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377 results for “Mass spectrometry”
Liquid chromatography mass spectrometry data of HMCES SRAP domain
<p>Liquid chromatography mass spectrometry data for the HMCES SRAP domain alone (Apo_SRAPd) and for the SRAP domain incubated with abasic site containing DNA (SRAPd_DPC). All LC/MS data were acquired according to the previously published protocol (Chalk R., Springer New York, 2017).</p>
Mass spectrometry Imaging dataset for the study on fungicide application to tomato leaves - I
<p>The dataset uploaded here is in association to a manuscript in press by Ajith et al. titled, "Visualizing active fungicide formulation mobility in tomato leaves with Desorption Electrospray Ionisation Mass Spectrometry Imaging". This dataset contains .imzML format files of Mass Spectrometry Imaging data along with the zipped .ibd files for a fungicide application study with a commerical Azoxystrobin formulation. The files were generated with a DESI Imprint imaging method for a commercial pesticide formulation applied young tomato leaves after 2 hours, 24 hours, 56 hours and a week after application.</p> <table> <tbody> <tr> <td>File Name</td> <td>Time point</td> </tr> <tr> <td>DTIM_2h</td> <td>2h Adaxial Imprint</td> </tr> <tr> <td>DTIM_24h_1</td> <td>24h Adaxial Imprint</td> </tr> <tr> <td>DTIM_24h_2</td> <td>24h Adaxial Imprint</td> </tr> <tr> <td>DTIM_24h_3</td> <td>24h Adaxial Imprint</td> </tr> <tr> <td>DTIM_56h_1</td> <td>56h Adaxial Imprint</td> </tr> <tr> <td>DTIM_56h_2</td> <td>56h Adaxial Imprint</td> </tr> <tr> <td>DTIM_56h_3</td> <td>56h Adaxial Imprint</td> </tr> <tr> <td>DTIM_1week_1</td> <td>1 week Adaxial Imprint</td> </tr> <tr> <td>DTIM_1week_2</td> <td>1 week Adaxial Imprint</td> </tr> <tr> <td>DTIM_1week_3</td> <td>1 week Adaxial Imprint</td> </tr> <tr> <td>DTIM_48h_Abaxial</td> <td>48h Abaxial imprint</td> </tr> <tr> <td>DTIM_48h_Adaxial</td> <td>48h Adaxial Imprint</td> </tr> </tbody> </table> <p> </p>
MALDI-TOF-MS spectra of archaeological bone fragments from Bandicoot Bay, Barrow Island (Australia) for ZooMS (Zooarchaeology by Mass Spectrometry)
<p>MALDI-TOF-MS spectra for archaeological bone fragments from Bandicoot Bay, Barrow Island, Western Australia. All spectra are uploaded in .mzml format. </p>
Development of a spectral library for the discovery of altered genomic events in Mycobacterium avium associated with virulence using mass spectrometry-based proteogenomic analysis
<p><em>Mycobacterium avium</em> is one of the prominent disease-causing bacteria in humans. It causes lymphadenitis, chronic and extrapulmonary, and disseminated infections in adults, children, and immunocompromised patients. <em>M. avium</em> has ~4,500 predicted protein-coding regions on an average, which can be helpful in discovering several variants at the proteome level. Many of them are potentially associated with virulence, thus identifying such proteins can be a helpful feature in the development of panel-based theranostics. In line with such a long-term goal, we carried out an in-depth proteomic analysis of <em>M. avium</em> with both data-dependent and data-independent acquisition methods. Further, a set of proteogenomic investigations were carried out using the protein database for <em>Mycobacterium tuberculosis,</em> and a genome six-frame translated database and a variant protein database of <em>M. avium</em>. A search of mass spectrometry data analysis against <em>M. avium</em> protein database resulted in the identification of 2,954 proteins. Further, proteogenomic analyses aided in the identification of 1,301 novel peptide sequences and correction of translation start sites for 15 proteins. At the end, we created a spectral library of <em>M. avium</em> proteins including novel genome search-specific peptides and variant peptides detected in this study. We validated the spectral library by a data-independent acquisition of the <em>M. avium</em> proteome. Thus, we present a <em>M. avium </em>spectral library of 29,033 peptide precursors supported by 0.4 million fragment ions for further use by the biomedical community.</p>
DNA-HDXMS_XchangeDB: A dataset of Hydrogen-Deuterium eXchange native Mass Spectrometry experiments on DNA oligonucleotides
<p>The DNA-HDXMS_XchangeDB dataset contains HDX/native MS exchange kinetics and metadata of a reference set of DNA oligonucleotides.</p> <p> </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>
Raw data for the Article "Cyclopentadienone Iron Complex-Catalyzed Hydrogenation of Ketones: An Operando Spectrometric Study Using Pressurized Sample Infusion-Electrospray Ionization-Mass Spectrometry"
<p>This data set contains the raw data (NMR, LC-MS, ESI-MS, HRMS, Elemental Analysis) for the article "Cyclopentadienone Iron Complex-Catalyzed Hydrogenation of Ketones: An <em>Operando</em> Spectrometric Study Using Pressurized Sample Infusion-Electrospray Ionization-Mass Spectrometry" published in <em>Organometallics</em>, DOI:</p> <p><a href="https://doi.org/10.1021/acs.organomet.2c00341">https://doi.org/10.1021/acs.organomet.2c00341</a></p> <p>The compound names correspond to the ones used in the article and its supporting information.</p>
Multiplexed Staining Dataset - OMAP 5 - Liver-Lanthanides-conjugated antibodies and C60-secondary ion mass spectrometry imaging
<p>This dataset contains images of multiplexed antibody panel on a human pediatric liver section including the nuclear marker and antibodies conjugated with lanthanides tags. The dataset is one example of serial experiments of multiplexed antibody staining and imaging. The antibody panel targets the major cell types and tissue structures in the liver tissue. Data acquisition was performed using single multiplexing imaging by C60-secondary ion mass spectrometry.</p> <p> </p>
Dataset for: Improving the accuracy of δ18O and δ17O values of O2 measured by continuous-flow isotope-ratio mass spectrometry with a multi-point isotope-ratio calibration
<p>Dataset containing raw and treated isotope-ratio mass spectrometry and laser absorption spectroscopy data, accompanying the manuscript "Improving the accuracy of δ18O and δ17O values of O2 measured by continuous-flow isotope-ratio mass spectrometry with a multi-point isotope-ratio calibration". This dataset also contains O2 concentration and partial pressure data used for figures in the associated manuscript.</p>
The photooxidation of dissolved organic matter in surface waters analyzed by Fourier-transform ion cyclotron resonance mass spectrometry.
Dissolved organic matter (DOM) plays an important role in carbon cycling in natural waters. The processing of DOM in these waters can occur via photooxidation, or interaction with sunlight. This processing can lead to the production of CO2, and also the alteration of organic compounds that make up DOM. It is likely that the extent of photooxidation is at least partially determined by the chemical composition of DOM. Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was used to characterize the dissolved organic matter at the molecular level for all water samples, both before and after light exposure to better understand the photooxidation of DOM. Chemical formulas were assigned to mass to generated mass to charge ratios using a custom script in R, resulting in a list of chemical formula assignments for each DOM sample, at multiple light exposure time points.
Laser Ablation Electrospray Ionization Mass Spectrometry Imaging (LAESI MSI) of Arabidopsis thaliana leaf
<p>Mass spectrometry imaging (MSI) data set in imzML format, obtained from the 5th leaf of an Arabidopsis thaliana wildtype plant using Laser Ablation Electrospray Ionization. Laser ablation took place with 20 pulses per pixel at an energy of 58.4 µJ/pulse. The ROI measures 9 mm by 5 mm and was sampled with a step size of 200 µm.</p>
Mass spectrometry output SILAC labelled (F/Y) biological replicate 1 - anti-HLA-A29 antibody DK1G8
<p>Mass spectrometry output from SILAC labelled (F/Y) ERAP2 wildetype versus (CRISPR Cas9-mediated) ERAP2-KO lymphoblastoid cell line from a Birdshot Uveitis patient (ERAP1 hap10/10 ERAP2 hapA/A). Peptides were eluted from immuno-purifications with anti-HLA-A29 antibody DK1G8. The dataset was used for subsequent filtering and differential expression analysis by <em>limma</em>. </p>
Evaluation of MALDI‐ToF Mass Spectrometry for Rapid Detection of Cereulide from Bacillus cereus Cultures - MALDI-ToF Mass Spectra
<p>Datasets in support of the <em>bioRxiv </em>submitted paper Doellinger et al. (<strong>2019</strong>) "<em>Evaluation of MALDI‐ToF Mass Spectrometry for Rapid Detection of Cereulide from Bacillus cereus Cultures"</em> - MALDI-ToF Mass Spectra.</p> <p>The experiment and sample description and spectra numbering is consistent with the publication. Mass spectral data files are provided as unprocessed raw data in the manufacturer's original data format (Bruker Daltonics). Data is compressed using the freely available 7zip software.</p> <p><strong>Content:</strong></p> <p><em><strong>Figure 1.zip</strong></em>: Cereulide detection in <em>B. cereus</em> samples cultivated using different cultivation media and different sample preparation, or cereulide extraction methods.</p> <p><em><strong>Figure 2.zip</strong></em>: Effectivity of cereulide extraction by different solvents from <em>B. cereus</em> F4810/72 colony material.</p> <p><em><strong>Figure 3.zip</strong></em>: MALDI LIFT-ToF /ToF MS spectrum of cereulide.</p> <p><em><strong>Figure 4.zip</strong></em>: Determination of the limit of detection (LOD) of cereulide by MALDI- and LDI-ToF</p> <p><em><strong>Table 1.zip</strong></em>: Analysis of cereulide in <em>B. cereus</em> strains by MALDI-ToF MS.</p> <p><em><strong>Fig.SI.01.zip: </strong></em> Ultraperformance Liquid Chromatography – Mass Spectrometry (UPLC-MS/MS) analysis of ethanolic washing solutions of <em>B. cereus</em> F4810/72.</p> <p><em><strong>Fig.SI.02.zip:</strong></em> A selection of MALDI-ToF and LDI-ToF technical replicate mass spectra obtained from a commercial cereulide standard.</p> <p><em><strong>Fig.SI.03.zip:</strong></em> Limit of detection (LOD) of cereulide determined by MALDI- and LDI-ToF MS of ethanol wash solutions from <em>B. cereus</em> ATCC 10987 spiked by a cereulide standard. </p> <p><em><strong>Fig.SI.04.zip:</strong></em> Direct cereulide detection by means of MALDI- (panels <strong>A</strong>-<strong>F</strong>) and LDI-ToF MS (panels <strong>G</strong>-<strong>M</strong>) in linear and reflectron measurement mode.</p>
Training dataset: Mass spectrometry based proteomics of healthy human serum samples
<p>The two raw files serve as a concise but meaningful training data set in the Galaxy training network (https://galaxyproject.github.io/training-material/).</p> <p>Serum of a healthy person was obtained by centrifugation of full blood in a serum-gelmonovette. One serum sample was depleted for high abundant proteins, the other not.<br> For the non-depleted sample: 5µl of serum was diluted with 0.1% Rapigest, resulting in a concentration of 1mg/ml.<br> Depletion was performed with the Seppro IgY14 Spin columns which are able to deplete 14 high abundent blood proteins by immunoaffinity. For the depleted sample 9µl of serum was diluted with TBS/HCl/NaCl buffer and added to the Seppro IgY14 spin column. After depletion the sample was buffered with Hepes pH 8.0 and Rapigest was added to a final 0.1% Rapigest concentration. From here on, both samples were reduced by adding TCEP, alkylated by IAA and quenched with DTT in solution. Digestion was performed by adding trypsin in a ratio of 1:50 to the samples. After incubation at 37°C, 600rpm, over night, the sample clean-up was performed with the PreOmics desalting columns. iRT peptides were added and the sample was measured with a Q-Exactive Plus mass spectrometer. Besides the two raw files, we uploaded a fasta file that serves as human protein sequence database and the Galaxy MaxQuant training result files: protein groups, peptides, mqpar and PTXQC.</p>
Training dataset: Generation of a spectral library from HEK-Ecoli Spike-in mass spectrometry data
<p>The five raw files serve as a concise but meaningful training data set in the Galaxy training network (https://galaxyproject.github.io/training-material/).</p> <p>HEK and E.coli cell pellets were lysed with 5 % SDS, 50 mM triethylammonium bicarbonate (TEAB), pH 7.55. The obtained protein extracts were reduced by adding f.c. 5 mM TCEP and alkylated by the addition of f.c. 10 mM iodacetamide. Protein digestion and purification was performed on S-Trap columns. To ensure protein binding to the S-Trap columns, samples were acidified to a final concentration of 1.2 % phosphoric acid (~ pH 2). Six times the sample volume S-Trap buffer (90% aqueous methanol containing a final concentration of 100 mM TEAB, pH 7.1) was added to the samples which were then loaded on the columns and washed with S-Trap buffer. Protein digestion was performed with trypsin and LysC for one hour at 47 °C. Peptides were eluted in three steps with (1) 50 mM TEAB, (2) 0.2 % aqueous formic acid and (3) 50 % acetonitrile containing 0.2 % formic acid. Eluted peptides of HEK and E.coli were mixed in the following ratios (amount in µg):</p> <p>Sample HEK E.coli MS method<br> Sample1 2.5 0.00 DDA<br> Sample2 2.5 0.05 DDA<br> Sample3 2.5 0.15 DDA<br> Sample4 2.5 0.40 DDA<br> Sample5 2.5 0.80 DDA</p> <p>Additionally, iRT peptides were added and 1µg of each samples was measured with a Q-Exactive Plus mass spectrometer. Besides the five raw files, we uploaded two fasta files that serve as human and ecoli protein sequence databases, an transition list for the iRT peptides as well as an experimental design for the MaxQuant search.<br> Additionally, we uploaded the Galaxy MaxQuant training result files: protein groups, peptides, mqpar, msms, evidence and PTXQC.</p>
Low-temperature plasma mass spectrometry imaging (LTP-MSI) of Chili pepper
<p>Low-temperature plasma mass spectrometry imaging of a chili pepper. The data set contains raw data and the scripts to prepare the imzML file. The final imzML/ ibd files are also included.</p> <p>The creation of the data is described in: Maldonado-Torres, Mauricio, José Fabricio López-Hernández, Pedro Jiménez-Sandoval, and Robert Winkler. 2014. “‘Plug and Play’ Assembly of a Low-Temperature Plasma Ionization Mass Spectrometry Imaging (LTP-MSI) System.” <em>Journal of Proteomics</em> 102C (March): 60–65. doi:10.1016/j.jprot.2014.03.003.</p> <p>The data set was re-analyzed using R scripts, as reported in: Gamboa-Becerra, Roberto, Enrique Ramírez-Chávez, Jorge Molina-Torres, Robert Winkler, Enrique Ramírez-Chávez, Jorge Molina-Torres, and Robert Winkler. 2015. “MSI.R Scripts Reveal Volatile and Semi-Volatile Features in Low-Temperature Plasma Mass Spectrometry Imaging (LTP-MSI) of Chilli (Capsicum Annuum).” <em>Analytical and Bioanalytical Chemistry</em> 407 (19): 5673–84. doi:10.1007/s00216-015-8744-9.</p>
Data for "A learned score function improves the power of mass spectrometry database search"
<div> <h1>DATA for "A learned score function improves the power of mass spectrometry database search"</h1> <br> <div>These data files are associated with the following publication:</div> <br> <div> <ul> <li>Varun Ananth, Justin Sanders, Melih Yilmaz, 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> <br> <div>For the benchmarking data, we used a dataset that is publicly available on ProteomeXchange (PXD028735). The paper that introduced this dataset is:</div> <br> <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> <br> <div>More specifically, the following `.raw` files were downloaded:</div> <br> <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> <br> <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> <br> <div>We upload here the annotated <code>.mgf</code> files created from these <code>.raw</code> files, as described in our paper.</div> <br> <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> <br> <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> <br> <div>We include these files here, with only minor modifications to replace `U` amino acids with `X` so that all amino acids fall into Casanovo-DB's vocabulary.</div> </div>
Predicting glycan structure from tandem mass spectrometry via deep learning
<p>Curated set of LC-MS/MS data from glycomics studies. Used for training and applying CandyCrunch, a deep learning model to predict glycan structure from LC-MS/MS data, described in Urban et al., Nat Methods, 2024 and https://github.com/BojarLab/CandyCrunch.</p> <p>Files:</p> <p>full_dataset.xlsx: Full dataset with all annotated LC-MS/MS glycan spectra</p> <p>X_train.pkl: spectra and metadata from our training set</p> <p>y_train.pkl: labels from our training set</p> <p>X_test.pkl: spectra and metadata from our independent test set</p> <p>y_test.pkl: labels from our independent test set</p> <p>glycans.pkl: glycans in IUPAC-condensed nomenclature in the same order as the label-encoding</p>
Supporting files for Turečková et al. 2024 "A New Abscisic Acid Conjugate, ABA‑L‑Glutamate, Determined in Different Plant Species by Combined Immunoaffinity Chromatography‑Tandem Mass Spectrometry"
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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