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2,394 results for “ms”
Raw MS data for "Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor"
<p>These are the raw HDX/MS data for our paper: "Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor."</p>
Galaxy Training Material for Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)
<p>This dataset contains the training data for the <strong>Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)</strong> GTN tutorial. It includes 3 GC-[EI+]-HRMS files from seminal plasma samples, the RECETOX Metabolome HR-[EI+]-MS library collected from mostly endogoenous compounds from MetaSci Human Metabolite Library, reference alkanes, sample metadata table, and preprocessed XCMS object.</p>
Ionome analysis of Salmonella mutants by Inductively coupled plasma mass spectrometry (ICP-MS)
<p>In many Gram-negative bacteria, the stress sigma factor of RNA polymerase, σS/RpoS, remodels global gene expression to reshape the physiology of quiescent cells and ensure their survival under non-optimal growth conditions. In the foodborne pathogen <i>Salmonella enterica</i> serovar Typhimurium, σS is also required for biofilm formation and virulence.</p><p>We have previously shown that a Δ<i>rpoS</i> mutation affects the <i>Salmonella</i> ionome. Indeed, inductively coupled plasma mass spectrometry analyses have unraveled a significant effect of the Δ<i>rpoS </i>mutation on the cellular concentration of manganese, magnesium, cobalt and potassium, suggesting that σS controls fluxes of ions that might be important for the fitness of quiescent cells (Metaane et al. 2022, PLoS ONE 17(3): e0265511).</p><p>Study: These findings prompted us to evaluate the impact on the<i> Salmonella</i> ionome of deletions of genes encoding the <i>Salmonella</i> Mn2+ transporters (<i>sitABCD</i> and <i>mntH</i>), the Co2+ transporter (<i>cbiMNQO</i> operon) and small proteins of unkown function (<i>yqaE</i> and <i>yqjDEK</i>) that accumulate in quiescent <i>Salmonella</i> under the tight control of σS (Levi-Meyrueis et al. PloS one. 2014; 9(5):e96918, Lago et al. Scientific reports. 2017; 7(1):2127 and Metaane et al. 2022, PLoS ONE 17(3): e0265511).</p><p>Material and Methods: Cell-associated contents of several elements were measured by inductively coupled plasma mass spectrometry (ICP-MS) as previously described in Metaane <i>et al </i>2022 PLoS ONE 17(3): e0265511.Dried cell pellets were prepared by V. Monteil and F. Norel (Institut Pasteur, Université de Paris, CNRS UMR3528, Biochimie des Interactions Macromoléculaires, F-75015, Paris, France). Cell-associated contents of several elements were measured by S. Ayrault and L. Bordier (ICP-MS platform, Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRSUVSQ,Université Paris-Saclay, 91191, Gif-sur-Yvette, France)</p><p><strong>This work was supported by the French National Research Agency (ANR-19-CE44-0005-01, PERIOMET project).</strong></p><p><strong>Linked studies:</strong></p><ul><li>NOREL Francoise, MONTEIL Veronique, DOUCHE Thibaut, & MATONDO Mariette. (2023). Global effects of deletions of the sitABCD, mntH, cbiMNQO and corA genes, encoding transporters for manganese, cobalt and magnesium on protein abundance in Salmonella enterica serovar Typhimurium grown to stationary phase in LB. [Data set]. Zenodo. https://doi.org/10.5281/zenodo.8279780</li><li>Metaane S, Monteil V, Douché T, Giai Gianetto Q, Matondo M, Maufrais C, Norel F. Loss of CorA, the primary magnesium transporter of <i>Salmonella, </i>is alleviated by MgtA and PhoP-dependent compensatory mechanisms. PloS one. 2023;18(9):e0291736.</li></ul>
Data for: "Unlocking the potential of LC-MS through an XIC-based algorithm for chromatographic optimisation"
<p>This dataset is for upload of supplementary info and data for my master research thesis at the University of Amsterdam.</p> <p>All the compounds in each pesticide mix of the RESTEK multiresidue kit can be found along with some descriptors.</p> <p>For easy use of the developed algorithm without having to generate any mzxml files, a few files are included on which SAFD and CompCreate have already been performed using three different LC methods, Their gradients are also provided. To run the code, a package has been developed and is ready for installation at: https://github.com/tobihul/LC_MS_Resolved_Peaks. </p> <p> </p>
Data for ms. Do people really care less about their cats than about their dogs? A comparative study in three European countries
<p>The present dataset is based on a questionnaire which is also part of this package. The enclose questionnaire includes identifiable and relevant variables names (yellow highlighted).</p> <p>Participants were recruited by Norstat, a European-based survey company, with the aim of gaining a representative sample of Austrian, Danish and UK citizens, including pet owners. The survey company administers and hosts online panels comprising citizens from many European countries. We aimed for a sample that is representative in terms of age, gender, and region. Therefore, a stratified sampling principle was set up where individuals within each stratum were randomly invited to participate. The invitations were issued through e-mail that contained a link to the online questionnaire. Data was collected from 11-25<sup>th</sup> of March 2022 in Austria, from 11-24<sup>th</sup> of March 2022 in Denmark and from 8-23<sup>rd</sup> of March 2022 in the UK. The invitation provided information about the background of the study, the participating universities, ethical approval, estimated time for questionnaire completion and further, participants were informed that the completion of the questionnaire was voluntary and anonymous, and that they could exit the survey at any point. Before participants were directed to the survey, they ensured informed consent by confirming that they are over 17 years old, and consent to participate in this survey. </p> <p>Besides the questionnaire the dataset includes a csv and an Excel file consisting of the data that is used in the ms. and an rtf and a pdf file with data variable names/labels, and value labels.</p>
MALDI FTICR MS imaging data of pancreatic mouse tissue
<p>Preprocessed imaging mass spectrometry data (.imzML format) for mouse pancreatic Islets of Langerhans. Detailed information is given in the publication by Prade & Kunzke et al. "De novo discovery of metabolic heterogeneity with immunophenotype-guided imaging mass spectrometry" (currently in revision).</p>
GC-MS data set for Generation of a chromosome-scale genome assembly of the insect-repellant terpenoid-producing Lamiaceae species, Callicarpa americana
<p>RAW GC/MS data set for characterization of class II terpene synthases from <em>Callicarpa americana </em></p>
Non-target screening of organic compounds in offshore produced water by GC×GC-MS (associated data)
<p>Associated data for the manuscript titled "<em>Non-target screening of organic compounds in offshore produced water by GC×GC-MS</em>"</p> <p>Preprint doi://10.26434/chemrxiv.13317938</p> <p> </p>
Supplement to "The virtual spot approach: a simple method for image U-Pb carbonate geochronology by high-repetition rate LA-ICP-MS" by Hoareau et al
<p>This repository contains supplementary data, excel datasets and python / R codes as supplement to the publication by Hoareau et al.</p> <p>Files are:</p> <ul> <li>pdf with Supplementary material (S1 to S6)</li> <li>Excel spreadsheet with all image ratio and CPS data (Table S7)</li> <li>Iolite4 python plugin for virtual spot calculation (Iolite4_plugin_virtual_spot.py)</li> <li>Jupyter .ipynb file for U-Pb age calculation (Multiage.ipynb, R language)</li> <li>Jupyter .ipynb file for cp-sat minimum rectangle problem calculation (Rects.ipynb, Python language)</li> </ul>
Age estimation of captive Asian elephants (Elephas maximus) based on DNA methylation: An exploratory analysis using methylation-sensitive high-resolution melting (MS-HRM)
<p>Age is an important parameter for bettering the understanding of biodemographic trends-development, survival, reproduction and environmental effects-critical for conservation. However, current age estimation methods are challenging to apply to many species, and no standardised technique has been adopted yet. This study examined the potential use of methylation-sensitive high-resolution melting (MS-HRM), a labour, time, and cost-effective method to estimate chronological age from DNA methylation in Asian elephants (<em>Elephas maximus</em>). The objective of this study was to investigate the accuracy and validation of MS-HRM use for age determination in long-lived species, such as Asian elephants. The average lifespan of Asian elephants is between 50-70 years but some have been known to survive for more than 80 years. DNA was extracted from 53 blood samples of captive Asian elephants across 11 zoos in Japan, with known ages ranging from a few months to 65 years. Methylation rates of two candidate age-related epigenetic genes, <em>RALYL</em> and <em>TET2,</em> were significantly correlated with chronological age. Finally, we established a linear, unisex age estimation model with a mean absolute error (MAE) of 7.36 years. This exploratory study suggests an avenue to further explore MS-HRM as an alternative method to estimate the chronological age of Asian elephants.</p>
Native MS dataset for: "Insights into the pathogenesis of primary hyperoxaluria type I from the structural dynamics of alanine:glyoxylate aminotransferase variants"
<p>Native mass spectrometry dataset used in: <strong>Insights into the pathogenesis of primary hyperoxaluria type I from the structural dynamics of alanine:glyoxylate aminotransferase variants.</strong> Pavla Vankova, Juan Luis Pacheco-Garcia, Dmitry S. Loginov, Atanasio Gómez-Mulas, Alan Kádek, José Manuel Martín-Garcia, Eduardo Salido, Petr Man and Angel L. Pey. FEBS Letters (2024)</p> <p><strong>Description:</strong></p> <p>Native mass spectrometry (MS) analysis verifying the oligomeric state of alanine:glyoxylate aminotransferase (AGT) protein and its P11L and I340M (LM) polymorphism and LM G170R mutation variants in primary hyperoxaluria type I.</p> <p><strong>Sample processing:</strong></p> <p>AGT protein as well as its LM and LM G130R mutants were buffer exchanged into 150 mM aqueous ammonium acetate solution (pH 7.5, MS-grade, Sigma-Aldrich) through six cycles of tenfold dilution and re-concentration using centrifugal concentrators Vivaspin 500 (30 kDa cut-off, <em>Sartorius</em>). Desalted proteins were introduced into a Synapt G2Si mass spectrometer (Waters) via static nanoelectrospray ionization from in-house prepared gold-coated borosilicate glass capillaries Kwik-Fil 1B120F-4 (<em>World Precision Instruments</em>). Protein concentration in samples was determined by 280 nm absorbance measurements using DeNovix DS-11 spectrophotometer. Samples were diluted in ammonium acetate and electrosprayed at 1 and 2 µM concentration. The mass spectrometer was carefully tuned for best signal quality and intensity, while keeping ion activation and unfolding minimal. Namely, electrospray voltage was kept at 1.3 kV, source desolvation temperature 80°C, sampling cone 80 V and 10 V collision voltage with 6 ml/min flow of argon in the trap region for thermalization of ions. Quadrupole was operated in a broadband transmission mode up to 8000 m/z while the spectra were acquired in mass range 500 – 20000 m/z. Spectra were externally mass recalibrated using known masses of caesium iodide clusters.</p> <p><strong>Data processing:</strong></p> <p>Raw mass spectra were averaged over 75 scans and further processed in Waters MassLynx 4.1. The averaged spectra were exported for ZENODO deposition as plain in plain m/z vs intensity .txt files as well uploaded as part of the .raw file format of the whole analysis (including initial metadata) with scan descriptions and parameter changes described in a stand-alone .txt descriptor file.</p>
Dataset for publication "Multi-phase quantitative compositional mapping by LA-ICP-MS: analytical approach and data reduction protocol implemented in XMapTools"
<p>Datasets for the publication "Multi-phase quantitative compositional mapping by LA-ICP-MS: analytical approach and data reduction in XMapTools"</p>
An Approach Based on an Increased Bandpass for Enabling the Use of Internal Standards in Single Particle ICP-MS: Application to AuNPs Characterization
<p>This dataset contains the raw data corresponding to the figures of the publication https://doi.org/10.3390/nano13121838</p>
HDX-MS dataset for: "Glycan-induced structural activation softens the human papillomavirus capsid for entry through reduction of intercapsomere flexibility"
<p>Hydrogen/deuterium exchange mass spectrometry dataset used in: <strong>Glycan-induced structural activation softens the human papillomavirus capsid for entry through reduction of intercapsomere flexibility.</strong> Yuzhen Feng*, Dominik van Bodegraven*, Alan Kádek*, Ignacio L.B. Munguira, Laura Soria-Martinez, Sarah Nentwich, Sreedeepa Saha, Florian Chardon, Daniel Kavan, Charlotte Uetrecht#, Mario Schelhaas#, Wouter H. Roos#. <em>Nature Communications</em> 10076 (2024). doi: 10.1038/s41467-024-54373-0</p> <p>* - authors contributing equally</p> <p># - corresponding authors</p> <p><strong>Description:</strong></p> <p>Hydrogen/deuterium exchange mass spectrometry (HXMS) analysis of the effect of heparin on the conformational dynamics of human papillomavirus 16 pseudovirus (PsV).</p> <p><strong>Sample processing:</strong></p> <p>HPV16 PsV were prepared according to (Buck & Thompson: Current Protocols in Cell Biology 2007). In short, p16Shell and pClneo-EGFP were transfected into HEK293TT cells. After 48 h, cells were harvested and lysed followed by maturation of the virus particles for 24 h. For purification, the particles were purified using a CsCl step gradient (27 % w/V and 38.8 % w/V CsCl in 10 mM Tris-HCl pH 7.4, 207570 x g, 3 h 50 min, 4 °C) followed by dialysis in Float-A-Lyzer devices (1 mL, Spectra/Por) against a total of 3 L HPV virion buffer (1x PBS, 635 mM NaCl, 0.9 mM CaCl2, 0.5 mM MgCl2, 2.1 mM KCl, pH 7.4).</p> <p>PsV were pre-incubated for 1 h either with or without heparin (H4784, Sigma-Aldrich) at room temperature. To initiate deuterium labelling the samples were 6-fold diluted with the virion buffer they were obtained in, only made of 99.9% D2O (150 mM NaCl, 4.8 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4, 0.9 mM CaCl2, 0.5 mM MgCl2, pD 7.2). This resulted in a final concentration of 0.5 µM L1 monomer in the form of PsV with or without 1 mg/ml heparin during deuterium labelling. The exchange reaction was left to proceed at room temperature until aliquots of 45 µl were removed at predetermined time points (1 min, 5 min, 15 min, 1 h and 4 h). In the aliquots, the exchange was immediately stopped by twofold dilution with ice-cold quench buffer (0.25 M glycine, 100 mM TCEP, 8 M urea, indicated pH 2.7), resulting in final pH 2.5. For samples with heparin, the quench buffer additionally contained 1 mg/ml protamine sulphate (P4020, Sigma-Aldrich). After 30 s incubation on ice, the samples were centrifuged at 10.000 x g for 1 min at 0 °C. Each supernatant was transferred to a fresh tube and flash frozen in liquid nitrogen. Low binding microtubes and low binding pipette tips (both Axygen) were used throughout for all handling of viral particles.</p> <p>The frozen samples were quickly thawed and injected into a refrigerated (1°C) HPLC system (Infinity 1260, Agilent Technologies), through a porcine pepsin column (≥ 3200 units/mg, Sigma-Aldrich) in-house immobilized onto POROS-20AL perfusion resin (Thermo Scientific) as described previously (Wang et al.: Molecular & Cellular Proteomics 2002), which was kept at 4°C. Pepsin digestion was performed at isocratic 200 µl/min flow rate (0.4 % formic acid in water). After the digestion, peptides were online desalted for 3 min on a peptide microtrap (OPTI-TRAP, Optimize Technologies) and then eluted on a reversed-phase analytical column (ZORBAX 300SB-C18, 0.5 x 35 mm, 3.5 µm, 300Å, Agilent Technologies). There LC separation proceeded at 25 µl/min flow rate through an 8 min gradient of 8–30% solvent B, followed by a 3 min gradient of 30-90 % solvent B (solvent A: 0.4 % formic acid in water, solvent B: 0.4 % formic acid in acetonitrile). The outlet of the HPLC system was connected to an electrospray ionization (ESI) source of an Orbitrap Fusion Tribrid Mass Spectrometer (Thermo Scientific). The instrument was operated in positive ESI MS-only mode for deuterated samples, scan range 300-2000 m/z, using 4 microscans at resolving power setting 120,000. In a separate measurement on non-deuterated sample, the instrument was used in positive data-dependent ESI MS/MS mode with 30% HCD dissociation, 1 microscan and 240,000 resolving power setting for the identification of all peptides produced by non-specific pepsin cleavage.</p> <p>In total 22 pmol and 50 pmol L1 protein were injected per MS and MS/MS analysis, respectively. To minimize sample carry-over on the protease column, two washing solutions were always injected between sample injections modified from Majumdar et al. 69 (wash solution 1: 5% acetonitrile, 5% isopropanol, 20% acetic acid; wash solution 2: 4 M Urea, 1 M glycine, pH 2.5). All HDX samples were analysed in technical triplicates, except for the 15 min time point for PsV without heparin, which was measured in duplicate.</p> <p><br><strong>Data processing:</strong></p> <p>Peptides were identified from the MS/MS data by the Andromeda search algorithm implemented in MaxQuant (version 1.6.5.0) using a custom protein database containing the sequences of HPV16 L1 and L2 proteins. Deuterium uptake for the identified peptides was calculated with DeutEx (in-house developed), manually inspected and the statistical significance of the observed differences in deuteration was evaluated by applying an unpaired two-tailed Student’s T-test with single pooled variance evaluated with alpha ≤ 0.05 using the Holm-Šidák correction for multiple comparisons in Prism 8.0.1 (GraphPad Software). The processed data were visualized using MSTools (https://peterslab.org/MSTools/, Kavan & Man: International Journal of Mass Spectrometry 2011) and open-source PyMol 2.6.0a0 (Schrödinger, Inc).</p> <p>For ZENODO the datafiles were deposited as native Thermo .raw files (including instrumental parameters metadata) while all peaks in the spectra were additionally exported into plain m/z vs intensity .txt files per each scan in the LC-MS analysis as also used for the DeutEx HDX-MS processing.</p>
LC-MS/MS, PSM and BLG properties data from "Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins"
<p>This dataset contains the data analyzed in:</p> <p>Rodriguez Palomo I, Nair B, Chang Y, Dartigues B, Dekker K, Mackie M, Evans M, Macleod R, Olsen JV, Collins MJ. (2023) "<em>Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins"</em></p> <p>It contains the following data:</p> <ul> <li>raw_files.zip Thermo RAW files for the 0, 4 and 128 days samples</li> <li>benchmark_results.zip PSMs data from the analysis of the RAW files <ul> <li>Data from runs in Mascot, Fragpipe, pFind, Metamorpheus, MaxQuant and DeNovoGUI</li> <li>Parameters and workflow files for MaxQuant and Fragpipe</li> </ul> </li> <li>bovin_blg_prop.zip BLG properties files: amyloid formation, 3D structure and solvent accessibility</li> <li>benchmark_table.csv Table with runs settings for benchmarking</li> <li>parameters_table.xlsx Spreadsheet with software parameters, derived from files used to run each software</li> </ul> <p> </p>
UVSL MS 48032 Tamiḻneṟi Viḷakkam
<div>Paper manuscript of the <em>Tamiḻneṟi Viḷakkam </em>from the U. Ve. Swaminatha Iyer Library. Photographs taken by the NETami project.</div>
GOML MS TR118/R435 Kaḷaviyaṟ Kārikai
<p>A manuscript of the Kaḷaviyaṟ Kārikai from the Government Oriental Manuscripts Library, Chennai.</p> <p>https://www.tamildigitallibrary.in/goml/download?filename=paper_manuscript/Tamil/TR/TR+0118++R+00435.pdf</p>
Portimine A toxin causes skin pathology through ZAKα-dependent NLRP1 inflammasome activation: LC-MS/MS raw data for Figure 1. C
<p>This dataset pertains to the LC-MS/MS analyses conducted as part of a study on microalgal toxins present in samples from Senegal, published in the paper entitled <em>"Portimine A toxin causes skin pathology through ZAK</em><em>α</em><em>-dependent NLRP1 inflammasome activation."</em> The data correspond to the quantification results of environmental samples presented in Figure 1C.</p> <p>The raw data were acquired using Analyst software (Applied Biosystems proprietary software). The materials and methods used to generate these data are detailed in the associated publication in <em>EMBO Molecular Medicine</em> (ISSN: 1757-4676, 2024).</p>
RECETOX Exposome HR-[EI+]-MS library
<p>The RECETOX Mass Spectrum Reference Libraries is a collection of MS spectra collected from authentic compounds. Each library comprises the spectra in MSP format and an accompanying SDF database of compounds. The collection is shared under terms & conditions of <a href="https://creativecommons.org/licenses/by-nc/4.0/">CC-BY-NC</a>.</p> <p>The RECETOX Exposome HR-[EI+]-MS library is a collection of mostly anthropogenic compounds. Spectra were acquired at 70 eV on Thermo Fisher Q Exactive™ GC Orbitrap™ GC-MS/MS at 60000 resolving power.</p>
RECETOX Metabolome HR-[EI+]-MS library
<p>The RECETOX Mass Spectrum Reference Libraries is a collection of MS spectra collected from authentic compounds. Each library comprises the spectra in MSP format and an accompanying SDF database of compounds. The collection is shared under terms & conditions of <a href="https://creativecommons.org/licenses/by-nc/4.0/">CC-BY-NC</a>.<br> <br> The RECETOX Metabolome HR-[EI+]-MS library is a collection of mostly endogoenous compounds from MetaSci Human Metabolite Library. Analytes underwent methoximation/silylation prior to acquisition. Spectra were acquired at 70 eV on Thermo Fisher Q Exactive™ GC Orbitrap™ GC-MS/MS at 60000 resolving power.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.