NMR Spectroscopy. N.M.R. = Nuclear Magnetic Resonance. Basic Principles. Spectroscopic technique, thus relies on the interaction between material and. Nuclear Magnetic Resonance (NMR) spectroscopy has made a tremendous impact in many areas of chemistry, biology and medicine. The nuclear spin energy levels of a spin-½ nucleus in a magnetic field (Atkins, ). The 1 H-NMR spectrum of ethanol. Chapter Nuclear Magnetic Resonance (NMR) Spectroscopy direct observation of the H's and C's of a molecules. Nuclei are positively charged and spin on.

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N.M.R.. ◇ Nuclear Magnetic Resonance. ◇ spectroscopy. ◇ imaging. ◇ solid- state. ◇ .and much Protein structure file in the Protein Data Bank. Structure. Nuclear magnetic resonance spectroscopy (NMR) was first developed in Samples are strategically chosen in a high-low format in each variable with all. The general phenomenon of nuclear magnetic resonance is introduced using both a classical and a quantum mechanical perspective. This provides the basis .

The overarching goal of the integrated toolbox of MetaboID is to centralize the one dimensional spectral assignment process, from providing access to large chemical shift libraries to providing a straightforward, intuitive means of spectral comparison. Such a toolbox is expected to be attractive to both experienced and new metabolomic researchers as well as general complex mixture analysts. Keywords: NMR, metabolomics, assignment, mixture analysis 1. Introduction Metabolomics is increasingly utilized in biomedical and clinical studies to better understand various diseases.

With increasing availability of high magnetic-field spectrometers e. A significant challenge for NMR-based metabolomic studies remains the assignment of all small molecules contributing to the 1D proton 1H spectrum.

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One-dimensional 1H NMR spectra are by far the most common data routinely collected on biological fluids, cell extracts, and tissues due to the high NMR sensitivity of the hydrogen nucleus. The traditional solution to the overlap problem is to extend the NMR experiment into higher frequency dimensions, either with homonuclear e. This strategy is limited due to the large time requirements of the 2D experiment, which may be as much as 10 — 40 times longer than that of the 1D 1H experiment.

The collection of a full suite of 2D experiments required for full spectral assignment of every sample is clearly a daunting task, particularly when considering the large sample cohorts typically utilized in metabolomics studies.

However, it is not the case that every sample is completely unique within a cohort; often there is significant correspondence between the samples and thus selecting one or several representative samples to undergo the full battery of 2D experimental measurements is all that is necessary. Thus, the final analysis still requires resonance assignment of all the peaks in 1D 1H spectra, with the knowledge of the 2D spectra of selected samples guiding the process.

The FID time domain is Fourier transformed to obtain a 1H-NMR spectrum frequency domain that is visualized as a series of peaks along a chemical shift axis. The peaks correspond to the resonating hydrogen nuclei.

The unit of the chemical shift axis is parts per million ppm , that is, the difference between the resonance frequency of the hydrogen nucleus of the metabolite and the hydrogen nucleus of a reference compound, divided by the resonance frequency of the reference compound. Each metabolite in the biological sample produces a characteristic spectral signature that is formed by a combination of peaks not necessarily adjacent to each other along the chemical shift axis.

Each signature appears with an area under the intensity curve that is proportional to the concentration of the corresponding metabolite in the sample. The identification and quantification of blood plasma metabolites based on 1H-NMR spectra is a challenge for the following reasons: 1H-NMR spectrometers have detection limits. Although the number of significantly detectable peaks increases for higher magnetic field strengths, the number of existing plasma metabolites that can be reliably detected and quantified remains rather small approximately More than one metabolite can contribute to a signal at a specific location which further complicates peak identification and metabolite quantification.

Typically, 1H-NMR metabolomics of blood plasma is conducted using spectrometers with magnetic field strengths ranging from 9. Higher-field spectrometers e.

The ability to resolve peaks with different chemical shifts increases with field strength. However, higher-field spectrometers are also far more costly.


It involves subdividing the spectra into regions along the chemical shift axis and computing the area under the curve within each integration region. The limits of the integration regions are defined by spectroscopists in a way that best accommodates the metabolite peaks of interest.

However, peak overlap and variation in the chemical shift positions of the peaks across spectra often prevents a one-to-one mapping between integration regions and metabolites. This may be especially problematic in the context of sample classification.


In particular, an integration region may fail to show potential for classification if it includes metabolites which show opposite behavior under- and over-expression in patients versus controls. For instance, assume an integration region encompasses signal coming from two discriminative metabolites. On average, one metabolite has a higher concentration in patients than in controls while the second metabolite has a lower concentration in patients than in controls.

Despite the fact that the integration region contains signal from two discriminative metabolites, the opposite behavior of the two metabolites diminishes the classification potential of the integration region, potentially resulting in a non-differential integrated spectral region ISR.

On the other hand, for an integration region that shows classification potential it may be difficult to uniquely assign its effect to a single metabolite.

Since overlapping molecular resonances complicate the extraction of metabolic information from 1H-NMR data, spectral deconvolution techniques are currently the state of the art. It exploits extensive prior information on the characteristic resonance signatures of each metabolite and combines this information with the intensities observed in the actual spectrum to model the metabolic signal. Other deconvolution models include Bayesil and the commercially available software package Chenomx amongst others.

The prior information on peak shape and relative intensity plays an important role in any spectral deconvolution and signal extraction model.

Flexibility in setting up the prior information is desirable especially when 1H-NMR spectroscopy is performed on a spectrometer different to the one used to create the software. However, the measures are normalized such that the values become relative to a normalization constant e.


In this article, the application of the widely used spectral binning approach is compared with the automated spectral deconvolution technique, BATMAN, for extracting metabolic signal for the purposes of sample classification.

The two approaches were applied to MHz medium-field and MHz high-field 1H-NMR spectra of blood plasma samples from lung cancer patients and control subjects.This goal can only be reached if the dissemination of original data becomes a standard component, if not a requirement, of established publication mechanisms.

Trends Biotechnol. Thus, for experiments performed under similar conditions as the ones used for creating the reference library, a necessary step for automatic assignment is the development of an efficient bioinformatic tool for comparison, identification and assignment directly from the spectra.

Peak-picking should be implemented as part of this self-learning loop also.

Assignment confidence increases as the processing approaches spike-in or related experimental confirmation.

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