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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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Alignment results for P. redivivus (Pre) and P. pacificus (Ppa) TOCSY spectra of flow-through fractions from C18 solid phase extractions. (A) The guide tree produced by HATS groups spectra from the same species, resulting in intraspecies alignment before interspecies alignment. The utility of a guide tree-based alignment is exemplified by the anomeric crosspeaks of glucose, sucrose, and trehalose in the TOCSY spectra (B, C). By aligning spectra with similar composition first, false positive alignments of nearby but unrelated crosspeaks, such as the anomeric crosspeaks shown above, are avoided.
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fig2: Alignment results for P. redivivus (Pre) and P. pacificus (Ppa) TOCSY spectra of flow-through fractions from C18 solid phase extractions. (A) The guide tree produced by HATS groups spectra from the same species, resulting in intraspecies alignment before interspecies alignment. The utility of a guide tree-based alignment is exemplified by the anomeric crosspeaks of glucose, sucrose, and trehalose in the TOCSY spectra (B, C). By aligning spectra with similar composition first, false positive alignments of nearby but unrelated crosspeaks, such as the anomeric crosspeaks shown above, are avoided.

Mentions: The HATS-PR approach to eliminating positional variation is to first cluster all of the spectra through a guide tree, as shown in Figure 2A. The problem of positional variation in our nematode TOCSY spectra is easily seen in the expansion of the anomeric region of the sugars from the flow-through fractions (Figure 2B,C). In the unaligned data (Figure 2B), local differences in resonance frequency of the anomeric protons affect multiple spectra of both P. redivivus and P. pacificus samples and result in a general “blurriness” that significantly impacts subsequent statistical analyses. Removing this variation is clearly desirable, but the close proximity (∼0.03 ppm) and similar patterns and lineshapes of the P. pacificus glucose and P. redivivus trehalose crosspeaks raise the possibility of inappropriate alignment of the glucose to the trehalose crosspeaks. The use of the HATS-PR guide tree (Figure 2A) helps avoid this possibility by aligning the most similar before the less similar spectra. Using this approach, the glucose and trehalose resonances are not compared for alignment until they have been well aligned separately. As shown in Figure 2C, this results in the correction of positional variation within both glucose and trehalose crosspeaks and rejection of the inappropriate alignment of the two sugars.


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)

Alignment results for P. redivivus (Pre) and P. pacificus (Ppa) TOCSY spectra of flow-through fractions from C18 solid phase extractions. (A) The guide tree produced by HATS groups spectra from the same species, resulting in intraspecies alignment before interspecies alignment. The utility of a guide tree-based alignment is exemplified by the anomeric crosspeaks of glucose, sucrose, and trehalose in the TOCSY spectra (B, C). By aligning spectra with similar composition first, false positive alignments of nearby but unrelated crosspeaks, such as the anomeric crosspeaks shown above, are avoided.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig2: Alignment results for P. redivivus (Pre) and P. pacificus (Ppa) TOCSY spectra of flow-through fractions from C18 solid phase extractions. (A) The guide tree produced by HATS groups spectra from the same species, resulting in intraspecies alignment before interspecies alignment. The utility of a guide tree-based alignment is exemplified by the anomeric crosspeaks of glucose, sucrose, and trehalose in the TOCSY spectra (B, C). By aligning spectra with similar composition first, false positive alignments of nearby but unrelated crosspeaks, such as the anomeric crosspeaks shown above, are avoided.
Mentions: The HATS-PR approach to eliminating positional variation is to first cluster all of the spectra through a guide tree, as shown in Figure 2A. The problem of positional variation in our nematode TOCSY spectra is easily seen in the expansion of the anomeric region of the sugars from the flow-through fractions (Figure 2B,C). In the unaligned data (Figure 2B), local differences in resonance frequency of the anomeric protons affect multiple spectra of both P. redivivus and P. pacificus samples and result in a general “blurriness” that significantly impacts subsequent statistical analyses. Removing this variation is clearly desirable, but the close proximity (∼0.03 ppm) and similar patterns and lineshapes of the P. pacificus glucose and P. redivivus trehalose crosspeaks raise the possibility of inappropriate alignment of the glucose to the trehalose crosspeaks. The use of the HATS-PR guide tree (Figure 2A) helps avoid this possibility by aligning the most similar before the less similar spectra. Using this approach, the glucose and trehalose resonances are not compared for alignment until they have been well aligned separately. As shown in Figure 2C, this results in the correction of positional variation within both glucose and trehalose crosspeaks and rejection of the inappropriate alignment of the two sugars.

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