Evaluation of BAYESIL for automated annotation of 1H NMR data using limited sample volumes: Application to African elephant serum
Ontology highlight
ABSTRACT:
ORGANISM(S): Loxodonta africana
SUBMITTER:
PROVIDER: S-BSST1045 | biostudies-other |
REPOSITORIES: biostudies-other
Similar Datasets
Project description:IntroductionTechnological advancements enabled the analyses of limited sample volumes on 1H NMR. Manual spectral profiling of the data is, however, complex, and timely.ObjectiveTo evaluate the performance of BAYESIL for automated identification and quantification of 1H NMR spectra of limited volume samples.MethodAliquots of a pooled African elephant serum sample were analyzed using standard and reduced volumes. Performance was evaluated on confidence scores, non-detects and laboratory CV.ResultsOf the 47 compounds detected, 28 had favorable performances. The approach could differentiate samples based on biological variation.ConclusionsBAYESIL is valuable for limited sample 1H NMR data analyses.
| S-EPMC10063514 | biostudies-literature
Project description:In (1)H NMR metabolomic datasets, there are often over a thousand peaks per spectrum, many of which change position drastically between samples. Automatic alignment, annotation, and quantification of all the metabolites of interest in such datasets have not been feasible. In this work we propose a fully automated annotation and quantification procedure which requires annotation of metabolites only in a single spectrum. The reference database built from that single spectrum can be used for any number of (1)H NMR datasets with a similar matrix. The procedure is based on the generalized fuzzy Hough transform (GFHT) for alignment and on Principal-components analysis (PCA) for peak selection and quantification. We show that we can establish quantities of 21 metabolites in several (1)H NMR datasets and that the procedure is extendable to include any number of metabolites that can be identified in a single spectrum. The procedure speeds up the quantification of previously known metabolites and also returns a table containing the intensities and locations of all the peaks that were found and aligned but not assigned to a known metabolite. This enables both biopattern analysis of known metabolites and data mining for new potential biomarkers among the unknowns.
| S-EPMC5858920 | biostudies-literature
Project description:A new generation of microscale, nuclear magnetic resonance (CapNMR) probe technology employs two independent detection elements to accommodate two samples simultaneously. Each detection element in the dual-sample CapNMR probe (DSP) delivers the same spectral resolution and S/N as in a CapNMR probe configured to accommodate one sample at a time. A high degree of electrical isolation allows the DSP to be used in a variety of data acquisition modes. Both samples are shimmed simultaneously to achieve high spectral resolution for simultaneous data acquisition, or alternatively, a flowcell-specific shim set is readily called via spectrometer subroutines to enable acquisition from one sample while the other is being loaded. An automation system accommodates loading of two samples via dual injection ports on an autosampler and two completely independent flowpaths leading to dedicated flowcells in the DSP probe.
| S-EPMC2932813 | biostudies-literature
Project description: Not available
| S-EPMC11635603 | biostudies-literature
Project description:The hypothesis of the present study is that metabolic phenotyping of blood plasma allows to (i) discriminate between colorectal cancer patients and control subjects and (ii) identify new biomarkers for colorectal cancer. In order to test this hypothesis, the investigators will apply proton nuclear magnetic resonance (1H-NMR) spectroscopy to perform metabolic phenotyping of blood plasma in 50 colorectal cancer patients and 50 control subjects. Multivariate statistics will be performed to assess the discriminative power of the applied methodology in distinguishing between both groups and to identify metabolites with potential as biomarkers for colorectal cancer.
| 2183890 | ecrin-mdr-crc
Project description:In light of global reef decline new methods to accurately, cheaply, and quickly evaluate coral metabolic states are needed to assess reef health. Metabolomic profiling can describe the response of individuals to disturbance (i.e., shifts in environmental conditions) across biological models and is a powerful approach for characterizing and comparing coral metabolism. For the first time, we assess the utility of a proton-nuclear magnetic resonance spectroscopy (1H-NMR)-based metabolomics approach in characterizing coral metabolite profiles by 1) investigating technical, intra-, and inter-sample variation, 2) evaluating the ability to recover targeted metabolite spikes, and 3) assessing the potential for this method to differentiate among coral species. Our results indicate 1H-NMR profiling of Porites compressa corals is highly reproducible and exhibits low levels of variability within and among colonies. The spiking experiments validate the sensitivity of our methods and showcase the capacity of orthogonal partial least squares discriminate analysis (OPLS-DA) to distinguish between profiles spiked with varying metabolite concentrations (0 mM, 0.1 mM, and 10 mM). Finally, 1H-NMR metabolomics coupled with OPLS-DA, revealed species-specific patterns in metabolite profiles among four reef-building corals (Pocillopora damicornis, Porites lobata, Montipora aequituberculata, and Seriatopora hystrix). Collectively, these data indicate that 1H-NMR metabolomic techniques can profile reef-building coral metabolomes and have the potential to provide an integrated picture of the coral phenotype in response to environmental change.
| S-EPMC4213140 | biostudies-literature
Project description:Analysis of enteric microbiota function indirectly through the fecal metabolome has the potential to be an informative diagnostic tool. However, metabolomic analysis of feces is hampered by high concentrations of macromolecules such as proteins, fats, and fiber in samples. Three methods-ultrafiltration (UF), Bligh-Dyer (BD), and no extraction (samples added directly to buffer, vortexed, and centrifuged)-were tested on multiple rat (n = 10) and chicken (n = 8) fecal samples to ascertain whether the methods worked equally well across species and individuals. An in silico baseline correction method was evaluated to determine if an algorithm could produce spectra similar to those obtained via UF. For both rat and chicken feces, UF removed all macromolecules and produced no baseline distortion among samples. By contrast, the BD and no extraction methods did not remove all the macromolecules and produced baseline distortions. The application of in silico baseline correction produced spectra comparable to UF spectra. In the case of no extraction, more intense peaks were produced. This suggests that baseline correction may be a cost-effective method for metabolomic analyses of fecal samples and an alternative to UF. UF was the most versatile and efficient extraction method; however, BD and no extraction followed by baseline correction can produce comparable results.
| S-EPMC8875708 | biostudies-literature
Project description:To optimize sensitivity, there has been an increasing interest in the miniaturization of NMR detectors. In our lab, a stripline NMR detector has been developed, which provides high resolution and is scalable to a large range of sample volumes. These features make it an ideal detector for hyphenated techniques. In this manuscript, we demonstrate a stripline probe, which is designed for combining supercritical fluid chromatography (SFC) experiments with NMR. It features a novel stripline chip, designed to reduce the signal from the contact pads, which results in an improved lineshape. An external lock circuit provides stability over time to perform signal averaging or multidimensional experiments. As proof of concept, we demonstrate the SFC-NMR technique with this stripline probe using a mixture of cholesterol and cholestanol, which is relevant for studying cerebrotendinous xanthomatosis. Additionally, this probe makes it possible to record high-resolution spectra of samples with a high spin density. This means that it is possible to directly observe shifts due to the nuclear demagnetizing field in the "homomolecular" case, which is challenging using conventional probes due to broadening effects from radiation damping.
| S-EPMC7547862 | biostudies-literature
Project description:This paper describes a very simple and robust microfluidic device for digitizing samples into an array of discrete volumes. The device is based on an inherent fluidic phenomenon, where an incoming aqueous sample divides itself into an array of chambers that have been primed with an immiscible phase. Self-digitization of sample volumes results from the interplay between fluidic forces, interfacial tension, channel geometry, and the final stability of the digitized samples in the chambers. Here, we describe experiments and simulations that were used to characterize these parameters and the conditions under which the self-digitization process occurred. Unlike existing methods used to partition samples into an array, our method is able to digitize 100% of a sample into a localized array without any loss of sample volume. The final volume of the discretized sample at each location is defined by the geometry and size of each chamber. Thus, we can form an array of samples with varying but predefined volumes. We exploited this feature to separate the crystal growth of otherwise concomitant polymorphs from a single solution. Additionally, we demonstrated the removal of the digitized samples from the chambers for downstream analysis, as well as the addition of reagents to the digitized samples. We believe this simple method will be useful in a broad range of applications where a large array of discretized samples is required, including digital PCR, single-cell analysis, and cell-based drug screening.
| S-EPMC2901535 | biostudies-literature
Project description:This study investigates the application of the paramagnetic shift reagent tris(dipivaloylmethanato)-europium(III) in NMR spectral studies of permethoxyacridone alkaloids (1-3) and pyranoacridone alkaloids (4-6). The induced chemical shifts (∆δ) of all protons were observed for the same molecule, and were compared to deduce the positions resulting from the distance nearby the Eu(dpm)3. Assignment of the H-2, H-4 and H-8 of polysubstituted acridones could be distinguished based on the least-squares method of lanthanide-induced shifts plotted against the mole ratios of Eu(dpm)3 to the substrate. The developed method is not only potentially useful for determining the planar structures of polysubstituted compounds, such as acridones, anthraquinones, xanthones, flavonoids, and phenanthrenes, but also applicable for their stereochemistry.
| S-EPMC7698746 | biostudies-literature