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Hierarchical alignment and full resolution pattern recognition of 2D NMR spectra: application to nematode chemical ecology.

Robinette SL, Ajredini R, Rasheed H, Zeinomar A, Schroeder FC, Dossey AT, Edison AS - Anal. Chem. (2011)

Bottom Line: We present a native 2D peak alignment algorithm we term HATS, for hierarchical alignment of two-dimensional spectra, enabling pattern recognition (PR) using full-resolution spectra.We show the utility of this integrated approach with the rapid, semiautomated assignment of small molecules differentiating the two species and the identification of spectral regions suggesting the presence of species-specific compounds.These results demonstrate that the combination of 2D NMR spectra with full-resolution statistical analysis provides a platform for chemical and biological studies in cellular biochemistry, metabolomics, and chemical ecology.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610-0245, United States.

ABSTRACT
Nuclear magnetic resonance (NMR) is the most widely used nondestructive technique in analytical chemistry. In recent years, it has been applied to metabolic profiling due to its high reproducibility, capacity for relative and absolute quantification, atomic resolution, and ability to detect a broad range of compounds in an untargeted manner. While one-dimensional (1D) (1)H NMR experiments are popular in metabolic profiling due to their simplicity and fast acquisition times, two-dimensional (2D) NMR spectra offer increased spectral resolution as well as atomic correlations, which aid in the assignment of known small molecules and the structural elucidation of novel compounds. Given the small number of statistical analysis methods for 2D NMR spectra, we developed a new approach for the analysis, information recovery, and display of 2D NMR spectral data. We present a native 2D peak alignment algorithm we term HATS, for hierarchical alignment of two-dimensional spectra, enabling pattern recognition (PR) using full-resolution spectra. Principle component analysis (PCA) and partial least squares (PLS) regression of full resolution total correlation spectroscopy (TOCSY) spectra greatly aid the assignment and interpretation of statistical pattern recognition results by producing back-scaled loading plots that look like traditional TOCSY spectra but incorporate qualitative and quantitative biological information of the resonances. The HATS-PR methodology is demonstrated here using multiple 2D TOCSY spectra of the exudates from two nematode species: Pristionchus pacificus and Panagrellus redivivus. We show the utility of this integrated approach with the rapid, semiautomated assignment of small molecules differentiating the two species and the identification of spectral regions suggesting the presence of species-specific compounds. These results demonstrate that the combination of 2D NMR spectra with full-resolution statistical analysis provides a platform for chemical and biological studies in cellular biochemistry, metabolomics, and chemical ecology.

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Representative spectra and PC1 loadings for P. redivivus and P. pacificus 50% MeOH fractions. The region selected is useful for ascaroside differentiation, as crosspeaks here indicate correlations from the methylene protons on the ascaroside side chain to protons near the terminal functional groups. PC1 loadings suggest that P. redivivus and P. pacificus produce different mixtures of ascaroside-like compounds.
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fig5: Representative spectra and PC1 loadings for P. redivivus and P. pacificus 50% MeOH fractions. The region selected is useful for ascaroside differentiation, as crosspeaks here indicate correlations from the methylene protons on the ascaroside side chain to protons near the terminal functional groups. PC1 loadings suggest that P. redivivus and P. pacificus produce different mixtures of ascaroside-like compounds.

Mentions: C. elegans releases at least 10 different ascarosides important in the nematode’s chemical ecology,(32) and methods to efficiently compare other species for ascaroside-like compounds would be useful. The most diagnostic NMR signatures for ascarosides are typically resonance peaks from anomeric, methyl, and methylene protons (Figure 5) present in the eluate of C18 SPE chromatography matrix with 50% MeOH C18. As with the flow-through fraction, PC1 separates the P. redivivus and P. pacificus 50% MeOH fraction spectra (Figure 3S, Supporting Information). The PC1 loadings from the 50% MeOH fractions show numerous crosspeaks in the ascaroside signature region. These peaks are difficult to resolve using 1D 1H NMR, and loadings from pattern recognition on the 1D spectra are difficult to interpret (Figure 4S, Supporting Information). Interestingly, both P. redivivus and P. pacificus show signals representing ascaroside-like compounds; however, differences in chemical shift and signal intensity suggest different sets of ascarosides produced by these species. We tried database matching the 50% MeOH, as we did with the flow-through fractions, but we were unsuccessful in finding any matches. Identification of these compounds is in progress using traditional approaches and will be reported elsewhere.


Hierarchical alignment and full resolution pattern recognition of 2D NMR spectra: application to nematode chemical ecology.

Robinette SL, Ajredini R, Rasheed H, Zeinomar A, Schroeder FC, Dossey AT, Edison AS - Anal. Chem. (2011)

Representative spectra and PC1 loadings for P. redivivus and P. pacificus 50% MeOH fractions. The region selected is useful for ascaroside differentiation, as crosspeaks here indicate correlations from the methylene protons on the ascaroside side chain to protons near the terminal functional groups. PC1 loadings suggest that P. redivivus and P. pacificus produce different mixtures of ascaroside-like compounds.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3066641&req=5

fig5: Representative spectra and PC1 loadings for P. redivivus and P. pacificus 50% MeOH fractions. The region selected is useful for ascaroside differentiation, as crosspeaks here indicate correlations from the methylene protons on the ascaroside side chain to protons near the terminal functional groups. PC1 loadings suggest that P. redivivus and P. pacificus produce different mixtures of ascaroside-like compounds.
Mentions: C. elegans releases at least 10 different ascarosides important in the nematode’s chemical ecology,(32) and methods to efficiently compare other species for ascaroside-like compounds would be useful. The most diagnostic NMR signatures for ascarosides are typically resonance peaks from anomeric, methyl, and methylene protons (Figure 5) present in the eluate of C18 SPE chromatography matrix with 50% MeOH C18. As with the flow-through fraction, PC1 separates the P. redivivus and P. pacificus 50% MeOH fraction spectra (Figure 3S, Supporting Information). The PC1 loadings from the 50% MeOH fractions show numerous crosspeaks in the ascaroside signature region. These peaks are difficult to resolve using 1D 1H NMR, and loadings from pattern recognition on the 1D spectra are difficult to interpret (Figure 4S, Supporting Information). Interestingly, both P. redivivus and P. pacificus show signals representing ascaroside-like compounds; however, differences in chemical shift and signal intensity suggest different sets of ascarosides produced by these species. We tried database matching the 50% MeOH, as we did with the flow-through fractions, but we were unsuccessful in finding any matches. Identification of these compounds is in progress using traditional approaches and will be reported elsewhere.

Bottom Line: We present a native 2D peak alignment algorithm we term HATS, for hierarchical alignment of two-dimensional spectra, enabling pattern recognition (PR) using full-resolution spectra.We show the utility of this integrated approach with the rapid, semiautomated assignment of small molecules differentiating the two species and the identification of spectral regions suggesting the presence of species-specific compounds.These results demonstrate that the combination of 2D NMR spectra with full-resolution statistical analysis provides a platform for chemical and biological studies in cellular biochemistry, metabolomics, and chemical ecology.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610-0245, United States.

ABSTRACT
Nuclear magnetic resonance (NMR) is the most widely used nondestructive technique in analytical chemistry. In recent years, it has been applied to metabolic profiling due to its high reproducibility, capacity for relative and absolute quantification, atomic resolution, and ability to detect a broad range of compounds in an untargeted manner. While one-dimensional (1D) (1)H NMR experiments are popular in metabolic profiling due to their simplicity and fast acquisition times, two-dimensional (2D) NMR spectra offer increased spectral resolution as well as atomic correlations, which aid in the assignment of known small molecules and the structural elucidation of novel compounds. Given the small number of statistical analysis methods for 2D NMR spectra, we developed a new approach for the analysis, information recovery, and display of 2D NMR spectral data. We present a native 2D peak alignment algorithm we term HATS, for hierarchical alignment of two-dimensional spectra, enabling pattern recognition (PR) using full-resolution spectra. Principle component analysis (PCA) and partial least squares (PLS) regression of full resolution total correlation spectroscopy (TOCSY) spectra greatly aid the assignment and interpretation of statistical pattern recognition results by producing back-scaled loading plots that look like traditional TOCSY spectra but incorporate qualitative and quantitative biological information of the resonances. The HATS-PR methodology is demonstrated here using multiple 2D TOCSY spectra of the exudates from two nematode species: Pristionchus pacificus and Panagrellus redivivus. We show the utility of this integrated approach with the rapid, semiautomated assignment of small molecules differentiating the two species and the identification of spectral regions suggesting the presence of species-specific compounds. These results demonstrate that the combination of 2D NMR spectra with full-resolution statistical analysis provides a platform for chemical and biological studies in cellular biochemistry, metabolomics, and chemical ecology.

Show MeSH
Related in: MedlinePlus