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377 results for “Mass spectrometry”
Mass spectrometry datasets on TFEB proteostasis
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Data from: Liquid chromatography-mass spectrometry (LC-MS) data of a multi-epitope peptibody with bFGF/VEGFA
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Chemical profiling of milkweed and monarch butterfly wing extracts via mass spectrometry
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Mass spectrometry data of Chalmydomonas reinhardtii central pair mutants
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MALDI-TOF-MS reference spectra and sequence data for African bovid collagen for Zooarchaeology by Mass Spectrometry (ZooMS)
<p>MALDI-TOF-MS spectra of extracted collagen from modern African bovids used as reference spectra to develop markers for Zooarchaeology by Mass Spectrometry (ZooMS). Some of this material was also analyzed by LC-MS/MS. That data can be found at MassIVE MSV000084675 (<a href="https://doi.org/doi:10.25345/C5239K">doi:10.25345/C5239K</a>). Information about the species of the samples can be found in Key for Labels.csv file.</p> <p>The sequence data contains annotated alignments of the proteins COL1A1 and COL1A2 and the alignments for the available bovid collagen protein sequences. More information on these files can be found in the corresponding manuscript to this dataset.</p>
LILBID laser dissociation curves: a mass spectrometry-based method for the quantitative assessment of dsDNA binding affinities
<p>The data and data analysis scripts in this dataset are referenced in the manuscript, "LILBID laser dissociation curves: a mass spectrometry-based method for the quantitative assessment of dsDNA binding affinities", which is in preparation for publication. The contents of this dataset are as follows:</p> <p>1) raw data from UV melting curves<br> 2) settings, concentrations, and both raw and processed data from ITC experiments<br> 3) raw spectrum and imaging data from qLILBID experiments<br> 4) programming scripts used to process the qLILBID data</p> <p><em>Notes on the ITC data:</em><br> <em>The iTC200 microcalorimeter (Malvern Panalytical, Malvern, UK) used in the ITC experiments produces .itc files to be opened and analyzed in Origin (Originlab, Northampton, MA, US) using an add-on. The resulting Origin files, including data interpretation and figures, are provided here. Raw data and interpreted data have been gathered from the .itc files and the Origin files and assembled into tab-separated .dat files, so that the data are also accessible to users who do not have Origin.</em></p> <p><em>The Origin files can be understood as follows. After data collection, the ITC raw data are loaded into the Origin-based software. Initially, the baseline is created (Data1Coeff worksheet) and the data plotted in µcal/second as a function of time (minutes), shown in the mRawITC (graph) and the Data1RAW (data) windows. The peaks are integrated (area in µcal) and then plotted in units of kcal/mole of injectant as a function of molar ratio (injected ligand per molecule in the cell), shown in the DeltaH window. The first injection is negligible and therefore always deleted. According to the data points in the DeltaH window, a curve is fitted to obtain the molar ratio (N), Ka, ΔH and ΔS, the data is shown in the Data1 worksheet. The Data1 worksheet hereby contains the following information: DH: heat change resulting from the given injection (µcal/injection); INJV: volume of the injection; Xt: concentration of injected ligand in the cell before next injection; Mt: concentration of molecule in the cell before next injection; volume corrected; XMt: molar ratio of ligand per molecule in the cell after the injection as displayed in the DeltaH window; NDH: Normalized DH in kcal/moles of injectant as displayed in the DeltaH window, Fit: data points of the fitted curve. In the end, the results are presented in the ITCFINAL window (final figure). Additional information can be found in the MicroCal iTC200 System User Manual.</em></p> <p><em>The same data labeling system has been used for the tab-separated .dat files.</em></p>
Supplementary material for "Compounds with antiviral, anti-inflammatory and anticancer activity identified in wine via high resolution mass spectrometry and bioinformatics analyses"
<p>Wine contains a variety of molecules with potential beneficial effects on human health. Our aim was to examine the wine components with high-resolution mass spectrometry including high-resolution tandem mass spectrometry in two wine types made from grapes with or without the fungus <em>Botrytis cinerea</em>, or “noble rot.” For LC-MS/MS analysis, 12 wine samples (7 without and 5 with noble rotting) from 4 different wineries were used and wine components were identified and quantified. Results: 288 molecules were identified in the wines and the amount of 169 molecules was statistically significantly different between the two wine types. A database search was carried out to find the molecules, which were examined in functional studies so far, with high emphasis on molecules with antiviral, anti-inflammatory and anticancer activities. Conclusions: A comprehensive functional dataset related to identified wine components is also provided highlighting the importance of components with potential health benefits.</p>
Figure 2 from: Shkondrov A, Krasteva I (2021) Liquid chromatography – high resolution mass spectrometry screening of Astragalus hamosus and Astragalus corniculatus. Pharmacia 68(1): 135-139. https://doi.org/10.3897/pharmacia.68.e60621
Figure 2 A base peak chromatogram of the extract of A. corniculatus with identification of 4 (m/z 737 [M-H]-) and MS2 spectrum displaying kaempferol fragment (m/z 284).
Figure 1 from: Shkondrov A, Krasteva I (2021) Liquid chromatography – high resolution mass spectrometry screening of Astragalus hamosus and Astragalus corniculatus. Pharmacia 68(1): 135-139. https://doi.org/10.3897/pharmacia.68.e60621
Figure 1 A base peak chromatogram of the extract of A. hamosus with identification of 3 (m/z 753 [M-H]-) and MS2 spectrum displaying quercetin fragment (m/z 301).
Data from: Metabolism studies of paeoniflorin in rat liver microsomes by ultra-performance liquid chromatography coupled with hybrid quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS/MS)
To explore metabolism mechanism of paeoniflorin in the liver and further understand intact metabolism process of paeoniflorin, a rapid, convenient and effective assay is described using ultra-performance liquid chromatography coupled with hybrid quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS/MS). The strategy was confirmed in the following primary processes: firstly, different concentration of paeoniflorin, rat liver microsomes, coenzymes and different incubated conditions were optimized to build a biotransformation model of rat liver microsomes in vitro by high performance liquid chromatography with diode array detection (HPLC-DAD); secondly, the metabolites of paeoniflorin in rat liver microsomes were detected and screened using UPLC-Q-TOF-MS/MS by comparing the total ion chromatogram (TIC) of the experimental group with those of control groups; finally, the molecular formulae and corresponding chemical structures of paeoniflorin metabolites were identified by comparing the MS and MS/MS spectra with the self-constructed database and simulation software. Based on this analytical strategy, 20 metabolites of paeoniflorin were found and 6 metabolites (including four new compounds) were tentatively identified. It was shown that hydrolysis and oxidation were the major metabolic pathways of paeoniflorin in rat liver microsomes, and the main metabolic sites were the structures of pinane and the ester bond. These findings were significant for a better understanding of the metabolism of paeoniflorin in rat liver microsomes and the proposed metabolic pathways of paeoniflorin might provide fundamental support for the further research in the pharmacological mechanism of Paeoniae Radix Rubra (PRR).
Data from: Liquid chromatography-tandem mass spectrometry metabolic profiling of nazartinib reveals the formation of unexpected reactive metabolites
Nazartinib (EGF816, NZB) is a promising third-generation human epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor. This novel irreversible mutant-selective EGFR inhibitor targets EGFR containing both the resistance mutation (T790M) and the activating mutations (L858R and Del19), while it does not affect wild-type EGFR. However, the metabolic pathway and bioactivation mechanisms of NZB are still unexplored. Thus, using liquid chromatography-tandem mass spectrometry, we screened for products of NZB metabolism formed in vitro by human liver microsomal preparations and investigated the formation of reactive intermediates using potassium cyanide as a nucleophile trap. Unexpectedly, the azepane ring was not bioactivated. Instead, the carbon atom between the aliphatic linear tertiary amine and electron-withdrawing system (butenoyl amide group) was bioactivated, generating iminium intermediates as reactive species. Six NZB phase I metabolites, formed by hydroxylation, oxidation, and N-demethylation, were characterized. Moreover, two reactive iminium ions were characterized and their corresponding bioactivation mechanisms were proposed. Based on our results, we speculate that bioactivation of NZB can be blocked by small sterically hindering groups, isosteric replacement, or a spacer. This approach might reduce the toxicity of NZB by avoiding the generation of reactive species.
Raw data and code for publication "Optimisation of surfactin yield in Bacillus using active learning and high-throughput mass spectrometry"
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FLiPPR: A Processor for Limited Proteolysis (LiP) Mass Spectrometry Datasets Built on FragPipe
<p>Fully processes data using FLiPPR and accompanying python scripts.</p>
Data for "A learned score function improves the power of mass spectrometry database search"
<div>These data files are associated with the following publication:</div> <div> <ul> <li>Varun Ananth, Justin Sanders, Melih Yilmaz, Bo Wen, Sewoong Oh and William Stafford Noble. "<a title="biorXiv Preprint Link" href="https://www.biorxiv.org/content/10.1101/2024.01.26.577425v2" target="_blank" rel="noopener">A learned score function improves the power of mass spectrometry database search</a>". Bioinformatics (Proceedings of the ISMB). 2024.</li> </ul> </div> <div>For the benchmarking data, we used a dataset that is publicly available on ProteomeXchange (PXD028735). The paper that introduced this dataset is:</div> <div> <ul> <li>Van Puyvelde, B., Daled, S., Willems, S., Gabriels, R., Gonzalez de Peredo, A., Chaoui, K., Mouton-Barbosa, E., Bouyssié, D., Boonen, K., Hughes, C. J., Gethings, L. A., Perez-Riverol, Y., Bloomfield, N., Tate, S., Schiltz, O., Martens, L., Deforce, D., & Dhaenens, M. (2022). A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics. In Scientific Data (Vol. 9, Issue 1). Springer Science and Business Media LLC. https://doi.org/10.1038/s41597-022-01216-6</li> </ul> </div> <div>More specifically, the following `.raw` files were downloaded:</div> <ul> <li><code>LFQ_Orbitrap_DDA_Ecoli_01.raw</code></li> <li><code>LFQ_Orbitrap_DDA_Human_01.raw</code></li> <li><code>LFQ_Orbitrap_DDA_Yeast_01.raw</code></li> </ul> <div>Those files can be accessed via FTP <a title="Link to ProteomeXchange: PXD028735" href="https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD028735/" target="_blank" rel="noopener">here</a>.</div> <div>We upload here the annotated <code>.mgf</code> files created from these <code>.raw</code> files, as described in our paper.</div> <div>The human, yeast, and E. coli .fasta files used in all database searches were downloaded from UniProt on 11/6/23, 4:30 PM.</div> <div> <ul> <li>Bateman, A., Martin, M.-J., Orchard, S., Magrane, M., Ahmad, S., Alpi, E., Bowler-Barnett, E. H., Britto, R., Bye-A-Jee, H., Cukura, A., Denny, P., Dogan, T., Ebenezer, T., Fan, J., Garmiri, P., da Costa Gonzales, L. J., Hatton-Ellis, E., Hussein, A., … Zhang, J. (2022). UniProt: the Universal Protein Knowledgebase in 2023. In Nucleic Acids Research (Vol. 51, Issue D1, pp. D523–D531). Oxford University Press (OUP). https://doi.org/10.1093/nar/gkac1052</li> </ul> </div> <div>We include these files here, with only minor modifications to replace <code>U</code> amino acids with <code>X</code> so that all amino acids fall into Casanovo-DB's vocabulary.</div>
Processed mass spectrometry data - systematic identification of allosteric effectors in Escherichia coli metabolism
<p>MATLAB files of processed mass spectrometry data, i.e. full data table after peak picking, annotation and quantification. Additionally, for each of the tested enzymes, the relevant ion traces of substrates and products are extracted, sorted by timepoint and replicate and saved in separate tables.</p>
Raw mass spectrometry data for "Quinone extraction drives atmospheric carbon monoxide oxidation in bacteria"
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targets for Scan-Centric, Frequency-Based Method for Characterizing Peaks from Direct Injection Fourier transform Mass Spectrometry Experiments
<p>_targets folder for the scan-centric, frequency-based peak-characterization manuscript</p>
Organic pesticide database with 716 molecules analyzed with chemical ionization mass spectrometry. Reagent ions: bromide, protonated acetone, hydronium ion, dioxide.
<p>The dataset joins the measurements output of two standard mixtures from GALAB Laboratories, containing 404 and 312 pesticides. The measurements were conducted at Karsa Oy with a thermal desorption multi-scheme chemical ionization inlet operating at atmospheric pressure, coupled to a linear trap quadrupole orbitrap mass spectrometer.</p> <p>The dataset contains:</p> <ul> <li>name of the compound</li> <li>CAS identifier</li> <li>SMILES</li> <li>signal of the compound with a sample analyzed at a specific concentration and with a specific ionization method.</li> </ul> <p>Reagent ions:</p> <ul> <li>bromide</li> <li>protonated acetone</li> <li>hydronium ion</li> <li>dioxide</li> </ul> <p>Sample concentrations:</p> <ul> <li>10 pg/µl</li> <li>20 pg/µl</li> <li>100 pg/µl</li> <li>1 ng/µl</li> <li>2,5 ng/µl</li> </ul> <p> </p> <p>The dataset has been analysed in the publications:</p> <ul> <li>Bortolussi, F., Sandström, H., Partovi, F., Mikkilä, J., Rinke, P., and Rissanen, M.: Technical note: Towards atmospheric compound identification in chemical ionization mass spectrometry with pesticide standards and machine learning, Atmos. Chem. Phys., 25, 685–704, https://doi.org/10.5194/acp-25-685-2025, 2025.</li> </ul>
Mass spectrometry search data associated with the manuscript "Propensity for Proto-gene Emergence in Bacteria"
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Application of matrix-assisted laser desorption/ionization mass spectrometry imaging in combination with LC–MS in pharmacokinetic study of metformin
<p>Application of matrix-assisted laser desorption/ionization mass spectrometry imaging in combination with LC-MS in a pharmacokinetic study of metformin</p> <p><a href="https://doi.org/10.4155/bio-2017-0190">https://doi.org/10.4155/bio-2017-0190</a></p> <p>MALDI MSI datasets</p>
ScienceDex guides
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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.