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102 results for “spectrometry data”
Validation data Set: Development and validation of a quantitative method for 15 antiviral drugs in poultry muscle using liquid chromatography coupled to tandem mass spectrometry
<p>Validation dataset for paper published in the Journal of Chromatography A.</p> <p> </p> <p>Clément Douillet, Mary Moloney, Melissa Di Rocco, Christopher Elliott, Martin Danaher,<br> Development and validation of a quantitative method for 15 antiviral drugs in poultry muscle using liquid chromatography coupled to tandem mass spectrometry, Journal of Chromatography A, Volume 1665, 2022, 462793, ISSN 0021-9673,</p> <p><br> Abstract:</p> <p>The objective of this work was to develop a quantitative multi-residue method for analysing antiviral drug residues and their metabolites in poultry meat samples. Antiviral drugs are not licensed for the treatment of influenza in food producing animals. However, there have been some reports indicating their illegal use in poultry. In this study, a method was developed for the analysis of 15 antiviral drug residues in poultry muscle (chicken, duck, quail and turkey) using liquid chromatography coupled to tandem mass spectrometry. This included 13 drugs against influenza and associated metabolites, but also two drugs employed for the treatment of herpes (acyclovir and ganciclovir). The method required the development of a novel chromatographic separation using a hydrophilic interaction chromatographic (HILIC) BEH amide column, which was necessary to retain the highly polar compounds. The analytes were detected using a triple quadrupole mass spectrometer operating in positive electrospray ionization mode. A range of different sample preparation protocols suitable for polar compounds were evaluated. The most effective procedure was based on a simple acetonitrile-based protein precipitation step followed by a further dilution in a methanol/water solution. The confirmatory method was validated according to the EU 2021/808 guidelines on different species including chicken, duck, turkey and quail. The validation was performed using various calibration curves ranging from 0.1 µg kg−1to 200 µg kg−1, according to the analyte. Depending on the analyte sensitivity, decision limits achieved ranged from 0.12 µg kg−1 for arbidol to 34.7 µg kg−1 for ribavirin. Overall, the reproducibility precision values ranged from 2.8% to 22.7% and the recoveries from 84% to 127%. The method was applied to 120 commercial poultry samples from the Irish market, which were all found to be residue-free.<br> Keywords: Antiviral drug residues; Influenza; HILIC; LC-MS/MS; Poultry muscle</p>
Utilizing Skyline to analyze lipidomics data containing liquid chromatography, ion mobility spectrometry and mass spectrometry dimensions
<p>Lipidomics studies suffer from analytical and annotation challenges due to the great structural similarity of many of the lipid species. To improve lipid characterization and annotation capabilities beyond those afforded by traditional mass spectrometry (MS)-based methods, multidimensional separation methods such as those integrating liquid chromatography, ion mobility spectrometry, collision induced dissociation and MS (LC-IMS-CID-MS) may be employed. While LC-IMS-CID-MS and other multidimensional methods offer valuable hydrophobicity, structural and mass information, the files are also complex and difficult to assess. Thus, the development of software tools to rapidly process and facilitate confident lipid annotations is essential. In this Protocol Extension, we utilize the freely available, vendor-neutral, and open-source software Skyline to process and annotate the multidimensional lipidomic data. While Skyline was established for targeted processing of LC-MS-based proteomics data, it has since been extended such that it can be used to analyze small molecule data as well as data containing the IMS dimension. This protocol utilizes Skylines’ recently expanded capabilities, including small molecule spectral libraries, indexed retention time (iRT), and ion mobility filtering, and provides a step-by-step description for importing data, predicting retention times, validating lipid annotations, exporting results, and editing our manually validated 500+ lipid library. While the time required to complete the steps outlined here varies based on multiple factors such as dataset size and familiarity with Skyline, this protocol takes approximately 5.5 hours to complete when annotations are rigorously verified for maximum confidence.</p>
Data accompanying empirical Bayes functional models for hydrogen deuterium exchange mass spectrometry
<p>Data accompanying empirical Bayes functional models for hydrogen deuterium exchange mass spectrometry</p>
RAW SILAC mass spectrometry data of Chemical and topological design of multi-capped mRNA and capped circular RNA
<p>Here is the RAW SILAC mass spectrometry data included in "<strong>Chemical and topological design of multi-capped mRNA and capped circular RNA</strong>" from Chen et al. Please find the "README.txt" file for more details. </p>
Gamma spectrometry data of loess and U-Th ages of soil carbonates from Tajikistan
<p>These two Excel files contain gamma spectrometry data of loess-paleosols of the Khonako-II sequence (Dataset S1), and measured U-Th isotope compositions and calculated U-series ages of soil carbonates collected in the Kuldara and Khonako-II sites (Dataset S2) on the Khovaling Loess Plateau, Tajikistan.</p>
Data for Theoretical assessment of indistinguishable peptides in mass spectrometry-based proteomics
<p>This dataset provides comprehensive spectral libraries for the theoretical assessment of indistinguishable peptides in mass spectrometry-based proteomics. The data were generated through various experimental conditions. Each file contains the peptide fragmentation patterns and retention times predicted with Prosit at different normalized collision energies (NCE) and charge states.</p>
Data-driven fingerprint nanomechanical mass spectrometry
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Data and code for "Large volume injection and assessment of reference standards for n-alkane δD and δ13C analysis via gas chromatography isotope ratio mass spectrometry"
<p>This file includes data and code related ot the publication, "<span>Large volume injection and assessment of reference standards for <em>n</em>-alkane δD and δ<sup>13</sup>C analysis via gas chromatography isotope ratio mass spectrometry" in Rapid Communications in Mass Spectrometry (in review). Included are datasets of <em>n</em>-alkane δD and δ<sup>13</sup>C measurements with a recently developed large-volume injeciton method. Measuremtns of reference standards and lake sediment samples from Eifel maar lakes of Germany are included. Additionally, code to implement the correction schemes and reporduce the figures and analysis described in the paper are included. </span></p>
Supplementary data Quantitative elemental mapping of chondritic meteorites using laser ablation-inductively coupled plasma-time of flight-mass spectrometry (LA-ICP-TOF-MS)
<p>Supplementary data Quantitative elemental mapping of chondritic meteorites using laser ablation-inductively coupled plasma-time of flight-mass spectrometry (LA-ICP-TOF-MS)English</p>
Raw data: Validation of a method for surveillance of nanoparticles in mussels using single particle inductively coupled plasma mass spectrometry
<p>The compressed archive contains SP-ICP-MS data to reproduce results for the paper with the working title "Validation of a method for surveillance of nanoparticles in mussels using single particle inductively coupled plasma mass spectrometry"".</p> <p>The remaining data to produce all other results, visualizations and statistics for the paper is included in the supplementary or GitHub. Associated code is deposited in a GitHub repository, github.com/arebruvold/mussel_validation .</p>
Data from: A proteomic method to extract, concentrate, digest, and enrich peptides from fossils with colored (humic) substances for mass spectrometry analyses
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Data from: Direct nano-electrospray ionization tandem mass spectrometry for quantification and identification of metronidazole in its dosage form and human urine
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Data from: Rapid MALDI-TOF mass spectrometry strain typing during a large outbreak of Shiga-Toxigenic Escherichia coli
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Data from: Liquid chromatography-mass spectrometry (LC-MS) data of a multi-epitope peptibody with bFGF/VEGFA
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Mass spectrometry data of Chalmydomonas reinhardtii central pair mutants
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Ground Gamma-ray Spectrometry Data of the Araguainha Impact Structure
<p>This is a gamma-ray dataset that was collected during three field campaings in the Araguainha impact structure in Brazil. Araguainha is the largest impact strucutre of the country (~40 km wide). The available file provides the raw dataset in counts per unit of time, the concentration values of K, U and Th, and some derived products for geological interpretation.</p>
MALDI-TOF-MS reference spectra and sequence data for African bovid collagen for Zooarchaeology by Mass Spectrometry (ZooMS)
<p>MALDI-TOF-MS spectra of extracted collagen from modern African bovids used as reference spectra to develop markers for Zooarchaeology by Mass Spectrometry (ZooMS). Some of this material was also analyzed by LC-MS/MS. That data can be found at MassIVE MSV000084675 (<a href="https://doi.org/doi:10.25345/C5239K">doi:10.25345/C5239K</a>). Information about the species of the samples can be found in Key for Labels.csv file.</p> <p>The sequence data contains annotated alignments of the proteins COL1A1 and COL1A2 and the alignments for the available bovid collagen protein sequences. More information on these files can be found in the corresponding manuscript to this dataset.</p>
Data from: Metabolism studies of paeoniflorin in rat liver microsomes by ultra-performance liquid chromatography coupled with hybrid quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS/MS)
To explore metabolism mechanism of paeoniflorin in the liver and further understand intact metabolism process of paeoniflorin, a rapid, convenient and effective assay is described using ultra-performance liquid chromatography coupled with hybrid quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS/MS). The strategy was confirmed in the following primary processes: firstly, different concentration of paeoniflorin, rat liver microsomes, coenzymes and different incubated conditions were optimized to build a biotransformation model of rat liver microsomes in vitro by high performance liquid chromatography with diode array detection (HPLC-DAD); secondly, the metabolites of paeoniflorin in rat liver microsomes were detected and screened using UPLC-Q-TOF-MS/MS by comparing the total ion chromatogram (TIC) of the experimental group with those of control groups; finally, the molecular formulae and corresponding chemical structures of paeoniflorin metabolites were identified by comparing the MS and MS/MS spectra with the self-constructed database and simulation software. Based on this analytical strategy, 20 metabolites of paeoniflorin were found and 6 metabolites (including four new compounds) were tentatively identified. It was shown that hydrolysis and oxidation were the major metabolic pathways of paeoniflorin in rat liver microsomes, and the main metabolic sites were the structures of pinane and the ester bond. These findings were significant for a better understanding of the metabolism of paeoniflorin in rat liver microsomes and the proposed metabolic pathways of paeoniflorin might provide fundamental support for the further research in the pharmacological mechanism of Paeoniae Radix Rubra (PRR).
Data from: Liquid chromatography-tandem mass spectrometry metabolic profiling of nazartinib reveals the formation of unexpected reactive metabolites
Nazartinib (EGF816, NZB) is a promising third-generation human epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor. This novel irreversible mutant-selective EGFR inhibitor targets EGFR containing both the resistance mutation (T790M) and the activating mutations (L858R and Del19), while it does not affect wild-type EGFR. However, the metabolic pathway and bioactivation mechanisms of NZB are still unexplored. Thus, using liquid chromatography-tandem mass spectrometry, we screened for products of NZB metabolism formed in vitro by human liver microsomal preparations and investigated the formation of reactive intermediates using potassium cyanide as a nucleophile trap. Unexpectedly, the azepane ring was not bioactivated. Instead, the carbon atom between the aliphatic linear tertiary amine and electron-withdrawing system (butenoyl amide group) was bioactivated, generating iminium intermediates as reactive species. Six NZB phase I metabolites, formed by hydroxylation, oxidation, and N-demethylation, were characterized. Moreover, two reactive iminium ions were characterized and their corresponding bioactivation mechanisms were proposed. Based on our results, we speculate that bioactivation of NZB can be blocked by small sterically hindering groups, isosteric replacement, or a spacer. This approach might reduce the toxicity of NZB by avoiding the generation of reactive species.
Raw data and code for publication "Optimisation of surfactin yield in Bacillus using active learning and high-throughput mass spectrometry"
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.