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493 results for “LC”
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>
Supplementary material 2 from: Kumschick S, Wilson JRU, Foxcroft LC (2020) A framework to support alien species regulation: the Risk Analysis for Alien Taxa (RAAT). In: Wilson JR, Bacher S, Daehler CC, Groom QJ, Kumschick S, Lockwood JL, Robinson TB, Zengeya TA, Richardson DM. NeoBiota 62: 213-239. https://doi.org/10.3897/neobiota.62.51031
Risk Analysis for Alien Taxa framework, adapted to South African NEMBA A&IS Regulations (v.1.2) (Appendix S2)
Supplementary material 1 from: Kumschick S, Wilson JRU, Foxcroft LC (2020) A framework to support alien species regulation: the Risk Analysis for Alien Taxa (RAAT). In: Wilson JR, Bacher S, Daehler CC, Groom QJ, Kumschick S, Lockwood JL, Robinson TB, Zengeya TA, Richardson DM. NeoBiota 62: 213-239. https://doi.org/10.3897/neobiota.62.51031
How the Risk Analysis Framework covers Section 6, Regulation 14-17, in the NEM:BA A&IS Regulations of 2014 (Appendix S1)
Data from: Novel insights into relationships between egg corticosterone and timing of breeding revealed by LC-MS/MS
Inter- and intra-clutch variation in egg corticosterone (CORT), the major glucocorticoid in birds, may provide insights into how maternal stress levels vary with the timing of breeding and with laying order. Common analytical methods (e.g. immunoassays), however, suffer from cross-reaction with other steroids, leading to potential overestimation of CORT concentrations which can obscure true hormone–environment relationships and complicate among-study comparisons. We here apply a new LC-MS/MS technique, which has recently been shown to avoid the problem of cross-reactivity due to its high specificity, to quantify CORT concentrations in yolk and albumen in clutches of lesser black-backed gulls Larus fuscus. We found that CORT concentration exhibited a previously unreported U-shaped relationship with time of breeding, which we explain as a potential interplay of two forces exerting extra strain on the early and late breeders. Furthermore, results showed an increase in CORT with laying order indicating the energetic expense of egg production. The levels of CORT assessed in this study were significantly lower than those previously reported in studies using immunoassays for CORT analysis. This supports the fact that incorporating chromatography effectively reduces overestimation of CORT due to cross-reactivity with other steroid hormones, particularly in egg yolk.
Supplemntary tables S1-S6 related with the article entitled: LC-MS-Based Plasma Proteome Analysis in Nursery Pigs Fed Diets Enriched with Native Chicory Inulin
<p><span>Table S1: Composition of the pig diet: control diet (C) and diets supplemented with 1% (T1) or 3% (T2) of native chicory inulin.; Table S2: Nutrient contents of the control diet (C) and the diets supplemented with 1% (T1) or 3% (T2) of native chicory inulin.; Table S3: Chemical composition (%) of inulin (IN) used as a feed supplement.; Table S4: Porcine plasma proteins submitted for further analysis.; Table S5: Proteins significantly altered in response to the T1 diet.; Table S6: Proteins significantly altered in response to the T2 diet.</span></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>
Commercial standards of Streptomyces antibiotics (LC-MS-MS/MS)
<p>Commercial standards for 8 antibiotics produced by Streptomyces used for method validation for the untargeted metabolomics workflow UmetaFlow. Germicidin A, Germicidin B, Kanamycin, Tetracycline, Thiostreptone, Globomycin, Ampicillin, Apramycin. Publicly available also at MassIVE MSV000090047.</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>
Demonstration LC-IM-MS Lipidomics Data for mzapy
<p>LC-IM-MS lipidomics data, in MZA format, acquired from porcine brain total lipid extract. Used for demonstration of mzapy functionality. </p>
Tooth enamel LC-MS dataset for: "Enamel histomorphometry, growth patterns and developmental trajectories of the first decidous molar in an Italian early medieval skeletal series"
<p>(n)LC-MS .raw data of tooth enamel samples from archaeological human remains. </p> <p>The dataset is related to the publication of Magri et al. </p>
Targeted Metabolite Analysis of alkaloids in Different tissues and Processed seeds of Strychnos nux-vomica using LC-Q-TOF-MSn
Open the record for dataset details and reuse information.
LC-HRMS study of Arabidopsis root metabolome in wild-type Col-0 and npr1 mutant upon in vitro inoculation with Streptomyces sp. AgN23.
<p>This archive compiles datasets related to studies of <em>Streptomyces</em> sp. AgN23 interaction with <em>Arabidopsis thaliana</em>. Ultra-high-performance liquid chromatography-high-resolution MS (UHPLC-HRMS) analyses were performed on a Q Exactive Plus quadrupole (Orbitrap) mass spectrometer, equipped with a heated electrospray probe (HESI II) coupled to a U-HPLC Ultimate 3000 RSLC system (Thermo Fisher Scientific, Hemel Hempstead, United Kigdom). For each biological sample, the RAW file obtained in ESI+ and ESI- mode were retrieved from the Xcalibur version 4.4 software and are deposited in separate sub-folders termed "RawPos" and "RawNeg". Each folder contains all the data relative to the cohort comprising "Blank" samples (n=13), Quality Check samples (pool of all samples from the cohort) "QC" (n=8), Control Col-0 plant samples "Col0CTRL" (n=6), Col-0 plant inoculated with AgN23 samples "Col0AgN23WT" (n=6), Control npr1 plant samples"NPR1CTRL" (n=6), npr1 plant inoculated with AgN23 samples "NPR1AgN23WT" (n=6). The files belonging to Negative mode bare the "neg" suffix and those belonging to Positive mode "pos" suffix, i.e. "Col0AgN23WT1_neg" and Col0AgN23WT1_pos". The details regarding samples preparation, analytic parameters and mass spectrometry, statistical treatment and visualization of the data will be made available in the publication relating to this archive. </p>
The molecular basis for the increased stability of the FUS-LC fibril at the anionic membrane- and air-water interfaces [part-2]
<p>Here, we provide atomistic molecular dynamics (CHARMM36m force field and GROMACS software) simulation trajectories of FUS-LC fibril on DOPC and DOPG membrane in .xtc format. Coordinates of the system at the end of the simulations and topology files are also supplied.The data accompanies the publication "The molecular basis for the increased stability of the FUS-LC fibril at the anionic membrane- and air-water interfaces" by Sanjoy Paul, Sayantan Mondal, Irina Shenogina, and Qiang Cui. </p>
LC-MS data for Hirschi et al. (2024)
<p>Additional data related to the LC-MS experiments (Suppl. Figs. 7 and 8). MRM method, calibration curves and quantifications as well as .wiff files.</p>
text-fig. 13. Theropod quadrates, illustrating different character states for characters 48-50. a, Allosaurus fragilisa left quadrate; posterior view; based on Madsen (1976) and MOR 693. b, unspecified oviraptorid; left quadrate; posterior (left) and medial view (right); redrawn from Maryanska and Osmólska (1997). Abbreviations: lc, lateral condyle; mc, medial condyle; ot cap, otic capitulum; pn, pneumatic cavity; pt, pterygoid wing; pt fac, pterygoid facet; qf, quadrate foramen; sq cap, squamosal capitulum. Scale bars represent 50 mm (a) and 10 mm (b). in The interrelationships and evolution of basal theropod dinosaurs
text-fig. 13. Theropod quadrates, illustrating different character states for characters 48-50. a, Allosaurus fragilisa left quadrate; posterior view; based on Madsen (1976) and MOR 693. b, unspecified oviraptorid; left quadrate; posterior (left) and medial view (right); redrawn from Maryanska and Osmólska (1997). Abbreviations: lc, lateral condyle; mc, medial condyle; ot cap, otic capitulum; pn, pneumatic cavity; pt, pterygoid wing; pt fac, pterygoid facet; qf, quadrate foramen; sq cap, squamosal capitulum. Scale bars represent 50 mm (a) and 10 mm (b).
Label-Free Quantification (LFQ) LC-MS Data for the Profiling of Domain-specific VCP/p97 Interactions in Living Cells
<p>This deposit includes LFQ LC-MS data for tandem-IP samples from VCP-L278AbK and VCP-D592AbK crosslinking experiments, their VCP-L278BocK and VCP-D592BocK controls, and SpectroMine output files.</p>
Positive mode DDA LC-MS/MS analysis of organic plant extracts (Malaga)
<p>Organic Plant extracts from Malaga resuspended in 8/2 MeOH/water and analysed on Exploris 480 in positive DDA mode.</p>
LC-DAD separation of Kahweol and cafestol oleate and palmitate from coffee
<p>Analysis of diterpene esters (kahweol oleate -KO; cafestol oleate -CO; kahweol palmitate -KP; cafestol palmitate -CP) by LC DAD in standards and coffees.</p> <p><strong>Separation conditions: </strong></p> <p>Coffee brews were extracted using 5 mL of diethyl ether. The mixture was vortexed for 2 min, and after centrifugation, the upper phase was transferred to a clean test tube. Next, the aqueous solution was re-extracted using diethyl ether, and the combined ether phase was washed with 5mL of 2 M NaCl solution followed by centrifugation (4000 rpm, 10 min. Finally, the clean ether phase was dried under an azote stream. Samples were kept at –22ºC until analysis using LC–DAD. Separation was achieved using a Purospher STAR LichroCART RP 18 end-capped (250 × 4 mm, 5 µm) column attached. Before injection, the dried extract was dissolved in 2.5 mL of acetonitrile and filtered through 0.45 µm filter membrane (PTFE, VWR, USA). Twenty microliters of sample were injected, and the separation was achieved using isocratic conditions for 35 min with the mobile phase made of acetonitrile/isopropanol (70:30, v/v) and pumped at 0.4 mL/min. A diode array detector, in the range of 200–400 nm, was used. After each run, the acquisition software exported data as a comma-separated-values format (EZChrom Elite 3.1.6).</p> <p>For the calibration curves, mixtures of the four diterpenes esters at similar concentrations were used in the range of 2 to 200 mg/L. Eight samples were prepared and run in duplicates</p> <p> </p> <p><strong>Files: </strong></p> <p><a href="https://zenodo.org/api/files/9c2c7a63-966d-4b4b-a1bf-5b8d8228ac48/FTIRATR_Pulse.mat">Data.mat</a>: Matlab structure with, as fields:<br> <Time> : a 3751 length vector. Time axis in min<br> <Wavelength> : a 201 length vector, Wavelength of detection<br> <Names_calibration> : Name of the samples for calibrations<br> <Data_calibration> : a 3751x201x16 matrix with in first dimension the retention time, in second dimension the wavelength for detection and third dimension the calibration samples.<br> <Data_samples> : a 3751x201x4 matrix with in first dimension the retention time, in second dimension the wavelength for detection and third dimension the coffee samples.<br> <Names_Samples> : Name of the samples<br> <Concentrations_calibration>: Table with the real concentration (mg/L) used in the standard samples.</p>
LC-HRAM-MS data for "Emergence of a proton exchange-based isomerization and lactonization mechanism in the plant coumarin synthase COSY"
<p>LC-HRAM-MS data underlying Figures 2b and 3b for "Emergence of a proton exchange-based isomerization and lactonization mechanism in the plant coumarin synthase COSY"</p>
LC-Q-TOF-MS/MS data of phyllobilins in apples cv. 'Gala'
<p>The data contains:</p> <p>- Data-dependent Inclusion List (ex professo) and Figures</p> <p>- Tables containing base peak chromatograms (BPCs) and All MS data, tables containing extracted ion chromatograms (EICs)</p> <p>- Chromatograms BPC + All MS and EIC (Bruker mass spectrometer files)</p>
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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.