Metflexo: An automated simulation of realistic H1-NMR spectra

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Abstract

The development of the 'omics' technologies such as transcriptomics, proteomics and metabolomics has made it possible to realize some of the goals of systems biology, where biological systems are interrogated at different levels of biochemical activity (such as gene expression, protein activity and/or metabolite concentration). Metabolomics deals with the metabolome that represents the complete set of small-molecule metabolites. Even though metabolomics can be thought of as a relatively young method, it is nevertheless a rapidly growing one that has the potential to reveal the molecular mechanism of certain diseases. H1 nuclear magnetic resonance (NMR) spectroscopy is commonly used in the metabolic profiling of biofluids as it has the potential to detect all proton-containing metabolites. Metabolites in biofluids are in dynamic equilibrium with those in cells and tissues, so their metabolic profile reflects changes in the state of an organism due to disease or environmental effects. Results: MetFlexo is as an easy-to-use C package that allows the simulation of datasets of 1H-NMR spectra in order to test data analysis techniques, hypotheses and experimental designs. The idea is based on transforming statistical parameters of metabolites (shifts, couplings, concentrations and magnetic field) to an NMR spectrum using chemical-physics theory. Our method helps in the deconvolution of NMR spectra and in a better determination of metabolite concentrations, as these concentrations are key in detecting diseases and abnormalities. Unlike others, this program generates NMR spectrum of biofluids with no limit on magnetic field or pH. Thus, our approach is able to produce complex NMR profiles with flexible conditions. It is also simple to implement in C, requires small storage, is easy to compute and uses an independent platform. It will be available in R and MATLAB soon. The algorithm is freely available upon request to the corresponding author.

Original languageEnglish
Title of host publicationProcedia Computer Science
PublisherElsevier
Pages1382-1391
Number of pages10
Volume18
DOIs
Publication statusPublished - 2013
Event13th Annual International Conference on Computational Science, ICCS 2013 - Barcelona, Spain
Duration: 5 Jun 20137 Jun 2013

Other

Other13th Annual International Conference on Computational Science, ICCS 2013
CountrySpain
CityBarcelona
Period5/6/137/6/13

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Keywords

  • Chemical shifts
  • Eigenvectors
  • H1-nmr
  • Metabolites
  • Spin-spin couplings

ASJC Scopus subject areas

  • Computer Science(all)

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