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43 results for “LC-MS/MS”
Liquid Chromatography - Tandem Mass Spectrometry (LC-MS/MS) and Gas Chromatography - Mass Spectrometry (GC-MS) Reference Libraries from Global Natural Products Social Molecular Networking (GNPS) and National Institute of Standards and Technology (NIST) WebBook Processed for Spectral Library Matching
<div>In order to obtain a high-quality LC-MS/MS reference database for spectral library matching, we selected 22 high-quality GNPS tandem mass spectrometry databases generated under the positive ion mode. Further preprocessing similar to Huber et al involving mass-to-charge (m/z) and intensity filtering yields the database found in the file LCMS_GNPS_reference_library.csv which contains 14,705 electrospray ionization (ESI) mass spectra, each of which corresponds to a unique compound. The NIST WebBook database was used to construct GC-MS database contained in the file GCMS_NIST_WebBook.csv. This database contains 23,721 electron ionization (EI) mass spectra, each of which corresponds to a unique non-hyphenated Chemical Abstract Service (CAS) Registry Number.</div> <div> </div> <div>Both LC-MS/MS and GC-MS databases are organized into three columns: one for the identifier, one for the m/z values, and one for the intensity values. For example, if spectrum A has 20 ion fragments, then there will be 20 rows corresponding to spectrum A in the corresponding database with the identifier A repeated 20 times with the corresponding m/z and intensity values.</div>
LC-MS/MS, PSM and BLG properties data from "Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins"
<p>This dataset contains the data analyzed in:</p> <p>Rodriguez Palomo I, Nair B, Chang Y, Dartigues B, Dekker K, Mackie M, Evans M, Macleod R, Olsen JV, Collins MJ. (2023) "<em>Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins"</em></p> <p>It contains the following data:</p> <ul> <li>raw_files.zip Thermo RAW files for the 0, 4 and 128 days samples</li> <li>benchmark_results.zip PSMs data from the analysis of the RAW files <ul> <li>Data from runs in Mascot, Fragpipe, pFind, Metamorpheus, MaxQuant and DeNovoGUI</li> <li>Parameters and workflow files for MaxQuant and Fragpipe</li> </ul> </li> <li>bovin_blg_prop.zip BLG properties files: amyloid formation, 3D structure and solvent accessibility</li> <li>benchmark_table.csv Table with runs settings for benchmarking</li> <li>parameters_table.xlsx Spreadsheet with software parameters, derived from files used to run each software</li> </ul> <p> </p>
Portimine A toxin causes skin pathology through ZAKα-dependent NLRP1 inflammasome activation: LC-MS/MS raw data for Figure 1. C
<p>This dataset pertains to the LC-MS/MS analyses conducted as part of a study on microalgal toxins present in samples from Senegal, published in the paper entitled <em>"Portimine A toxin causes skin pathology through ZAK</em><em>α</em><em>-dependent NLRP1 inflammasome activation."</em> The data correspond to the quantification results of environmental samples presented in Figure 1C.</p> <p>The raw data were acquired using Analyst software (Applied Biosystems proprietary software). The materials and methods used to generate these data are detailed in the associated publication in <em>EMBO Molecular Medicine</em> (ISSN: 1757-4676, 2024).</p>
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>
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>
Algoa Bay 2018/2019 LC-MS/MS DOM study
<p>This dataset contains the raw and processed data for a nontargeted tandem mass spectrometry study of dissolved organic matter (DOM) in surface water collected from the Algoa Bay system in the Eastern Cape of South Africa in 2018/2019</p>
Proteomic Profiling for Identification of Animal Skin Species in Ancient Egyptian Archaeological Leather using Liquid Chromatography Coupled with Tandem Mass Spectrometry (Nano LC-MS/MS)
<p><strong>Proteomic Profiling Dataset for Identification of Animal Skin Species in Ancient Egyptian Archaeological Leather using Liquid Chromatography Coupled with Tandem Mass Spectrometry (Nano LC-MS/MS)</strong></p>
Proteomics LC-MS/MS test dataset for protein quantitation via stable isotope labelling
<p>The provided mzML file can be used as a test dataset for protein identification and quantitation software. It was generated from human embryonic kidney (HEK) cells that were either unlabelled or labelled with heavy SILAC (K6R6, unimod accession 188, PSI-MS Name: "Label:13C(6)"). Apart from different labelling, the HEK cells were kept in exactly the same conditions and harvested simultaneously. Light and heavy labelled proteins from HEK cell lysate were mixed in a certain ratio, digested with Trypsin and measured on a ThermoFisher QExactive mass spectrometer. A more detailed description on the generation of the dataset will soon be accessible at PRIDE.</p> <p>The provided mzML file has been converted from Thermo RAW and slightly modified via msConvert (ProteoWizard). To reduce the filesize and to speed up analysis, it has further been filtered to contain only the data measured between 2,000 sec and 3,000 sec of the original LC-MS/MS run.</p>
LC-MS/MS data for WT human PANX1 with or without co-expressing Src-Y529F mutant
<p>Protein phosphorylation is one of the major molecular mechanisms regulating protein activity and function throughout the cell. Pannexin 1 (PANX1) is a large-pore channel permeable to ATP and other cellular metabolites. Its tyrosine phosphorylation and subsequent activation have been found to play critical roles in diverse cellular conditions, including neuronal cell death, acute inflammation, and smooth muscle contraction. Specifically, the non-receptor kinase Src has been reported to phosphorylate Tyr198 and Tyr308 of mouse PANX1 (equivalent to Tyr199 and Tyr309 of human PANX1), resulting in channel opening and ATP release. Although the Src-dependent PANX1 activation mechanism has been widely discussed in the literature, independent validation of the tyrosine phosphorylation of PANX1 has been lacking. Here, we show that commercially available antibodies against the two phosphorylation sites mentioned above—which were used to identify endogenous PANX1 phosphorylation at these two sites—are nonspecific and should not be used to interpret results related to PANX1 phosphorylation. We further provide evidence that neither tyrosine residue is a major phosphorylation site for Src kinase in heterologous expression systems. We call on the field to re-examine the existing paradigm of tyrosine phosphorylation-dependent activation of the PANX1 channel.</p>
LC-MS/MS data of pharmaceutical compounds for lIbrary building
<p>Dataset used for MergeION package testing are provided by Janssen Pharmaceutica. It consists of known standard pharmaceutical compounds for which high quality Q-Exactive MS/MS data is provided. Details about these compounds can be found in Metadata_Library.txt. All datasets were acquired in positive ion mode through either DDA (data-dependent acquisition) or targeted MS/MS. Raw data in profile mode were converted into centroid-mode mzML or mzXML files using MSConvertGUI</p> <p> </p>
LC-MS/MS plasma protein measurements from children with bacterial and viral infections - "MS-A"
<p>LC-MS/MS data generated from plasma samples from children with bacterial and viral infections. </p>
LC-MS/MS plasma protein measurements from children with bacterial and viral infections - "MS-B"
<p>LC-MS/MS data generated from plasma samples from children with bacterial and viral infections. </p>
LC-MS/MS data for WT human PANX1 with or without co-expressing Src-Y529F mutant
Open the record for dataset details and reuse information.
Data from: Novel insights into relationships between egg corticosterone and timing of breeding revealed by LC-MS/MS
Inter- and intra-clutch variation in egg corticosterone (CORT), the major glucocorticoid in birds, may provide insights into how maternal stress levels vary with the timing of breeding and with laying order. Common analytical methods (e.g. immunoassays), however, suffer from cross-reaction with other steroids, leading to potential overestimation of CORT concentrations which can obscure true hormone–environment relationships and complicate among-study comparisons. We here apply a new LC-MS/MS technique, which has recently been shown to avoid the problem of cross-reactivity due to its high specificity, to quantify CORT concentrations in yolk and albumen in clutches of lesser black-backed gulls Larus fuscus. We found that CORT concentration exhibited a previously unreported U-shaped relationship with time of breeding, which we explain as a potential interplay of two forces exerting extra strain on the early and late breeders. Furthermore, results showed an increase in CORT with laying order indicating the energetic expense of egg production. The levels of CORT assessed in this study were significantly lower than those previously reported in studies using immunoassays for CORT analysis. This supports the fact that incorporating chromatography effectively reduces overestimation of CORT due to cross-reactivity with other steroid hormones, particularly in egg yolk.
Proteomic Profiling for Identification of Animal Skin Species in Ancient Egyptian Archaeological Leather using Liquid Chromatography Coupled with Tandem Mass Spectrometry (Nano LC-MS/MS)
<p><strong>Proteomic Profiling for Identification of Animal Skin Species in Ancient Egyptian Archaeological Leather using Liquid Chromatography Coupled with Tandem Mass Spectrometry (Nano LC-MS/MS)</strong></p>
Positive mode DDA LC-MS/MS analysis of organic plant extracts (Malaga)
<p>Organic Plant extracts from Malaga resuspended in 8/2 MeOH/water and analysed on Exploris 480 in positive DDA mode.</p>
Lactobacillus johnsonii N6.2 total lipid and fractionated lipids profiling by qualitative lipidomic LC-MS/MS analysis
<p>Table presents both MS-1 (precursor mass-matched) and MS-2 (precursor mass- and spectral-matched) annotations. The values in the table represent the peak area. The column labels, RT: retention time; m/z: mass-to-charge ratio; SL (simple lipids), GL (glycolipids), and PL (phospholipids) represent lipid fractions and TL: total lipids. Table is provided as an xlsx file.</p>
Supplementary Table 1. Identification of protein bands content by LC-MS/MS from fractions obtained from B. arietans venom after size exclusion chromatography.
<p>FG1 to FG6 were cut from the gel and subjected to in-gel digestion with trypsin. Analysis was performed using an Easy-nLC Proxeon nanoHPLC system coupled to an LTQ-Orbitrap Velos. The results obtained were compared with the “<em>Bitis</em>” and “Snakes” database downloaded from Uniprot (Taxid: 8570).</p>
LC-MS/MS analysis of Buxus
<p>Lc-MS/MS analysis of the polar extracts of <em>Buxus</em></p>
Fig. 5. A in Assessing specialized metabolite diversity of Alnus species by a digitized LC-MS/MS data analysis workflow
Fig. 5. A boxplot showing the ion intensities of MS/MS feature 10 (gallic acid) in extracts which were active (IC50 <30 μg/mL) and inactive against α-glucosidase.
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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.