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54 results for “MS2”
Omnitrap MS2 and MS3 data of Herceptin
<p>All data were acquired in a Q Exactive Plus Orbitrap MS equipped with the Omnitrap platform. Ions were produced by nanoESI using pulled borosilicate glass-coated emitters. The analysis of intact Herceptin was performed using a combination of fragmentation techniques. Mass selection of 49+ charge state at MS2 level was performed using the quadrupole mass filter of the Q Exactive Plus, while MS2 isolation of 25+ charge state and MS3 level isolation were performed in the Omnitrap platform. Orbitrap resolution was set to 240,000, CID activation time was 10 ms and Electron capture dissociation (ECD) was performed with ~0 eV electrons. All experiments were performed with intact non-reduced Herceptin in positive ion mode. Herceptin stock solution was diluted to a final concentration of 5 uM in a) 100 mM ammonium acetate for experiments with 25+ charge state and in b) 50:50:0.1 ACN:H2O:FA for experiments with 49+ charge state.</p>
A global LC-MS2-based methodology to identify and quantify anionic phospholipids in plant samples
<p>This table contains peaks aera values from LC-MS used to develop a method for identification and quantification of anionic lipid in plant sample: Genva et al. 2023: “A global LC-MS2-based methodology to identify and quantify anionic phospholipids in plant samples”</p>
molxspec: Deep learning models for predicting MS2 spectra from molecular structures
<p>This repository contains a pre-processed dataset derived from the <a href="https://gnps.ucsd.edu">GNPS public repository</a> of natural product mass spectra as well as pretrained model weights for four different types of model architectures using pytorch (version 1.9.0). The contents are as follows:</p> <ul> <li>gnps_processed_data.tgz: Contains tab separated files of molecule/MS2 spectra pairs derived from GNPS after filtering for invalid structures, too large molecules (bigger than 2000 M/Z spectra), and structures that yielded valid 3D geometry optimization. The processing steps were done for positive ionization mode (pos_* files), though negative ionization data is also included (neg_* files)</li> <li>models.tgz: Contains pytorch format pretrained models for four different architecutres: MLP (a residual block multilayer perceptron trained on ECFP molecular fingerprints), BERT (the same MLP but trained on pretrained representations from the Zinc V1 pretrained ChemBERTa models on SMILES), GCN (a graph convolution architecture), and EGNN (an equivariant graph neural network). Models were trained on pos_processed_gnps_shuffled_with_3d_train.tsv found in the gnps_processed_data.tgz file described previously.</li> </ul>
Skeletonema marinoi MS2 mzML files in negative mode
<p>These are MS2 files in .mzML format acquired in negative mode. The extracted metabolites come from a sample from <em>Skeletonema marinoi.</em></p>
A molecular basis for the presentation of phosphorylated peptides by HLA-B antigens (ANNOTATED MS2 SPECTRA OF PHOSPHOPEPTIDES)
<p>Phosphopeptides identified from the immunopeptidome of the C1R-B*40 cell line. </p> <p>Phosphopeptides identified from the proteome of the C1R-B*40 cell line. </p> <p>Phosphopeptides identified from the immunopeptidome of the GR cell line. </p>
Bacterial RNA Virus MS2 Exposure Increases the Expression of Cancer Progression genes in LNCaP Prostate Cancer Cell Line
<p><strong>Supplementary Figure 1. </strong>Network of protein-protein interactions in LNCaP cells according to their interaction with T4 and M13 phages (DNA phages). The network of protein-protein interactions in Homo Sapiens was constructed using the string protein-protein interaction network v 11.5 [35] with the overexpressed genes (highest confidence level setting) in LNCaP cells. Interactions of overexpressed protein genes were mapped with the highest confidence cut-off of (0.7-0.9). In the resulting protein association network, proteins are presented as nodes connected by lines with varying thicknesses representing the highest confidence level of (0.7-0.9). It is observed that there is strong experimentally determining evidence for the link between SRC and other overexpressed genes, including MAPKs and other integrins by adding more nodes until the highest confidence level of (0.7-0.9) among all overexpressed genes was obtained based on known interactions.</p> <p> </p> <p><strong>Supplementary Figure 2. </strong>Enrichr web server-based gene set enrichment analysis for overexpressed cancer progression genes in LNCaP cells treated with (A) MS2 and (B) T4 and M13 phages; which predicts caveolin-mediated endocytosis for MS2 bacterial virus (with a p-value of 0.000001399). Similarly, an integrin-mediated signaling pathway (with a p-value of 0.000007588) based on overexpression of most integrin genes and caveolin-mediated endocytosis (with a p-value of 0.000001799) were predicted for both T4 and M13 phages based on GO Biological process 2021.</p>
MS2 MGX Solid Snake Parachute
Source: Objaverse 1.0 / Sketchfab
Tocchini and Mango_An adapted MS2-MCP system to visualize endogenous cytoplasmic mRNA with live imaging in Caenorhabditis elegans_Table S1_Raw data
<p><strong>Table S1. Raw data.</strong> List of quantitation of GFP intensities of heads (<em>spc-1</em>) or pharynges (<em>dlg-1</em>) in the different figures.</p>
Interaction of the maturation protein of the bacteriophage MS2 and the F pilus of Escherichia coli
<p>Five 20 ns independent trajectories of a model of the F pilus comprising a trimer of subunits binding to the maturation protein.</p>
Skeletonema marinoi MS2 mzML files in positive mode
<p>These are MS2 files in .mzML format acquired in positive mode. The extracted metabolites come from a sample from <em>Skeletonema marinoi.</em></p>
MS2-affinity purification coupled with RNA sequencing (MAPS) reveals DsrA sRNA targetome
GEO Series GSE67605. Escherichia coli str. K-12 substr. MG1655. 2 samples. Type: Expression profiling by high throughput sequencing.
MS2-affinity purification coupled with RNA sequencing (MAPS) reveals RybB sRNA targetome
GEO Series GSE66518. Escherichia coli K-12. 2 samples. Type: Other.
MS2-affinity purification coupled with RNA sequencing (MAPS) reveals RprA sRNA targetome.
GEO Series GSE80020. Escherichia coli K-12. 2 samples. Type: Other.
Identification of sRNA binding to ITSmetZW and ITSmetWV using MS2-affinity purification coupled with RNA sequencing (MAPS) technology
GEO Series GSE66517. Escherichia coli K-12. 2 samples. Type: Other.
MS2-affinity purification coupled with RNA sequencing (MAPS) reveals CyaR sRNA targetome in Escherichia coli.
GEO Series GSE90128. Escherichia coli K-12. 2 samples. Type: Expression profiling by high throughput sequencing.
Global transcriptional responses to KI-MS2-008 treatment and Myc inactivation via doxycycline addition
GEO Series GSE107222. Homo sapiens. 64 samples. Type: Expression profiling by high throughput sequencing.
MS2-affinity purification coupled to RNA-sequencing (MAPS) reveals targetomes of Z. mobilis sRNAs Zms4 and Zms6
GEO Series GSE107192. Zymomonas mobilis. 9 samples. Type: Expression profiling by high throughput sequencing.
MS2-affinity purification coupled with RNA sequencing (MAPS) reveals GcvB sRNA targetome.
GEO Series GSE80019. Escherichia coli K-12. 2 samples. Type: Other.
MS2-affinity purification coupled with RNA sequencing (MAPS) reveals S. aureus IsrR sRNA targetome
GEO Series GSE296222. Staphylococcus aureus. 8 samples. Type: Expression profiling by high throughput sequencing.
Identification of RNAs bound to MS2 aptamer using MS2-affinity purification coupled with RNA sequencing (MAPS)
GEO Series GSE67606. Escherichia coli str. K-12 substr. MG1655. 2 samples. Type: Expression profiling by high throughput sequencing.
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DANDI Archive for NWB datasets
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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.
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