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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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Related in: MedlinePlus

(A) Overlay of P. redivivus (Pre) and P. pacificus (Ppa) flow-through TOCSY spectra and (B) scores plot from PCA of the flow-through TOCSY data set. P. redivivus and P. pacificus spectra are clearly differentiated by PC1, which allows the loadings of PC1 to be interpreted as relative quantitative spectral differences between the species.
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fig3: (A) Overlay of P. redivivus (Pre) and P. pacificus (Ppa) flow-through TOCSY spectra and (B) scores plot from PCA of the flow-through TOCSY data set. P. redivivus and P. pacificus spectra are clearly differentiated by PC1, which allows the loadings of PC1 to be interpreted as relative quantitative spectral differences between the species.

Mentions: Next, using the aligned TOCSY spectra (Figure 3A) of C18 flow-through fractions, we conducted PCA and PLS analysis. The PCA scores show clear, unambiguous separation of the P. redivivus spectra from the P. pacificus spectra in the first principal component (Figure 3B). This separation allows the PC1 loadings to be interpreted as a pattern of TOCSY crosspeaks differentiating the two species (Figure 4). The back-scaling procedure outlined above produces contours reflecting the crosspeak lineshapes in the original spectra but colored according to the loading coefficients. As the P. redivivus and P. pacificus PC1 scores have opposite signs, we represent features with greater intensity in the P. redivivus spectra in red (loadings between 0 and 1) and with greater P. pacificus intensity in blue (loadings between −1 and 0). The PLS predictors also agree with the PC1 loadings (Figure 2S, Supporting Information). The assignment of the crosspeaks in the PC1 loadings spectrum enables the identification of compounds unique to each species as well as quantitative differences between compound levels.


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)

(A) Overlay of P. redivivus (Pre) and P. pacificus (Ppa) flow-through TOCSY spectra and (B) scores plot from PCA of the flow-through TOCSY data set. P. redivivus and P. pacificus spectra are clearly differentiated by PC1, which allows the loadings of PC1 to be interpreted as relative quantitative spectral differences between the species.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig3: (A) Overlay of P. redivivus (Pre) and P. pacificus (Ppa) flow-through TOCSY spectra and (B) scores plot from PCA of the flow-through TOCSY data set. P. redivivus and P. pacificus spectra are clearly differentiated by PC1, which allows the loadings of PC1 to be interpreted as relative quantitative spectral differences between the species.
Mentions: Next, using the aligned TOCSY spectra (Figure 3A) of C18 flow-through fractions, we conducted PCA and PLS analysis. The PCA scores show clear, unambiguous separation of the P. redivivus spectra from the P. pacificus spectra in the first principal component (Figure 3B). This separation allows the PC1 loadings to be interpreted as a pattern of TOCSY crosspeaks differentiating the two species (Figure 4). The back-scaling procedure outlined above produces contours reflecting the crosspeak lineshapes in the original spectra but colored according to the loading coefficients. As the P. redivivus and P. pacificus PC1 scores have opposite signs, we represent features with greater intensity in the P. redivivus spectra in red (loadings between 0 and 1) and with greater P. pacificus intensity in blue (loadings between −1 and 0). The PLS predictors also agree with the PC1 loadings (Figure 2S, Supporting Information). The assignment of the crosspeaks in the PC1 loadings spectrum enables the identification of compounds unique to each species as well as quantitative differences between compound levels.

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