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MetaboMiner--semi-automated identification of metabolites from 2D NMR spectra of complex biofluids.

Xia J, Bjorndahl TC, Tang P, Wishart DS - BMC Bioinformatics (2008)

Bottom Line: However, the lack of dedicated software for this purpose significantly restricts the application of 2D NMR methods to most metabolomic studies.MetaboMiner is a freely available, easy-to-use, NMR-based metabolomics tool that facilitates automatic peak processing, rapid compound identification, and facile spectrum annotation from either 2D TOCSY or HSQC spectra.Using comprehensive reference libraries coupled with robust algorithms for peak matching and compound identification, the program greatly simplifies the process of metabolite identification in complex 2D NMR spectra.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada. jianguox@ualberta.ca

ABSTRACT

Background: One-dimensional (1D) 1H nuclear magnetic resonance (NMR) spectroscopy is widely used in metabolomic studies involving biofluids and tissue extracts. There are several software packages that support compound identification and quantification via 1D 1H NMR by spectral fitting techniques. Because 1D 1H NMR spectra are characterized by extensive peak overlap or spectral congestion, two-dimensional (2D) NMR, with its increased spectral resolution, could potentially improve and even automate compound identification or quantification. However, the lack of dedicated software for this purpose significantly restricts the application of 2D NMR methods to most metabolomic studies.

Results: We describe a standalone graphics software tool, called MetaboMiner, which can be used to automatically or semi-automatically identify metabolites in complex biofluids from 2D NMR spectra. MetaboMiner is able to handle both 1H-1H total correlation spectroscopy (TOCSY) and 1H-13C heteronuclear single quantum correlation (HSQC) data. It identifies compounds by comparing 2D spectral patterns in the NMR spectrum of the biofluid mixture with specially constructed libraries containing reference spectra of approximately 500 pure compounds. Tests using a variety of synthetic and real spectra of compound mixtures showed that MetaboMiner is able to identify >80% of detectable metabolites from good quality NMR spectra.

Conclusion: MetaboMiner is a freely available, easy-to-use, NMR-based metabolomics tool that facilitates automatic peak processing, rapid compound identification, and facile spectrum annotation from either 2D TOCSY or HSQC spectra. Using comprehensive reference libraries coupled with robust algorithms for peak matching and compound identification, the program greatly simplifies the process of metabolite identification in complex 2D NMR spectra.

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Related in: MedlinePlus

An illustration of the calculation of uniqueness values. The red peak represents the peak of interest and three peaks are in its immediate vicinity. The calculations are only performed at five chemical shifts distance levels – 0.01, 0.02, 0.03, 0.04, 0.05 ppm along the 1H dimension, and 0.05, 0.10, 0.15, 0.20, 0.25 ppm along the 13C dimension. No peak is observed in the first three distance levels. So the maximum unique scope for this peak is (0.03, 0.15) ppm. Peak A is found within 0.03~0.04 ppm (1H dimension) and 0.15~0.20 ppm (13C dimension) of the red peak; Peak B is found within 0.04~0.05 ppm (1H dimension) and 0.20~0.25 ppm (13C dimension) of the red peak; Peak C is not considered since the chemical shift distance is more than 0.05 ppm along the 1H dimension. Therefore, the assigned uniqueness values are 0-0-0-1-2. Note that the distance is not drawn to scale.
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Figure 1: An illustration of the calculation of uniqueness values. The red peak represents the peak of interest and three peaks are in its immediate vicinity. The calculations are only performed at five chemical shifts distance levels – 0.01, 0.02, 0.03, 0.04, 0.05 ppm along the 1H dimension, and 0.05, 0.10, 0.15, 0.20, 0.25 ppm along the 13C dimension. No peak is observed in the first three distance levels. So the maximum unique scope for this peak is (0.03, 0.15) ppm. Peak A is found within 0.03~0.04 ppm (1H dimension) and 0.15~0.20 ppm (13C dimension) of the red peak; Peak B is found within 0.04~0.05 ppm (1H dimension) and 0.20~0.25 ppm (13C dimension) of the red peak; Peak C is not considered since the chemical shift distance is more than 0.05 ppm along the 1H dimension. Therefore, the assigned uniqueness values are 0-0-0-1-2. Note that the distance is not drawn to scale.

Mentions: After the spectral libraries were constructed, each peak for each compound in each library was assigned a series of uniqueness values that are specific for that reference library. A unique peak in MetaboMiner is defined as a relatively isolated peak around which no peak from any other compound is observed based on the spectral library of the given biofluid. For any given peak, its uniqueness value is calculated as the total number of surrounding peaks from other compounds within a given chemical shift "distance". Five distance levels were used to measure peak uniqueness. For 1H chemical shifts, the distance thresholds are 0.01, 0.02, 0.03, 0.04, and 0.05 ppm. For 13C chemical shifts, the distance thresholds are set at 0.05, 0.10, 0.15, 0.20, and 0.25 ppm. For instance, an HSQC peak with a series of assigned uniqueness values of 0-0-0-1-2 indicates that no peak from any other compound in the reference library is observed within 0.03 ppm (1H dimension) and 0.15 ppm (13C dimension) of that peak. It also indicates that one peak from another compound in the spectra library was observed within 0.03~0.04 ppm (1H dimension) and 0.15~0.20 ppm (13C dimension) and another peak from another compound was observed within 0.04~0.05 ppm (1H dimension) and 0.20~0.25 ppm (13C dimension). See Figure 1 for a more complete description of the uniqueness value concept. These uniqueness values are automatically updated after any spectral library change using MetaboMiner's graphical user interface.


MetaboMiner--semi-automated identification of metabolites from 2D NMR spectra of complex biofluids.

Xia J, Bjorndahl TC, Tang P, Wishart DS - BMC Bioinformatics (2008)

An illustration of the calculation of uniqueness values. The red peak represents the peak of interest and three peaks are in its immediate vicinity. The calculations are only performed at five chemical shifts distance levels – 0.01, 0.02, 0.03, 0.04, 0.05 ppm along the 1H dimension, and 0.05, 0.10, 0.15, 0.20, 0.25 ppm along the 13C dimension. No peak is observed in the first three distance levels. So the maximum unique scope for this peak is (0.03, 0.15) ppm. Peak A is found within 0.03~0.04 ppm (1H dimension) and 0.15~0.20 ppm (13C dimension) of the red peak; Peak B is found within 0.04~0.05 ppm (1H dimension) and 0.20~0.25 ppm (13C dimension) of the red peak; Peak C is not considered since the chemical shift distance is more than 0.05 ppm along the 1H dimension. Therefore, the assigned uniqueness values are 0-0-0-1-2. Note that the distance is not drawn to scale.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2612014&req=5

Figure 1: An illustration of the calculation of uniqueness values. The red peak represents the peak of interest and three peaks are in its immediate vicinity. The calculations are only performed at five chemical shifts distance levels – 0.01, 0.02, 0.03, 0.04, 0.05 ppm along the 1H dimension, and 0.05, 0.10, 0.15, 0.20, 0.25 ppm along the 13C dimension. No peak is observed in the first three distance levels. So the maximum unique scope for this peak is (0.03, 0.15) ppm. Peak A is found within 0.03~0.04 ppm (1H dimension) and 0.15~0.20 ppm (13C dimension) of the red peak; Peak B is found within 0.04~0.05 ppm (1H dimension) and 0.20~0.25 ppm (13C dimension) of the red peak; Peak C is not considered since the chemical shift distance is more than 0.05 ppm along the 1H dimension. Therefore, the assigned uniqueness values are 0-0-0-1-2. Note that the distance is not drawn to scale.
Mentions: After the spectral libraries were constructed, each peak for each compound in each library was assigned a series of uniqueness values that are specific for that reference library. A unique peak in MetaboMiner is defined as a relatively isolated peak around which no peak from any other compound is observed based on the spectral library of the given biofluid. For any given peak, its uniqueness value is calculated as the total number of surrounding peaks from other compounds within a given chemical shift "distance". Five distance levels were used to measure peak uniqueness. For 1H chemical shifts, the distance thresholds are 0.01, 0.02, 0.03, 0.04, and 0.05 ppm. For 13C chemical shifts, the distance thresholds are set at 0.05, 0.10, 0.15, 0.20, and 0.25 ppm. For instance, an HSQC peak with a series of assigned uniqueness values of 0-0-0-1-2 indicates that no peak from any other compound in the reference library is observed within 0.03 ppm (1H dimension) and 0.15 ppm (13C dimension) of that peak. It also indicates that one peak from another compound in the spectra library was observed within 0.03~0.04 ppm (1H dimension) and 0.15~0.20 ppm (13C dimension) and another peak from another compound was observed within 0.04~0.05 ppm (1H dimension) and 0.20~0.25 ppm (13C dimension). See Figure 1 for a more complete description of the uniqueness value concept. These uniqueness values are automatically updated after any spectral library change using MetaboMiner's graphical user interface.

Bottom Line: However, the lack of dedicated software for this purpose significantly restricts the application of 2D NMR methods to most metabolomic studies.MetaboMiner is a freely available, easy-to-use, NMR-based metabolomics tool that facilitates automatic peak processing, rapid compound identification, and facile spectrum annotation from either 2D TOCSY or HSQC spectra.Using comprehensive reference libraries coupled with robust algorithms for peak matching and compound identification, the program greatly simplifies the process of metabolite identification in complex 2D NMR spectra.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada. jianguox@ualberta.ca

ABSTRACT

Background: One-dimensional (1D) 1H nuclear magnetic resonance (NMR) spectroscopy is widely used in metabolomic studies involving biofluids and tissue extracts. There are several software packages that support compound identification and quantification via 1D 1H NMR by spectral fitting techniques. Because 1D 1H NMR spectra are characterized by extensive peak overlap or spectral congestion, two-dimensional (2D) NMR, with its increased spectral resolution, could potentially improve and even automate compound identification or quantification. However, the lack of dedicated software for this purpose significantly restricts the application of 2D NMR methods to most metabolomic studies.

Results: We describe a standalone graphics software tool, called MetaboMiner, which can be used to automatically or semi-automatically identify metabolites in complex biofluids from 2D NMR spectra. MetaboMiner is able to handle both 1H-1H total correlation spectroscopy (TOCSY) and 1H-13C heteronuclear single quantum correlation (HSQC) data. It identifies compounds by comparing 2D spectral patterns in the NMR spectrum of the biofluid mixture with specially constructed libraries containing reference spectra of approximately 500 pure compounds. Tests using a variety of synthetic and real spectra of compound mixtures showed that MetaboMiner is able to identify >80% of detectable metabolites from good quality NMR spectra.

Conclusion: MetaboMiner is a freely available, easy-to-use, NMR-based metabolomics tool that facilitates automatic peak processing, rapid compound identification, and facile spectrum annotation from either 2D TOCSY or HSQC spectra. Using comprehensive reference libraries coupled with robust algorithms for peak matching and compound identification, the program greatly simplifies the process of metabolite identification in complex 2D NMR spectra.

Show MeSH
Related in: MedlinePlus