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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

Screenshot of MetaboMiner's "Annotation View". The contents of the reference spectral library and the automatically identified compound list are shown on the left panel. The spectral image is displayed on the right panel. The red peaks correspond to the reference spectra of the current compound being annotated (Valine). Peak searching is carried out by right clicking on a corresponding Valine peak. The user can also directly edit the current compound by inserting, removing, or dragging its peaks to match the exact pattern of the reference spectrum.
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Figure 4: Screenshot of MetaboMiner's "Annotation View". The contents of the reference spectral library and the automatically identified compound list are shown on the left panel. The spectral image is displayed on the right panel. The red peaks correspond to the reference spectra of the current compound being annotated (Valine). Peak searching is carried out by right clicking on a corresponding Valine peak. The user can also directly edit the current compound by inserting, removing, or dragging its peaks to match the exact pattern of the reference spectrum.

Mentions: Users can further refine the automated search results by manually annotating the raw 2D spectrum. By clicking the "Refine" button in the "Search View", the "Annotation View" will be launched with the identified compounds being transferred as the starting point. Users can also directly enter the "Annotation View" mode by clicking the "Annotate" button from the "Console" menu. In order to perform manual annotation, users first need to load a high resolution spectral image in PNG format and set up the spectral axes properly. Peak searching is performed by right clicking the peak position on the spectrum to search the reference library as shown in Figure 4. All compounds that generate peaks within the search threshold will be checked. The compound with the closest peak match will be highlighted with its database reference spectrum displayed on the uploaded "raw" spectrum. Users can perform peak annotation for any currently displayed compound. Double clicking any database peak will open a small text editor where users can enter the peak assignment or a comment. The peak pattern of the identified compounds can also be edited to match the experimental spectrum. For example, users can insert, delete, or drag a database peak to match the observed peak in the raw spectrum. These changes will be valid only for the current session. To make permanent changes, MetaboMiner's "Library View" must be used.


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

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

Screenshot of MetaboMiner's "Annotation View". The contents of the reference spectral library and the automatically identified compound list are shown on the left panel. The spectral image is displayed on the right panel. The red peaks correspond to the reference spectra of the current compound being annotated (Valine). Peak searching is carried out by right clicking on a corresponding Valine peak. The user can also directly edit the current compound by inserting, removing, or dragging its peaks to match the exact pattern of the reference spectrum.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Screenshot of MetaboMiner's "Annotation View". The contents of the reference spectral library and the automatically identified compound list are shown on the left panel. The spectral image is displayed on the right panel. The red peaks correspond to the reference spectra of the current compound being annotated (Valine). Peak searching is carried out by right clicking on a corresponding Valine peak. The user can also directly edit the current compound by inserting, removing, or dragging its peaks to match the exact pattern of the reference spectrum.
Mentions: Users can further refine the automated search results by manually annotating the raw 2D spectrum. By clicking the "Refine" button in the "Search View", the "Annotation View" will be launched with the identified compounds being transferred as the starting point. Users can also directly enter the "Annotation View" mode by clicking the "Annotate" button from the "Console" menu. In order to perform manual annotation, users first need to load a high resolution spectral image in PNG format and set up the spectral axes properly. Peak searching is performed by right clicking the peak position on the spectrum to search the reference library as shown in Figure 4. All compounds that generate peaks within the search threshold will be checked. The compound with the closest peak match will be highlighted with its database reference spectrum displayed on the uploaded "raw" spectrum. Users can perform peak annotation for any currently displayed compound. Double clicking any database peak will open a small text editor where users can enter the peak assignment or a comment. The peak pattern of the identified compounds can also be edited to match the experimental spectrum. For example, users can insert, delete, or drag a database peak to match the observed peak in the raw spectrum. These changes will be valid only for the current session. To make permanent changes, MetaboMiner's "Library View" must be used.

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