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Daniel Raftery

Publications and source records attributed to Daniel Raftery.

16 recordsLinked to original sources
PubMed2007

Monitoring diet effects via biofluids and their implications for metabolomics studies.

The effect of diet on metabolites found in rat urine samples has been investigated using nuclear magnetic resonance (NMR) and a new ambient ionization mass spectrometry experiment, extractive electrospray ionization mass spectrometry (EESI-MS). Urine samples from rats with three different dietary regimens were readily distinguished using multivariate statistical analysis on metabolites detected by NMR and MS. To observe the effect of diet on metabolic pathways, metabolites related to specific pathways were also investigated using multivariate statistical analysis. Discrimination is increased by making observations on restricted compound sets. Changes in diet at 24-h intervals led to predictable changes in the spectral data. Principal component analysis was used to separate the rats into groups according to their different dietary regimens using the full NMR, EESI-MS data or restricted sets of peaks in the mass spectra corresponding only to metabolites found in the urea cycle and metabolism of amino groups pathway. By contrast, multivariate analysis of variance from the score plots showed that metabolites of purine metabolism obscure the classification relative to the full metabolite set. These results suggest that it may be possible to reduce the number of statistical variables used by monitoring the biochemical variability of particular pathways. It should also be possible by this procedure to reduce the effect of diet in the biofluid samples for such purposes as disease detection.

Alloxan↗
PubMed2006

Signal enhancement in HPLC/microcoil NMR using automated column trapping.

A new HPLC NMR system is described that performs analytical separation, preconcentration, and NMR spectroscopy in rapid succession. The central component of our method is the online preconcentration sequence that improves the match between postcolumn analyte peak volume and microcoil NMR detection volume. Separated samples are collected on to a C18 guard column with a mobile phase composed of 90% D2O/10% acetonitrile-D3 and back-flushed to the NMR microcoil probe with 90% acetonitrile-D3/10% D2O. To assess the performance of our unit, we separated a standard mixture of 1 mM ibuprofen, naproxen, and phenylbutazone using a commercially available C18 analytical column. The S/N measurements from the NMR acquisitions indicated that we achieved signal enhancement factors up to 10.4 (+/-1.2)-fold. Furthermore, we observed that preconcentration factors increased as the injected amount of analyte decreased. The highest concentration enrichment of 14.7 (+/-2.2)-fold was attained injecting 100 microL of solution of 0.2 mM (approximately 4 microg) ibuprofen.

Chromatography, High Pressure Liquid↗
PubMed2006

Principal component analysis of urine metabolites detected by NMR and DESI-MS in patients with inborn errors of metabolism.

Urine metabolic profiles of patients with inborn errors of metabolism were examined with nuclear magnetic resonance (NMR) and desorption electrospray ionization mass spectrometry (DESI-MS) methods. Spectra obtained from the study of urine samples from individual patients with argininosuccinic aciduria (ASA), classic homocystinuria (HCY), classic methylmalonic acidemia (MMA), maple syrup urine disease (MSUD), phenylketonuria (PKU) and type II tyrosinemia (TYRO) were compared with six control patient urine samples using principal component analysis (PCA). Target molecule spectra were identified from the loading plots of PCA output and compared with known metabolic profiles from the literature and metabolite databases. Results obtained from the two techniques were then correlated to obtain a common list of molecules associated with the different diseases and metabolic pathways. The combined approach discussed here may prove useful in the rapid screening of biological fluids from sick patients and may help to improve the understanding of these rare diseases.

Case-Control Studies↗
PubMed2006

Analysis of conformational polymorphism in pharmaceutical solids using solid-state NMR and electronic structure calculations.

A detailed analysis of molecular structure in three polymorphic forms of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile is made using a combination of multidimensional solid-state NMR (SSNMR) experiments and molecular modeling via electronic structure calculations. These compounds, collectively referred to as ROY because of their red, orange, and yellow colors, share a similar molecular structure with the exception of the dihedral angle between the phenyl and thiophene rings. The ROY materials make it possible to study the influence of nearly a single degree of freedom on the associated NMR spectra. Using the 2D PASS (Antzutkin et al. J. Magn. Reson. A 1995, 115, 7) experiment, spectral editing techniques, and DFT-based calculations of the local fields, an analysis is made of the sensitivity of all carbon and nitrogen sites to changing molecular conformation. Chemical shift and dipolar coupling information obtained from these experiments vary noticeably between forms and are subsequently used to quantitatively determine aspects of molecular structure in these materials, including the coplanar angle between the phenyl and thiophene rings. The influence of motion on the methyl and nitro chemical shifts is also investigated. The accuracy of the information obtained from local field analysis and the model structure calculation demonstrates the capabilities of SSNMR as a quantitative structural method.

Algorithms↗
PubMed2006

Combining desorption electrospray ionization mass spectrometry and nuclear magnetic resonance for differential metabolomics without sample preparation.

Desorption electrospray ionization mass spectrometry (DESI-MS) and nuclear magnetic resonance (NMR) spectroscopy are used to provide data on urine examined without sample preparation to allow differentiation between diseased (lung cancer) and healthy mice. Principal component analysis (PCA) is used to shortlist compounds with potential for biomarker screening which are responsible for significant differences between control urine samples and samples from diseased animals. Similar PCA score plots have been achieved by DESI-MS and NMR, using a subset of common detected metabolites. The common compounds detected by DESI and NMR have the same changes in sign of their concentrations thereby indicating the usefulness of corroborative analytical methods. The effects of different solvents and surfaces on the DESI mass spectra are also evaluated and optimized. Over 80 different metabolites were successfully identified by DESI-MS and tandem mass spectrometry experiments, with no prior sample preparation.

Animals↗
PubMed2005

Use of semiselective TOCSY and the pearson correlation for the metabonomic analysis of biofluid mixtures: application to urine.

The authors recently proposed an approach to the metabonomic analysis of biofluid mixtures based on the use of the selective TOCSY experiment (Sandusky, P.; Raftery, D. Anal. Chem. 2005, 77, 2455). This method has some significant advantages over standard metabonomic analysis. However, when analyzing overlapped components, the selective TOCSY method can suffer from the relatively high likelihood of simultaneous excitation of several spin systems at once. This multiple excitation can cause problems both with the purity of the individual TOCSY peaks observed and with their assignment into specific spin systems. To address this problem, the possibility of using a more selective excitation is initially explored. Unfortunately, in most cases, greater spin system selectivity can only be gained at the expense of sensitivity. This is obviously an unacceptable tradeoff when dealing with biofluid samples. However, the application of the Pearson product moment correlation to the TOCSY peak integral intensities provides a test for individual TOCSY peak purity and allows for the assignment of the peaks into spin systems. The specific application of this two-stage "semiselective" TOCSY method to rat and human urine is presented. Significantly, it is also demonstrated that the use of semiselective TOCSY spectra as data inputs for PCA calculations provides a more sensitive and reliable method of distinguishing small differences in biofluid composition than the standard metabonomic approach using complete 1D proton NMR spectra of urine samples.

Amino Acids↗
PubMed2005

Analysis of porosity in porous silicon using hyperpolarized 129Xe two-dimensional exchange experiments.

The porosity in porous silicon was characterized using hyperpolarized (HP) xenon as a probe. HP xenon under conditions of continuous flow allows for the rapid acquisition of xenon NMR spectra that can be used to characterize a variety of materials. Two-dimensional exchange spectroscopy (EXSY) (129)Xe NMR experiments using HP xenon were performed to obtain exchange pathways and rates of xenon mobility between pores of different dimensions within the structure of porous silicon and to the gas phase above the sample. Pore sizes are estimated from chemical shift information and a model for pore geometry is presented.

Isotopes↗
PubMed2005

Use of selective TOCSY NMR experiments for quantifying minor components in complex mixtures: application to the metabonomics of amino acids in honey.

The application of the traditional methods of multivariate statistics, such as the calculation of principle components, to the analysis of NMR spectra taken on sets of biofluid samples is one of the central approaches in the field of metabonomics. While this approach has proven to be a powerful and widely applicable technique, it has an inherent weakness, in that it tends to be dominated by those chemical species present at relatively higher concentrations. Using a set of commercial honey samples, a comparison of this classical metabonomics approach to one based on the use of the selective TOCSY experiment is presented. While the NMR spectrum of honey and its classical metabonomic analysis is completely dominated by a very few chemical species, specifically alpha-glucose and fructose, the statistical signal carried by minor honey components, such as amino acids, may be accessed using a selective TOCSY-based approach. This approach has the intrinsic virtue that it focuses the statistical analysis on a set of predefined chemical species, which might be chosen for their metabolic significance, and could be composed of either major or minor mixture constituents. Furthermore, the selective TOCSY method allows for more certain chemical identification, acquisition times of approximately 1 min, and accurate quantification of the species contributing to the statistical discriminatory signal.

Amino Acids↗
PubMed2005

Substrate and field dependence of the SPINOE transfer to surface 13C from hyperpolarized 129Xe.

The substrate and field dependencies of surface SPINOE enhancements using optical pumping and magic angle spinning NMR were monitored. Relaxation rates and enhancements were examined to gain an understanding of the parameters that determine the SPINOE enhancement. (13)C-labeled deuterated methanol was adsorbed on three different substrates (SnO(2), TiO(2), Ti/SiO(2)) with heats of adsorption for xenon ranging from 14.2 to 22.6 kJ/mol. The different heats of adsorption led to a range of xenon coverages and xenon relaxation rates. Using a simple model along with experimental values for the xenon surface polarization and cross- and self-relaxation rates, the (13)C signal enhancement could be predicted and compared with experimental enhancement values. Magnetic field dependence studies were also made by monitoring the (13)C enhancements via SPINOE from hyperpolarized xenon at fields of 0.075, 4.7, and 9.4 T. The pertinent parameters necessary to achieve maximum SPINOE enhancement are discussed.

Journal Article↗
PubMed2004

NMR difference spectroscopy with a dual saddle-coil difference probe.

A new difference probe for nuclear magnetic resonance (NMR) spectroscopy is presented. The difference probe uses two saddle-shaped coils to excite and detect two samples simultaneously. The samples are held in a specially modified 3-mm NMR tube with an Ultem plastic disk to separate the samples. The probe's resonant circuit contains two crossed diodes that passively switch the relative phase of each coil during the NMR experiment. The result is a difference spectrum from the two samples. The degree of cancellation of common signals was determined to be approximately 90%, and the application of the probe to relaxation-edited difference spectroscopy for identifying protein-ligand interactions was demonstrated using glutathione and glutathione S-transferase binding protein.

Glutathione↗
PubMed2003

Frozen-solution conformational analysis by REDOR spectroscopy.

Frozen-solution conformational analysis (FrSCA) can be performed on organic compounds using REDOR spectroscopy. REDOR measurements on frozen aqueous solutions of 13C-methyl beta-15N-aminoglucoside indicate a bimodal distribution of conformations in a 68:32 ratio, with 13C-15N distances of 4.31 and 3.55 A, respectively. The high resolution and straightforward sample preparation make FrSCA an attractive alternative to solution-based NMR methods of conformational analysis.

Acetylglucosamine↗
PubMed2003

High-throughput nuclear magnetic resonance analysis using a multiple coil flow probe.

An automated method for high-throughput nuclear magnetic resonance (NMR) spectroscopy has been developed using a four-coil Multiplex NMR probe. The probe is constructed with solenoidal microcoils optimized for detection of small volume, mass-limited samples and a flow-through design. Four samples can be simultaneously injected into the Multiplex probe with a robotics liquid handler and then analyzed in rapid succession using a selective excitation experiment. Due to the simultaneous injection of four samples and the reduced analysis time with rapid selective excitation, the analysis rate achieved thus far is as low as 1 sample/34 s for 1D 1H NMR.

Magnetic Resonance Spectroscopy↗
PubMed2003

Solid-state NMR studies of the adsorption and photooxidation of ethanol on mixed TiO2--SnO2 photocatalysts.

In situ solid-state NMR methodologies have been used to investigate the photocatalytic oxidation of ethanol (CH3CH2OH) over a series of SnO2-based photocatalysts. The adsorption of ethanol on commercially available SnO2 powder was studied using both cross-polarization 13C NMR and REDOR experiments, and showed the formation of two surface ethanol species, hydrogen-bonded ethanol at surface hydroxyl groups and ethanol chemisorbed to the SnO2 surface (Sn--OCH2CH3). 13C NMR of the adsorbed ethanol was used to characterize the surface of monolayer SnO2--TiO2 coupled photocatalysts supported on porous Vycor glass. In situ solid-state NMR studies showed that the photooxidation of ethanol over the monolayer photocatalysts was slower than that over a supported TiO2 monolayer photocatalyst due to the build-up of reaction intermediates such as acetic acid on the catalyst surface. 119Sn NMR experiments characterized the tin species on the porous Vycor glass support.

Adsorption↗
PubMed2002

NMR difference probe: a dual-coil probe for NMR difference spectroscopy.

A unique probe designed to acquire nuclear magnetic resonance difference spectra of two samples is presented. The NMR Difference Probe contains two sample coils in a resonant circuit that switches between parallel excitation and serial acquisition to cancel common signals such as solvent peaks and impurities. Two samples containing a common analyte, acetonitrile, were used to demonstrate signal cancellation in a difference spectrum collected with a single pulse experiment. The cancellation was over 96% effective. The approach described has applications in the areas of solvent subtraction and spectral simplification.

Magnetic Resonance Spectroscopy↗