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60 results for “liquid chromatography”
Data from: Liquid chromatography-mass spectrometry (LC-MS) data of a multi-epitope peptibody with bFGF/VEGFA
<p><span><span><span><span><span><span><span><span><span><span><span>The <span><span><span>protein </span></span></span><span><span><span>primary </span></span></span><span><span><span>structure of the recombinant </span></span></span>Peptibody were investigated systematically by Liquid Chromatography-Mass Spectrometry (LC-MS)<span><span><span>. T</span></span></span><span><span>he 15 amino acids of N-terminal were </span></span>Met-Gln-Lys-Arg-Lys-Arg-Lys-Lys-Ser-Arg-Tyr-Lys-Ser-Gly-Gly and <span><span>the C-terminal was Lys (K</span></span><span><span>), the same as</span></span> the theoretical sequence. <span><span>With more </span></span><a><span class="15"><span>protease</span></span></a><span><span>s, the whole sequence was detected at the coverage of </span></span>trypsin 87.5%, <span><span>c</span></span><span><span>hymotrypsin</span></span> 75.3% and <span><span>Glu-C</span></span> 76.7%<span><span>. The </span></span>peptide-mapping could be used as an valuable standard to certify the complete expression and primary structure of Peptibody. The pI and MW were 8.93 and 37.415 kDa, within the errors allowed . The binding specificity after production were analyzed using anti-VEGFA and anti-His antibodies.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Molecular profiling of diatom assemblages in tropical lake sediments using taxon-specific PCR and Denaturing High-Performance Liquid Chromatography (PCR-DHPLC)
Here we present a protocol to genetically detect diatoms in sediments of the Kenyan tropical Lake Naivasha, based on taxon-specific PCR amplification of short fragments (approx. 100 bp) of the small subunit ribosomal (SSU) gene and subsequent separation of species-specific PCR products by PCR-based DHPLC. An evaluation of amplicons differing in primer specificity to diatoms and length of the fragments amplified demonstrated that the number of different diatom sequence types detected after cloning of the PCR products critically depended on the specificity of the primers to diatoms and the length of the amplified fragments whereby shorter fragments yielded more species of diatoms. The DHPLC was able to discriminate between very short amplicons based on the sequence difference, even if the fragments were of identical length. and if the amplicons differed only in a small number of nucleotides. Generally the method identified the dominant sequence types from mixed amplifications. A comparison with microscopic analysis of the sediment samples revealed that the sequence types identified in the molecular assessment corresponded well with the most dominant species. In summary, the PCR-based DHPLC protocol offers a fast, reliable, and cost-efficient possibility to study DNA from sediments and other environmental samples with unknown organismic content, even for very short DNA fragments.
Raw data for the submitted manuscript entitled "Novel strategies for the determination of plastic additives derived from agricultural plastics in soil using ultrahigh-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS)"
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Raw data for Hybrid micellar liquid chromatography separation of brimonidine tartrate and brinzolamide. Retention study and quantification in fixed dose ophthalmic suspensions
<p>Raw data for optimization of the chromatographic conditions and calibration curve construction</p>
Liquid chromatography measurement obtained from the chitin extracts of insect exuviae
<p>Chitin, a biopolymer present in fungi and arthropods, is a compound of interest for various applications, such as in the agricultural and medical fields. With the recently growing interest in the development of insect farming, the availability of chitin-containing residual streams, particularly the molting skins (exuviae), is expected to increase in the near future. For application purposes, accurate quantification of chitin in these insect sources is essential. Previous studies on chitin extraction and quantification often overlooked the purity of the extracted chitin, making the outcomes inconsistent and prone to overestimation. The present study aims to determine chitin content in the exuviae of three insect species mass-reared worldwide: black soldier fly (BSF), mealworm, and house cricket. Chitin was chemically extracted using acid and alkali treatments to remove minerals and proteins. The purity of extracted chitin was evaluated by hydrolyzing the chitin into glucosamine, followed by quantitative determination of the latter using two liquid chromatography methods: electrochemical detection (ECD) and tandem mass spectrometry (MS/MS). Both methods proved accurate and precise, without the need for labor-intensive derivatization steps. Pearson's correlation and Bland-Altman plots showed that the glucosamine determination results obtained by the two methods were comparable, and there is no consistent bias of one approach vs. the other. The chitin content in extracted residues ranged between 7.9 and 18.5%, with the highest amount<br> found in BSF puparium. In summary, the study demonstrated that (1) the residual streams of the insect farming industry have a great potential for utilization as an alternative chitin source, and (2) both LC-ECD and LC-MS/MS are reliable for the quantitative determination of glucosamine in insect chitin.</p>
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>
Lipidomics and metabolomics datasets for "Adverse effects of arsenic uptake in rice metabolome and lipidome revealed by untargeted liquid chromatography coupled to mass spectrometry (LC-MS) and regions of interest multivariate curve resolution"
<p><strong>Files description</strong></p> <p>Raw files for lipidomics and metabolics studies on the impact of arsenic exposure on rice growth.</p> <p>File details on the worksheets lipids_files.xlsx and metabolomics_files.xlsx</p> <p>Files have been organized as follows:</p> <p><strong>Lipidomics</strong></p> <blockquote> <p>1) Control samples: lip_controls.rar<br> 2) Watering low As exposure: lip_water_1.rar<br> 3) Watering high As exposure: lip_water_1000.rar<br> 4) Soil low As exposure: lip_soil_5.rar<br> 5) Soil high As exposure: lip_soil_50.rar<br> 6) QC samples: lip_qcs.rar</p> </blockquote> <p><strong>Metabolomics (positive ionization mode)</strong></p> <blockquote> <p>1) Control samples: met_pos_controls.rar<br> 2) Watering low As exposure: met_pos_water_1.rar<br> 3) Watering high As exposure: met_pos_water_1000.rar<br> 4) Soil low As exposure: met_pos_soil_5.rar<br> 5) Soil high As exposure: met_pos_soil_50.rar<br> 6) QC samples: met_pos_qcs.rar</p> </blockquote> <p><strong>Metabolomics (negative ionization mode)</strong></p> <blockquote> <p>1) Control samples: met_neg_controls.rar<br> 2) Watering low As exposure: met_neg_water_1.rar<br> 3) Watering high As exposure: met_neg_water_1000.rar<br> 4) Soil low As exposure: met_neg_soil_5.rar<br> 5) Soil high As exposure: met_neg_soil_50.rar<br> 6) QC samples: met_neg_qcs.rar<br> </p> </blockquote> <p> </p> <p><strong>Experimental details</strong></p> <blockquote> <p><strong>Arsenic Exposure</strong></p> <p>Arsenic was supplied through two main routes: watering with contaminated water or soil containing arsenic. In addition, this new study includes metabolomic as well as lipidomic analysis, in order to have a more global overview of arsenic exposure.</p> <p>For the watering treatment, during the first 11 days, rice was irrigated with Milli-Q water. From that day until harvesting, plants were watered with 1 and 1000 μM of As (V) for the two concentration levels of exposure, and with Milli-Q water for control samples. The lowest concentration was established at 1 μM as it is the limit of the acceptable arsenic concentration in water by European legislation. The upper concentration was set at 1000 μM, a threshold established to ensure that the experiment was performed under sub-lethal arsenic concentration for the plant, based on previous studies.</p> <p>For the soil treatment, two containers were prepared with 1 kg of soil two days before planting. Soil from the container was exposed to two arsenic concentration levels (5 and 50 mg L<sup>-1</sup>). Once sowing, rice was irrigated the whole growth period with a solution containing 0.001 μM of As (V). The lowest arsenic limit in this treatment was set at 5 mg L<sup>-1</sup> as a maximum value of common arsenic leaches without toxic characteristics, although background soil content of arsenic varies between one and 40 ppm according to the US food and drug administration (FDA) report. The highest arsenic limit was established to 50 mg L<sup>-1</sup>, as a considerably high arsenic content in the soil, slightly above the maximum frequently encountered levels.</p> <p><strong>Lipidomic Analysis</strong></p> <p>The lipidomic analysis was performed using a Waters Acquity UPLC system (Waters Corporation, MA, USA), connected to a Waters LCT Premier orthogonal accelerated time of flight mass spectrometer (Waters), operated in both positive and negative electrospray (ESI) ionization modes. Full scan spectra were acquired from 50 to 1500 Da.</p> <p>The chromatographic column employed was a Kinetex C8 (100 x 2.1 mm, 1.7 μm) (Phenomenex) under the following conditions (already used in [47]): temperature at 30˚C, injection volume at 10 μL, and flow rate at 0.3 mL min<sup>-1</sup>. Mobile phases selected were (A) MeOH 1mM ammonium formate, and (B) H<sub>2</sub>O 2mM ammonium formate, both at 0.2% formic acid. The gradient started at 80% A, increased to 90% A in 3 min, from 3 to 6 min remained at 90% A, changed to 99 % A until minute 15, remained constant 1 min, and returned to initial conditions until minute 20.</p> <p><strong>Metabolomic analysis</strong></p> <p>The metabolomic analysis was performed using a Waters Acquity UPLC system connected to a Q-Exactive (Thermo Fisher Scientific, Hemel Hempstead, UK) equipped with a quadrupole-Orbitrap mass analyzer. Electrospray (ESI) was used as an ionization source in both positive and negative ion modes. Full scan mass range was set from <em>m/z</em> 90 to 1000, and all ion fragmentation (AIF) was performed with normalized collision energy (NCE) of 35 eV.</p> <p>The column employed was an HILIC TSK gel amide-80 column (250 x 2.0 mm i.d., 5 μm) provided by Tosoh Bioscience (Tokyo, Japan), under the following experimental conditions (already employed in [45]): flow rate at 0.15 mL min<sup>-1</sup>, at room temperature, and 5 μL injection volume. Mobile phases were (A) AcN, and (B) 5 mM ammonium acetate, adjusted at pH 5.5 with acetic acid. The gradient employed was: starting conditions at 25% B, then increased until 30% B in 8 min; a 60% B was reached at 10 min, held for 2 min more and then back to 25% B until minute 14 min; lastly, a re-equilibration step was added and from 14 to 20 min at 25% B.</p> </blockquote> <p> </p> <p><strong>Funding:</strong> This research was funded by the Spanish Ministry of Science and Innovation (MCI, Grant CTQ2017-82598-P) and Severo Ochoa Project CEX2018-000794-S (funded by MCIN/AEI/ 10.13039/501100011033), and supported from the Catalan Agency for Management of University and Research Grants (AGAUR, Grant 2017SGR753). MPC was funded by a predoctoral FPU 16/02640 scholarship from the Spanish Ministry of Education and Vocational Training (MEFP). </p> <p> </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>
Proteomic Profiling for Identification of Animal Skin Species in Ancient Egyptian Archaeological Leather using Liquid Chromatography Coupled with Tandem Mass Spectrometry (Nano LC-MS/MS)
<p><strong>Proteomic Profiling for Identification of Animal Skin Species in Ancient Egyptian Archaeological Leather using Liquid Chromatography Coupled with Tandem Mass Spectrometry (Nano LC-MS/MS)</strong></p>
Liquid chromatography tandem mass spectrometry of AMPA receptor containing vesicles
<p>Regulated delivery of AMPA receptors (AMPARs) to the postsynaptic membrane is an essential step in synaptic strength modification, and in particular, long-term potentiation (LTP). While LTP has been extensively studied using electrophysiology and light microscopy, several questions regarding the molecular mechanisms of AMPAR delivery via trafficking vesicles remain outstanding, including the gross molecular make up of AMPAR trafficking organelles and identification and location of calcium sensors required for SNARE complex-dependent membrane fusion of such trafficking vesicles with the plasma membrane. Here, we isolated AMPAR containing vesicles (ACVs) from whole mouse brains via immunoisolation and characterized them using immunoelectron microscopy, immunoblotting, and liquid chromatography tandem mass spectrometry (LC-MS/MS). We identified several proteins on ACVs that were previously found to play a role in AMPAR trafficking, including synaptobrevin-2, Rabs, the SM protein Munc18-1, the calcium-sensor synaptotagmin-1, as well as several new candidates, including synaptophysin and synaptogyrin on ACV membranes. Here, we present three biological replicates of liquid chromatography tandem mass spectrometry of AMPA receptor containing vesicles.</p>
Fig. 5 in Magnetic Ti C MXene functionalized with β-cyclodextrin as magnetic solid-phase extraction and in situ derivatization for determining 12 phytohormones in oilseeds by ultra-performance liquid chromatography-tandem mass spectrometry
Fig. 5. Spatio-temporal distribution of target phytohormones in different tissue of rapeseed germination.
Fig. 2 in Magnetic Ti C MXene functionalized with β-cyclodextrin as magnetic solid-phase extraction and in situ derivatization for determining 12 phytohormones in oilseeds by ultra-performance liquid chromatography-tandem mass spectrometry
Fig. 2. XRD spectrum (a), FI-TR pattern (b), Raman spectrum (c) of the composite material, and magnetization hysteresis loop of Fe3O4@Ti3C2@β-CD (d).
Fig. 1 in Magnetic Ti C MXene functionalized with β-cyclodextrin as magnetic solid-phase extraction and in situ derivatization for determining 12 phytohormones in oilseeds by ultra-performance liquid chromatography-tandem mass spectrometry
Fig. 1. Schematic of the synthetic route for Fe3O4@Ti3C2@β-CD and the sample pre-treatment procedure.
Fig. 4 in Magnetic Ti C MXene functionalized with β-cyclodextrin as magnetic solid-phase extraction and in situ derivatization for determining 12 phytohormones in oilseeds by ultra-performance liquid chromatography-tandem mass spectrometry
Fig. 4. Effects of different cleanup sorbents (a), effects of the amount of magnetic solid-phase extraction sorbents (b), effects of the simultaneous derivatization and magnetic solid phase extraction time (c), effects of the desorption time (d). 5 mg rapeseed spiked with 10 ng/g of each analyte.
Fig. 3 in Magnetic Ti C MXene functionalized with β-cyclodextrin as magnetic solid-phase extraction and in situ derivatization for determining 12 phytohormones in oilseeds by ultra-performance liquid chromatography-tandem mass spectrometry
Fig. 3. SEM image of Ti3C2 (a) and Fe3O4@Ti3C2@β-CD (b), TEM image of Ti3C2(c) and Fe3O4@Ti3C2@β-CD (d), elemental mapping and chemical composition of Fe3O4@Ti3C2@β-CD (e).
Data from: Molecular profiling of diatom assemblages in tropical lake sediments using taxon-specific PCR and Denaturing High-Performance Liquid Chromatography (PCR-DHPLC)
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Liquid chromatography tandem mass spectrometry of AMPA receptor containing vesicles
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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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Liquid chromatography measurement obtained from the chitin extracts of insect exuviae
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High Performance Liquid Chromatography (HPLC) pigment analysis from rosette bottle samples at various depths from CCE LTER process cruises in the California Current System, 2006 to 2017.
High Performance Liquid Chromatography (HPLC) samples are collected from rosette bottles (from three to eight different depths in the photic zone) at stations located within the CCE region on Process cruises (since 2006, ongoing). The HPLC method is used to measure concentrations of chlorophylls and carotenoids in samples of particulate matter, which includes filtering and freezing the filter while at sea. The taxon-specific phyto-pigments are extracted back onshore. Concentrations of chlorophyll a are used as a proxy for phytoplankton biomass and concentrations of other taxon-specific pigments are used to determine contributions of phytoplankton taxa to total phytoplankton biomass.
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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.