundation of metabolomics studies. However, the automated high-throughput identification and quantification of metabolites in NMR spectroscopy is limited by severe spectral overlap. Although numerous software programs have been developed for resolving overlapping resonances, as well as for identifying and quantifying metabolites, most of these programs are frequency-domain methods, considerably influenced by phase shifts and baseline distortions, and effective only in small-scale studies. Almost all these programs require multiple spectra for each application, and do not automatically identify and quantify metabolites in batches. RESULTS: We created IQMNMR, an R package that integrates a relaxation algorithm, digital filter, and similarity search algorithm. It differs from existing software in that it is a time-domain method; it uses not only frequency to resolve overlapping resonances but also relaxation time constants; it requires only one NMR spectrum per application; is uninfluenced by phase shifts and baseline distortions; and most important, yields a batch of quantified metabolites. CONCLUSIONS: IQMNMR provides a solution that can automatically identify and quantify metabolites by one-dimensional proton NMR spectroscopy. Its time-domain nature, stability against phase shifts and baseline distortions, requirement for only one NMR spectrum, and capability to output a batch of quantified metabolites are of considerable significance to metabolic modeling and simulation. IQMNMR is available at http://cran.r-project.org/web/packages/IQMNMR/. BioMed Central 2011-08-12 /pmc/articles/PMC3169537/ /pubmed/21838867 http://dx.doi.org/10.1186/1471-2105-12-337 Text en Copyright © 2011 Song et al; licensee BioMed Central Ltd. https://creativecommons.org/licenses/by/2.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0 (https://creativecommons.org/licenses/by/2.0/) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Software Song, Xu Zhang, Bo-Li Liu, Hong-Min Yu, Bo-Yang Gao, Xiu-Mei Kang, Li-Yuan IQMNMR: Open source software using time-domain NMR data for automated identification and quantification of metabolites in batches |
title | IQMNMR: Open source software using time-domain NMR data for automated identification and quantification of metabolites in batches |
title_full | IQMNMR: Open source software using time-domain NMR data for automated identification and quantification of metabolites in batches |
title_fullStr | IQMNMR: Open source software using time-domain NMR data for automated identification and quantification of metabolites in batches |
title_full_unstemmed | IQMNMR: Open source software using time-domain NMR data for automated identification and quantification of metabolites in batches |
title_short | IQMNMR: Open source software using time-domain NMR data for automated identification and quantification of metabolites in batches |
title_sort | iqmnmr: open source software using time-domain nmr data for automated identification and quantification of metabolites in batches |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3169537/ https://www.ncbi.nlm.nih.gov/pubmed/21838867 http://dx.doi.org/10.1186/1471-2105-12-337 |
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