Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
2,394
datasets available to search
ShareScore release 0.9.0
Dataset results
2,394 results for “ms”
Source data for the HDX-MS experiments in publication "Deciphering the allosteric regulation of mycobacterial inosine-5′-monophosphate dehydrogenase"
<p>Dataset of HDX-MS experiments related to the publication "Deciphering the allosteric regulation of mycobacterial inosine-5′-monophosphate dehydrogenase", published in Nature Communications with DOI: https://doi.org/10.1038/s41467-024-50933-6 </p> <p>The differential HDX-MS experiments compare the apo and ligand-bound states of IMPDH from Mycobacterium smegmatis.</p> <p>A description of the dataset is provided in the attached README file: IMPDH_HDX-MS_README.txt.</p> <p>Detailed experimental conditions are available in the related publication.</p>
Fig. 2 in Biota-MS: Montando o quebra-cabeça da biodiversidade de Mato Grosso do Sul
Fig. 2. Espécies de animais encontradas no estado de Mato Grosso do Sul. A) Trichomycterus cf. dali Rizzato, Costa-Jr., Trajano & Bichuette, 2011; B) Pyrrhura devillei (Massena & Souance, 1854); C) Eunectes notaeus Cope, 1862; D) Elga newtonsantosi Machado, 1992; E) Craspedacusta sowerbii Lankester, 1880; F) Melanophryniscus klappenbachi Prigioni & Langone, 2000. Fotos: Paulo R. Souza.
Fig. 1. Algumas paisagens e in Biota-MS: Montando o quebra-cabeça da biodiversidade de Mato Grosso do Sul
Fig. 1. Algumas paisagens e ambientes de Mato Grosso do Sul. A) serra do Amolar; B) Coval, nascente do Sucuriú; C) bancada laterítica em primeiro plano e morraria do Urucum ao fundo; D) planalto da BodoQuena; E) borda oeste do planalto de Maracaju, em Piraputanga, com floresta estacional decidual; F) fitofisionomia chaQuenha do tipo chaco arborizado, municÍpio de Porto Murtinho; G) Lagoa das Pedras, municÍpio de Bonito, com predomÍnio de Dimerostemma annuum (Hassl.) H. Rob. (Compositae), registro de março de 2000; H) planície alagada (Pantanal) com arroz nativo, próxima à foz do rio São Lourenço; I) carandazal (Copernicia alba Morong. (Arecaceae)), município de Porto Murtinho. Nem todas as imagens coincidem com a localização no mapa. Fotos: Vali J. Pott (B) e Paulo R. Souza (as demais).
SI and ZooMS spectra Cassenade (MALDI-TOF-MS)
<p>Supplementary Information (SI) for the paper:</p> <p>Ruebens, K., Discamps, E., Smith, G. M., Hublin, J-J. Integrating ZooMS and zooarchaeology to assess the Châtelperronian and carnivore occupations at Cassenade (Dordogne, France), published in the gold open access journal PaleoAnthropology.</p> <ul> <li>SI 1: individual raw data files (10 .zip files with 2,550 mzxml files, representing 840 bone samples and 10 blanks, each spotted in triplicate, organised in 10 MALDI runs)</li> <li>SI 2: excel database listing information on plate number, MALDI run and triplicates (spot location), the identified peptide markers and ZooMS identifications (Barcode ID).</li> <li>SI 3: excel database with ZooMS identifications, zooarchaeological data (incl. body size classes) and taphonomic observations</li> <li>SI 4: excel database with the spatial coordinates for the piece-plotted bone fragments</li> <li>SI 5: tables for the statistical tests</li> <li>SI 6: R script used for making the figures and statistical tests</li> </ul> <p>Note: samples CAS-190-248 relate to bone fragments from old excavations which are not reported in this paper so not included in this database. </p> <p>Note: All samples were extracted using an AmBic protocol, except for samples 856-876 which were demineralised using HCl. </p> <p>For any questions please contact Karen Ruebens.</p> <p>Please use the DOI (10.5281/zenodo.11102785) when citing this dataset.</p>
MS-UMG: MALDI-TOF Mass Spectra and Resistance Information on Antimicrobials from University Medical Center Göttingen
<p>During routine diagnostic procedures, we aggregated MALDI-TOF MS data of organisms isolated from clinical specimens from the University Medical Center Göttingen (UMG) in 2020 / 2021. We integrated these with corresponding antimicrobial susceptibility profiles. This amounted to 26,961 mass spectra and 26,961 corresponding metadata entries for the year 2020, and 50,381 mass spectra and 50,381 corresponding metadata entries for 2021, respectively. The dataset reflects 348 different species of bacterial and fungal organisms and 72 different antimicrobial susceptibility testing (AST) results.</p> <p> </p> <p>Please cite: </p> <div> <div>Effect of Data Heterogeneity in Clinical MALDI-TOF Mass Spectra Profiles on Direct Antimicrobial Resistance Prediction through Machine Learning</div> </div> <div><span><span><span>Youngjun</span> <span>Park</span></span>, <span><span>Michael</span> <span>Weig</span></span>, <span><span>Christine</span> <span>Noll</span></span>, <span><span>Oliver</span> <span>Bader</span></span>, <span><span>Anne-Christin</span> <span>Hauschild</span></span></span></div> <div><span>bioRxiv </span><span>2024.10.18.617592; </span><span><span>doi:</span> https://doi.org/10.1101/2024.10.18.617592</span></div>
Fingerprint Matrix Files for "Machine Learning-based Bioactivity Classification of Natural Products Using LC-MS/MS Metabolomics"
<p>These files are the necessary dataset to reproduce the observed machine learning metrics in the paper "Machine Learning-based Bioactivity Classification of Natural Products Using LC-MS/MS Metabolomics" in review at the Journal of Natural Products. </p> <ul> <li>Multiclassifier_23_Drug_Class_Train-Test_Fingerprint_Matrix.tsv is the accumulated positive training set for the 23 different classes demonstrated in the training and testing sets.</li> <li>Negative_Train-Test_Fingerprint_Matrix.tsv is the negatives training and testing examples derived from the RIKEN NP Depo which represent a diverse set of natural product compounds that serve as the counter points to the positive examples.</li> <li>GNPS_23_Drug_Class_Fingerprints_Matrix.tsv is the dataset of fingerprints generated from the publically available GNPS MSMS dataset. These training examples serve to confirm the ability of the machine learning model to generalize to experimental data. </li> <li> Negative_Train-Test_Fingerprint_Matrix.tsv is the dataset of negative training examples derived from the publically available spectra from the GNPS dataset. It is composed of nearly 2,800 random MSMS spectra to compose a diverse negative evaluation set. </li> <li>Random_GNPS_Fingerprints.tsv is the dataset of fingeprints of 9,443 random spectra from GNPS used to evaluate the false positive rate of each model.</li> </ul>
Primary MS data and secondary data for: "Post-proline cleaving enzymes also show specificity to reduced cysteine"
<p>raw LC-MS/MS data (Bruker Daltonics - timsTOF Pro and tims TOF SCP) and ESI-MS data (Bruker Daltonics - 15T ESI/MALDI FT-ICR MS) and related MASCOT generic files (<em>.mgf) and search results (</em>.csv) plus corresponding custom databases (*.fasta). Protein identifications were performed using MASCOT or PEAKS programs.</p> <p>Data were used to:</p> <ul> <li>extract cleavage preferences of Clarity Ferm AnPEP, ProAlanase or Neprosin. Target samples were: protein mixture (BSA, cytC, bCA2, myoglobin, 14-3-3) or human serum from a healthy donor or HEK cell lysate or human insulin or oxidized bovine insulin beta chain</li> <li>profile protein content of Clarity Ferm AnPEP and quantify the proteins</li> </ul> <p>Additional data are under Zenodo entry 10.5281/zenodo.13985598</p> <p>Linked to the publication: <br>Postproline Cleaving Enzymes also Show Specificity to Reduced Cysteine. <br>Kalaninová Z, Portašiková JM, Jirečková B, Polák M, Nováková J, Kavan D, Novák P, Man P. <br>Anal. Chem. 2024, 96, 48, 19084–19092 <br>doi: 10.1021/acs.analchem.4c04277. </p> <p> </p>
Primary MS data and secondary data for: "Post-proline cleaving enzymes also show specificity to reduced cysteine" Part2
<p>raw LC-MS/MS data (Bruker Daltonics - tims TOF SCP) and related PEAKS<em> search results (*</em>.csv) plus corresponding custom database (*.fasta). Protein identifications were performed using PEAKS programs.</p> <p>Data were used to:</p> <ul> <li>extract cleavage preferences of Clarity Ferm AnPEP. The target sample was HEK cell lysate.</li> </ul> <p>These data are related to https://doi.org/10.5281/zenodo.13938580.</p>
Data analysis of an LC-MS dataset from a human urine biofluid cohort study
<p>Supplementary dataset and tutorials for the "<strong>Statistical analysis in metabolic phenotyping"</strong></p> <p> </p> <p>This repository contains Jupyter Notebooks with two examplar metabolomic data analysis workflows, applied to a liquid chromatography mass spectrometry dataset (LC-MS). The LC-MS dataset used comes from a metabolic phenotyping investigation of human urine biofluid samples from a dementia cohort. In this sample set, baseline spot urine samples (first sample collected after recruitment to the study) were collected as part of the AddNeuroMed<sup>1</sup> and ART/DCR study consortia, with the aim of identifying biomarkers of neurocognitive decline and Alzheimer’s disease. These samples were analysed by LC-MS and <sup>1</sup>H NMR, using the methods described by Lewis <em>et al</em><sup>2</sup> and Dona <em>et al</em>. Detailed information about this cohort and other available phenotypic measurements can be found in Lovestone and the ANMERGE<sup>3</sup> repository, which can be accessed via the Sage BioNetworks portal (<a href="https://doi.org/10.7303/syn22252881">https://doi.org/10.7303/syn22252881</a>). Information about the metabolic profiling experiments can be found in the study's MetaboLights entry: <a href="https://www.ebi.ac.uk/metabolights/MTBLS719">https://www.ebi.ac.uk/metabolights/MTBLS719</a>.</p> <p> </p> <p>1. Lovestone, S. <em>et al.</em> AddNeuroMed - The european collaboration for the discovery of novel biomarkers for alzheimer’s disease. in <em>Annals of the New York Academy of Sciences</em> (2009). doi:10.1111/j.1749-6632.2009.05064.x</p> <p>2. Lewis, M. R. <em>et al.</em> Development and Application of UPLC-ToF MS for Precision Large Scale Urinary Metabolic Phenotyping. <em>Anal. Chem.</em> <strong>88</strong>, acs.analchem.6b01481 (2016).</p> <p>3. Birkenbihl, C. <em>et al.</em> ANMerge: A comprehensive and accessible Alzheimer’s disease patient-level dataset. <em>medRxiv</em> (2020). doi:10.1101/2020.08.04.20168229</p>
MALDI-TOF-MS spectra of modern Australian marsupials for ZooMS (Zooarchaeology by Mass Spectrometry)
<p>MALDI-TOF-MS spectra of extracted collagen from modern Australian marsupials. These spectra were used to develop peptide markers for Zooarchaeology by Mass Spectrometry (ZooMS). All spectra are uploaded in .mzml format.</p> <p>One sample per species was also analyzed with LC-MS/MS (indicated in the metadata file). The LC-MS/MS data is available at PXD027107 through MassIVE (doi:10.25345/C5TC2H). Information about the species and sample numbers can be found in the metadata file.</p>
Proteomic data (SWATH-MS) of mouse uterine horns treated with different types of plasma
<p>This dataset contains the proteomic data (SWATH-MS) from 48 mouse uterine horns corresponding to a murine model of Asherman'Syndrome (presence of intrauterine adhesions). These 48 uterine horns correspond to 26 NOD-SCID mice (mouse uterus are bicornuate - 2 uterine horns per mouse) distributed in 4 groups (n = 6 /group), attending to the treatment received: Control (n = 6; milliQ H2O was injected), non-activated umbilical cord plasma (n = 6), activated umbilical cord plasma (n = 6), and activated platelet-rich plasma from adult blood (n = 6). To simulate Asherman's Syndrome, we induced endometrial damage (using a needle) inside the lumen of left uterine horns from all animals, while right horns were left undamaged.</p>
Proteomic data (LC-MS/MS) of human plasma samples
<p>LC-MS/MS analysis of 8 different samples of plasma: 4 samples correspond to the activated platelet-rich plasma (PRP) fractions from 4 different patients with infertility due to Asherman's syndrome and/or endometrial atrophy; 2 samples correspond to the activated and not-activated, respectively, PRP fractions from a control fertile patient; 2 samples correspond to the activated and not-activated, respectively, fractions from a commercial umbilical cord plasma.</p>
Text-fig. 1. Dental nomenclature. Peignecyon felinoides n. gen. et n. sp. a) TU 73916 upper right M1 in occlusal view; b) TU 7391147 lower right m1, b1) lingual view, b2) occlusal view. Abbreviations: bde, basal distobuccal expansion*; bc, buccal cingulum; Ec, ectoflexus; dc, distal cingulum; dlc, distolingual cristid; end, entoconid; hyd, hypoconid; lc, lingual cingulum; ME, metacone; MEC, metaconule; mc, mesial cingulum; med, metaconid; mlc, mesiolingual cristid; mpc, mesial protoconid cristid; MS, metastyle; PA, paracone; PAC, paraconule; pad, paraconid; PR, protocone; prd, protoconid; PS, parastyle. *Not developed in Peignecyon felinoides. in A New Thaumastocyoninae (Amphicyonidae, Carnivora) From The Early Miocene Of Tuchořice, The Czech Republic
Text-fig. 1. Dental nomenclature. Peignecyon felinoides n. gen. et n. sp. a) TU 73916 upper right M1 in occlusal view; b) TU 7391147 lower right m1, b1) lingual view, b2) occlusal view. Abbreviations: bde, basal distobuccal expansion*; bc, buccal cingulum; Ec, ectoflexus; dc, distal cingulum; dlc, distolingual cristid; end, entoconid; hyd, hypoconid; lc, lingual cingulum; ME, metacone; MEC, metaconule; mc, mesial cingulum; med, metaconid; mlc, mesiolingual cristid; mpc, mesial protoconid cristid; MS, metastyle; PA, paracone; PAC, paraconule; pad, paraconid; PR, protocone; prd, protoconid; PS, parastyle. *Not developed in Peignecyon felinoides.
Text-fig. 9. Tachyglossus aculeatus. Transverse section through the orbital region of the head of a juvenile specimen. ms: sphenobturatory membrane; plb: palatine bone; psw: primary endocranial sidewall; sll: secondary lateral lamella of Kuhn (1971); this endocranial process (blue) is here interpreted as a derivative of the cartilago teniformis. (From Kuhn and Zeller 1987.) in Cartilago Teniformis And Its Derivatives: Additional Information On The Basic Composition And Evolution Of The Skull
Text-fig. 9. Tachyglossus aculeatus. Transverse section through the orbital region of the head of a juvenile specimen. ms: sphenobturatory membrane; plb: palatine bone; psw: primary endocranial sidewall; sll: secondary lateral lamella of Kuhn (1971); this endocranial process (blue) is here interpreted as a derivative of the cartilago teniformis. (From Kuhn and Zeller 1987.)
Text-fig. 8. Tachyglossus aculeatus. Transverse section through the temporal region of the adult head. Membranous parts blue, autostoses brown and allostoses purple. gg: ganglion gasseri; lop: lamina obturatoria periotici; ms: sphenobturatory membrane; mt: musculus temporalis; oo: os obturans; opa: parietal bone. (Modified from Kuhn and Zeller 1987.) in Cartilago Teniformis And Its Derivatives: Additional Information On The Basic Composition And Evolution Of The Skull
Text-fig. 8. Tachyglossus aculeatus. Transverse section through the temporal region of the adult head. Membranous parts blue, autostoses brown and allostoses purple. gg: ganglion gasseri; lop: lamina obturatoria periotici; ms: sphenobturatory membrane; mt: musculus temporalis; oo: os obturans; opa: parietal bone. (Modified from Kuhn and Zeller 1987.)
Text-fig. 3. Metacheiromys marshi, USNM-P 452349, coronal sections from CT scans. a – section 590 of 2020 through the anteriormost tympanic cavity showing air spaces in the entotympanic and squamosal; b – section 898 of 2020 at level of the fenestra vestibuli showing the mastoid sinus. Abbreviations: bo – basioccipital, bs – basisphenoid, cp – crista parotica, ec – ectotympanic, en – entotympanic, es – epitympanic sinus of squamosal, fv – fenestra vestibuli, hyf – hypophyseal fossa, m – malleus, ms – mastoid sinus, pr – promontorium, sq – squamosal, tc – tympanic cavity. in Skeletal Anatomy Of The Basicranium And Auditory Region In The Metacheiromyid Palaeanodont Metacheiromys (Mammalia, Pholidotamorpha) Based On High-Resolution Ct Scans
Text-fig. 3. Metacheiromys marshi, USNM-P 452349, coronal sections from CT scans. a – section 590 of 2020 through the anteriormost tympanic cavity showing air spaces in the entotympanic and squamosal; b – section 898 of 2020 at level of the fenestra vestibuli showing the mastoid sinus. Abbreviations: bo – basioccipital, bs – basisphenoid, cp – crista parotica, ec – ectotympanic, en – entotympanic, es – epitympanic sinus of squamosal, fv – fenestra vestibuli, hyf – hypophyseal fossa, m – malleus, ms – mastoid sinus, pr – promontorium, sq – squamosal, tc – tympanic cavity.
ULS and UAV-MS Directly Georeferenced Point Clouds of the River Teme
<p>Directly Georeferenced Point Clouds of the River Teme for PhD research, provided as supporting information to methods described. These are unfiltered point clouds of a vegetated river reach in the UK, given in WGS UTM_30N CRS. UAV-MS are SfM derived point clouds and ULS UAV laser scanning based point clouds.</p>
Data from: Age estimation using methylation-sensitive high-resolution melting (MS-HRM) in both healthy felines and those with chronic kidney disease
<p>Age is an important ecological tool in wildlife conservation. However, it is difficult to estimate in most animals, including felines — most of whom are endangered. Here, we developed the first DNA methylation-based age-estimation technique — as an alternative to current age-estimation methods — for two feline species that share a relatively long genetic distance with each other: domestic cat (<i>Felis catus</i>; 79 blood samples) and an endangered <i>Panthera</i>, the snow leopard (<i>Panthera uncia</i>; 11 blood samples). We measured the methylation rates of two gene regions <span>using </span>methylation-sensitive high-resolution melting (MS-HRM). Domestic cat age was estimated with a mean absolute deviation (MAD) of 3.83 years. Health conditions influenced accuracy of the model. Specifically, the models built on cats with chronic kidney disease (CKD) had lower accuracy than those built on healthy cats. The snow leopard-specific model (i.e. the model that resets the model settings for snow leopards) had a better accuracy (MAD = 2.10 years) than that obtained on using the domestic cat model directly. This implies that our markers could be utilised across species, although changing the model settings when targeting different species could lead to better estimation accuracy. The snow leopard-specific model also successfully distinguished between sexually immature and mature individuals.</p>
Visualizations of fragment ancient Egyptian coffin based on MS PLD recordings
<p><strong>Detail on a fragment of an Egyptian coffin (Theban, end 22nd or early 25th Dynasty, © Archaeological Collections Faculty of Arts, KU Leuven). A: photograph with white light; B: green-induced infrared luminescence (523nm radiation); C: red-induced infrared luminescence (623nm radiation); D: normalmap (surface relief estimations) of isolated Egyptian blue, based on result in C.</strong></p>
Visualizations of reverse E.9076 based on old photographic and new MS PLD recordings
<p><strong>Reverse of execration figurine E.9076 (©️ Art and History Museum, Brussels), pre-processing and post-processing MS results</strong></p>
ScienceDex guides
Understand access before you commit
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.