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102 results for “spectrometry data”
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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Mass spectrometry search data associated with the manuscript "Propensity for Proto-gene Emergence in Bacteria"
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Data from: Colour patch size and measurement error using reflectance spectrometry
1. Over the past twenty years, portable and relatively affordable spectrophotometers have greatly advanced the study of animal coloration. However, the small size of many colour patches poses methodological challenges that have not, to date, been assessed in the literature. Here, we tackle this issue for a reflectance spectrophotometry set-up widely used in ecology and evolution (the beam method). 2. We reviewed the literature on animal coloration reporting the use of reflectance spectrophotometry to explore how the minimum measurable size of a colour patch is determined. We then used coloured plastic sheets to create artificial colour patches, and quantify the relationship between colour patch size and distortions induced by resulting chimeric spectra (spectra contaminated by an adjacent colour patch). Finally, we assessed the generality of our findings using natural colour spots in the lizard Podarcis muralis, as a biologically realistic model. 3. We found a lack of consensus in the literature, frequently resulting in the rejection of valid data or the potential inclusion of unreliable data. As expected, we show that decreasing colour patch size reduces the reliability of reflectance measurements, but also that spectral distortions resulting from chimeric spectra depend on patch/background colour combinations. We found similar results using natural colour spots in P. muralis. 4. We propose a series of steps to avoid the pitfalls described above. First, we provide guidelines on how to identify chimeric spectra and estimate the minimum size of a measurable colour patch in order to avoid them. Second, we show that reducing the probe-to-surface distance allows for more accurate measurements and therefore improves the spectrophotometric assessment of small colour patches. Third, we suggest that, as a general rule of thumb, very small (< 2 mm) colour patches should be avoided when using traditional spectrophotometry methods.
Raw mass spectrometry data for "Lysyl hydroxylase 2 mediated collagen post-translational modifications and functional outcomes"
<p><strong>Abstract:</strong> Lysyl hydroxylase 2 (LH2) is a member of LH family of enzymes (LH1-3) that catalyze the hydroxylation<br> of lysine (Lys) residues on collagen, and this particular isozyme has been implicated in Bruck syndrome,<br> fibrosis and cancer metastasis. Previously, we proposed LH2 as a telopeptidyl LH for type I collagen and<br> this specific function is now generally accepted. However, several fundamental questions remain<br> unanswered: 1, Is LH2 responsible for both N- (α1 and 2 chains) and C-telopeptidyl (α1 chain) Lys<br> hydroxylation? 2, Is LH2 involved in the helical Lys hydroxylation? 3, what are the functional<br> consequences when LH2 is completely lacking? To answer these questions, we generated LH2-null MC3T3<br> cells (LH2 KO) using CRISPR/Cas9, and extensively characterized the molecular and fibrillar phenotypes<br> of type I collagen. Cross-link analysis demonstrated that the hydroxylysine-aldehyde (Hyl<sup>ald</sup>)-derived crosslinks<br> were completely absent from LH2 KO collagen with concomitant increases in the Lys<sup>ald</sup>-derived crosslinks.<br> Mass spectrometric analysis revealed that, in LH2 KO type I collagen, telopeptidyl Lys hydroxylation<br> was completely abolished at all sites while helical Lys hydroxylation was slightly diminished in a sitespecific<br> manner. Moreover, di-glycosylated Hyl was diminished at the expense of mono-glycosylated Hyl.<br> Furthermore, prolyl 3-hydroxylation was slightly increased in LH2 KO type I collagen. In LH2 KO samples,<br> collagen solubility was markedly increased, fibril diameters are significantly diminished, and<br> mineralization severely impaired. Together, these data underscore the critical role of LH2-catalyzed<br> collagen modifications and consequent cross-linking in matrix stability, organization and mineralization.</p>
Mass spectrometry data on study of CNOT3 function in human myeloid leukemia cells
<p>Mass spectrometry data on study of CNOT3 function in human myeloid leukemia cells</p>
Data accompanying "Standardised workflow for mass spectrometry-based single-cell proteomics data analysis using the scp package"
<p>Data and scripts accompanying the paper <em>Standardised workflow for mass spectrometry-based single-cell proteomics data analysis using scp</em>.</p> <ul> <li>d.zip contains raw MS data from samples run on timsTOF SCP.</li> <li>raw.zip contains raw MS data from samples run on orbitrap mass spectrometers (Orbitrap Fusion Lumos Tribrid and Exploris 240).</li> <li>mzML.zip contains raw MS data in mzML format from all samples.</li> <li>sage.zip contains output results from the sage software (results.sage.tsv and quant.tsv) as well as configuration files (results.json) for both orbitrap (cbio) and timsTOF (giga) data.</li> <li>sample_annotation.zip contains csv files with samples annotation for each acquisition batch and used to build the colData.</li> <li>example_subset.zip contains csv files for short example datasets displayed in the paper.</li> <li>scp.rds file contains the initial QFeatures object of the full dataset with 56 PSM sets corresponding to the 56 MS runs.</li> <li>build_QF_dataset.Rmd file is the script used to build the scp.rds file described above from sage outputs and sample annotation.</li> </ul> <p>These file descriptions are also available in the README.txt file.</p>
Data from: Simultaneous determination of underivatized vitamin B1 and B6 in whole blood by Reversed Phase Ultra High Performance Liquid Chromatography Tandem Mass spectrometry
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Mass spectrometry-based proteomics of the Aurantiochytrium limacinum ATCC MYA-1381 zoospore-to-vegetative cell transition (MaxQuant processed data)
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Data from: Liquid chromatography-tandem mass spectrometry metabolic profiling of nazartinib reveals the formation of unexpected reactive metabolites
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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)
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Synaptometry by time-of-flight (SynTOF) mass spectrometry data from NHP
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Data from: Colour patch size and measurement error using reflectance spectrometry
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Data for paper "Understanding Mass Resolution of Foil-Based Time-of-Flight Mass Spectrometry"
<p>Data set for paper "Understanding Resolution of Foil-Based Time-of-Flight Mass Spectrometry" to be published in Journal of Geophysical Research: Space Physics (Technical Methods). The uploaded file is a single Microsoft Excel file containing Data Set S1 through S28.</p> <p> </p>
Data from: Identifying metabolic subpopulations from population level mass spectrometry
Metabolism underlies many important cellular decisions, such as the decisions to proliferate and differentiate, and defects in metabolic signaling can lead to disease and aging. In addition, metabolic heterogeneity can have biological consequences, such as differences in outcomes and drug susceptibilities in cancer and antibiotic treatments. Many approaches exist for characterizing the metabolic state of a population of cells, but technologies for measuring metabolism at the single cell level are in the preliminary stages and are limited. Here, we describe novel analysis methodologies that can be applied to established experimental methods to measure metabolic variability within a population. We use mass spectrometry to analyze amino acid composition in cells grown in a mixture of 12C- and 13C-labeled sugars; these measurements allow us to quantify the variability in sugar usage and thereby infer information about the behavior of cells within the population. The methodologies described here can be applied to a large range of metabolites and macromolecules and therefore have the potential for broad applications.
Accelerator Mass Spectrometry (AMS) data associated with the paper "Bossis et al., Evidence of slow millennial cliff retreat rates using cosmogenic nuclides in coastal colluvium, submitted to Esurf".
<p>This dataset contains the Accelerator Mass Spectrometry (AMS) 10Be data required to calculate the coastal cliff retreat rates presented in Bossis et al., Evidence of slow millennial cliff retreat rates using cosmogenic nuclides in coastal colluvium, submitted to Esurf. The samples were collected along the "Côte Vermeille" French coast, the "Costa Brava" Spanish coast and the south coast of Peru in colluvium at the foot of the cliffs. For additional information and methodology, see the original publication.</p>
Data from: Identifying metabolic subpopulations from population level mass spectrometry
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Multifaceted stoichiometry control of bacterial operons revealed by data-independent acquisition mass spectrometry
GEO Series GSE122971. Escherichia coli BW25113. 4 samples. Type: Expression profiling by high throughput sequencing.
LC-MS raw data for "A new generation of nanobody research tools using improved mass spectrometry-based discovery methods"
<p>This dataset contains LC-MS raw data for VHH identifications from the project "A new generation of nanobody research tools using improved mass spectrometry-based discovery methods." The descriptions of the raw data files are in Summary_Table_MS_RawData.pdf. Files are in the format of Thermo RAW in zip archives.</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.