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12 results for “LC-HRMS”
Data files for:Critical assessment of the chemical space covered by LC-HRMS non-targeted analysis
<p>This upload contains the data for the review: "Critical assessment of the chemical space covered by LC-HRMS non-targeted analysis".</p> <p>All the files needed to run the code uploaded to GitHub (https://github.com/tobihul/CEC_review_code) can be found here.</p> <p>Included is: </p> <ul> <li>All 2657 structures found in the studied papers with their CID, InChIKey, and SMILES and whether they can be found in MassBank</li> <li>All the experimental parameters retrieved for each study in each category along with the general scope of each study</li> <li>The file with the CID, MW, XLogP3 and experimental parameters for each of the 61 papers</li> <li>The CSV file containing all classes of each of the compounds from the papers</li> <li>The CSV with all of the structures used to plot the chemical space of NORMAN SusDat (their CIDs)</li> </ul> <p> </p> <p> </p>
Data for: Mapping the Limits of Passive Samplers in Water: Chemical Space Coverage Using Nontargeted LC-HRMS Analysis
<p>This dataset provides files for passive samplers nad blanks analyzed by LC-HRMS fullscan DIA MS2.</p> <p>Excel file provides information about passive samplers, sampling site and sample files.</p>
Data from Nicolle et al. LC-HRMS study of Streptomyces sp. AgN23 Culture Media Extract. Study of AgN23 exometabolome and analysis of Arabidopsis metabolomic responses to the bacteria
<p>This archive compiles several datasets related to studies of <i>Streptomyces</i> sp. AgN23 interaction with <i>Arabidopsis thaliana</i>. 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 experimental cohort is grouped in a folder where the biological repeats can be retrieved, as well as QC (Quality Check, pool of all samples from the cohort), Blank samples and eventual alternative control such as Bennett, the mock control media of <i>Streptomyces</i> sp. AgN23. 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. The folder " AgN23-WT_AgN23-pSC004" contains chromatograms related to metabolomic study of Wild-type and pSC004-1, pSC004-10, pSC004-16 and pSC004-22 mutants of <i>Streptomyces</i> sp. AgN23. The folder " Col-0_AgN23" contains chromatograms related to metabolomic study of <i>Arabidopsis thaliana</i> Col-0 responses to colonization by <i>Streptomyces</i> sp. AgN23-WT. The folder " Col-0_pad3-1_AgN23" contains chromatograms related to metabolomic study of <i>Arabidopsis thaliana</i> Col-0 and the <i>Arabidopsis</i> pad3-1 mutant responses to colonization by <i>Streptomyces</i> sp. AgN23-WT. The folder " Col-0_pSC004" contains chromatograms related to metabolomic study of <i>Arabidopsis thaliana</i> Col-0 responses to colonization by <i>Streptomyces</i> sp. AgN23-WT and the AgN23 mutants pSC004-10 and pSC004-22. It should be noted that in the publication associated with this archive, the pSC004-1, pSC004-10, pSC004-16 and pSC004-22 mutants are referred to as ΔgbnB-1, ΔgbnB-2, ΔgbnB-3 and ΔgbnB-4, respectively.</p>
LC-HRMS files from wastewater samples collected in Portugal
<p>LC-HRMS files corresponding to wastewater samples associated to the paper:</p> <p><em><strong><a href="https://doi.org/10.1016/j.scitotenv.2021.152518">M.F.T. Sá et al. Tracking pollutants in a municipal sewage network impairing the operation of a wastewater treatment plant. Science of the Total Environment, 2022, 817, 152518. DOI: 10.1016/j.scitotenv.2021.152518</a></strong></em></p> <p>These files contain the LC-QTOF-HRMS data associated with the manuscript:</p> <p>Please note:</p> <p>Data was acquired with an Agilent 6550 QTOF in both:<br> - AutoMSMS (data-dependent acquisition, DDA) <br> - All Ions (data-independent acquisition, DIA)</p> <p>Data is provided in Agilent MassHunter B.10.00 format.</p> <p>In the case of AutoMSMS the iterative mode with two injections per sample was employed.<br> Further details on how samples were processed is presented in the manuscript.</p> <p>Data is therefore structure in two folders, one for DDA and one for DIA.<br> Each folder is then further divided between positive and negative mode.</p> <p>Files are named accordingly to the sample, using the same codes than in the manuscript.<br> The number after the code refers to the sample campaign.<br> Besides, there are "A" and "B" files in the DDA files, corresponding to the first and second iterative injection, respectively.</p> <p>As an example, the file:<br> "PVZ-2 2_B.d" in the AutoMSMS_DDA (either pos or neg) folder:<br> corresponds to the sample PVZ-2 from the second sampling campaign and second injection</p> <p><strong>If you reuse this data, please cite this dataset (<a href="https://doi.org/10.5281/zenodo.5830725">DOI: 10.5281/zenodo.5830725</a>) and the orginal article cited above (<a href="https://doi.org/10.1016/j.scitotenv.2021.152518">DOI: 10.1016/j.scitotenv.2021.152518</a>)</strong></p>
TBT exposure dataset of the manuscript "Assessment of endocrine disruptors effects on zebrafish (Danio rerio) embryos by untargeted LC-HRMS metabolomic analysis"
<p><strong>Raw LC-HRMS data of the TBT exposure of zebrafish embryos (for more details see https://doi.org/10.1016/j.scitotenv.2018.03.369)</strong></p> <p>The exposure protocol involved zebrafish embryos exposed in groups of 20 to various concentrations of chemical compounds, with five replicates per treatment. The concentrations ranged from the lowest observed effect concentrations (LOECs) to control levels. After exposure, embryos were collected, washed, frozen, and stored. Metabolites were extracted from individual embryo pools using methanol and methionine sulfone. The extraction process included vortexing, sonication, and centrifugation, followed by addition of water and chloroform. The aqueous fraction was dried and reconstituted using acetonitrile-water solution. Liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) was used for analysis. Chromatographic separations were carried out on a hydrophilic interaction liquid chromatography (HILIC) column. Mass spectrometry was performed using an Orbitrap mass spectrometer with electrospray ionization in positive and negative modes. The mass spectra were acquired at high resolution, and fragmentation scans were used for metabolite identification. The overall process aimed to analyze the metabolomic profile of zebrafish embryos exposed to different chemical concentrations.</p> <p><strong>Data files</strong></p> <blockquote> <p>TBT ESI+ (tbt_pos.rar) - CDF files</p> <p>- QC (4 replicates)</p> <p>- Control (5 replicates)</p> <p>- TBT 3 nM (5 replicates)</p> <p>- TBT 10 nM (5 replicates)</p> <p>- TBT 30 nM (5 replicates)</p> <p>- TBT 100 nM (5 replicates)</p> </blockquote> <p> </p> <blockquote> <p>TBT ESI- (tbt_neg.rar) - CDF files</p> <p>- QC (6 replicates)</p> <p>- Control (5 replicates)</p> <p>- TBT 3 nM (5 replicates)</p> <p>- TBT 10 nM (5 replicates)</p> <p>- TBT 30 nM (5 replicates)</p> <p>- TBT 100 nM (5 replicates)</p> </blockquote>
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>
3D-MSNet: A point cloud based deep learning model for untargeted feature detection and quantification in profile LC-HRMS data
<p>Supplementary data of 3D-MSNet</p>
Fig. 4 in Targeted isolation of sesquiterpene lactone dimers from Aucklandia lappa guided by LC-HRMS/MS-based molecular networking
Fig. 4. Comparison of experimental and calculated ECD spectrum of compounds 1–4.
Fig. 1 in Targeted isolation of sesquiterpene lactone dimers from Aucklandia lappa guided by LC-HRMS/MS-based molecular networking
Fig. 1. The molecular networks of the n-hexane-soluble fraction of A. lappa.
Fig. 3. Key HMBC, 1H–1H in Targeted isolation of sesquiterpene lactone dimers from Aucklandia lappa guided by LC-HRMS/MS-based molecular networking
Fig. 3. Key HMBC, 1H–1H COSY, and ROESY correlations of compounds 1–4.
Fig. 2 in Targeted isolation of sesquiterpene lactone dimers from Aucklandia lappa guided by LC-HRMS/MS-based molecular networking
Fig. 2. Structure of compounds 1–10.
Fig. 5 in Targeted isolation of sesquiterpene lactone dimers from Aucklandia lappa guided by LC-HRMS/MS-based molecular networking
Fig. 5. Putative biogenetic pathway of compounds 1–6.
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International Brain Laboratory public data
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OpenNeuro
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