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377 results for “Mass spectrometry”
Mass spectrometry imaging and single-cell transcriptome reveal metabolic profiles of the postauricular glands of the Bufo gargarizans, and hypothesize Bufotoxin biosynthesis pathways
GEO Series GSE261560. Bufo gargarizans. 1 samples. Type: Expression profiling by high throughput sequencing.
Optimal settings of mass spectrometry open search strategy for higher confidence
GEO Series GSE112623. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing.
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>
Spectral database of the subspecies of the Mycobacterium abscessus complex (MALDI-TOF Mass Spectrometry)
<p><strong>Spectral database of the subspecies of the Mycobacterium abscessus complex (MALDI-TOF Mass Spectrometry)</strong></p> <ul> <li>This data set originates from a collection of 41 clinical strains of <em>Mycobacterium abscessus complex</em> corresponding to 1001 mass spectra: <ul> <li>25 strains of <em>Mycobacterium abscessus</em> subsp. <em>abscessus</em> (633 mass spectra)</li> <li>9 strains of <em>Mycobacterium abscessus</em> subsp. <em>massiliense</em> (204 mass spectra)</li> <li>7 strains of <em>Mycobacterium abscessus</em> subsp. <em>bolletii </em>(164 mass spectra)</li> </ul> </li> </ul> <p> </p> <ul> <li>Each strain has been characterized using molecular method (DNA/DNA hydridation, using GenoType NTM-DR (Hain Lifescience, Nehren, Germany) according to the manufacturer's instructions for identification and analyzed by MALDI-TOF mass spectrometry according MycoEx protocol (Bruker<sup>®</sup>). The mass spectra spectra were obtained according to the following steps :</li> </ul> <p> </p> <ol> <li>Each of the 41 strains was cultured in aerobic atmosphere at 37°C for 7 ± 2 days on blood agar (COH, bioMerieux<sup>®</sup>). Then, one colony was extracted according to the MycoEx protocol (Bruker<sup>®</sup>). For each of the extracts, 8 technical replicates were realized and analyzed by MALDITOF MS (Bruker<sup>®</sup>). Dried spots were overlaid with 1µL of MALDI matrix (α-HCCA).</li> <li> <p>Data acquisition was performed using a Microflex LT (Bruker<sup>®</sup> Daltonics) mass spectrometer equipped with a N2 laser (λ =377 nm). Instrument parameters used were as follows: a masse range between 200-20000 Da, ion source 1: 20 kV, ion source 2: 18.5 kV, Iens: 8.45 kV, pulsed ion extraction: 330 ns, laser frequency: 20.0 Hz. Spectra were obtained after 500 shots. Each spot was analyzed three times. In total 24 spectra were obtained for each extraction.</p> </li> <li> <p>Spectra acquired for each isolate were visualized and analyzed using Flex Analysis software (Bruker<sup>®</sup> Daltonics), and spectra with low quality peaks were removed. A minimum of 15 spectra per extraction was necessary to validate the extraction.</p> </li> </ol> <p><strong>This database is only intended for medical research. Please contact: medecine-drv@sorbonne-universite.fr for data access.</strong></p> <p>After access agreement, the three following files will be available :</p> <ul> <li>The MABSC_spectra.zip file contains the MS peak list data in a Matlab compatible format.</li> <li>The MABSC_metadata.pdf file contains the molecular identifications of strains.</li> <li>The MABSC_notes.txt file contains informations concerning contains informations on the method of obtaining the data.</li> </ul>
Meta-Analysis and Comparative Study of Proteomic Profiles in COPD Patients, Asymptomatic Smokers, and Healthy Individuals Using Mass Spectrometry-Based DIA Approaches on Serum Samples
<p>The provided files include raw data from Data Independent Acquisition (DIA) mass spectrometry proteomics and targeted proteomics of human clinical COPD samples, along with the study design.</p>
Mass Spectrometry Raw Files from IP-MS of eRNA-encoded proteins
<p>Mass spectrometry raw data files from immunoprecipitation of tagged eRNA protein constructs.</p> <p>Name guide: ORFIP_R[ORF ID number]_[+/- RNase], P = RNase+, N = RNase-free</p> <p>Protein constructs were expressed in pCMV plasmids.</p> <p>Cell line: HEK293T</p> <p>Transfection: PEI-MAX, 24 hours</p> <p>Lysis performed with/without RNase treatment.</p> <p>Immunoprecipitation stage 1 with anti-DYKDDDDK antibody, eluted with 3xFLAG peptide buffer</p> <p>Immunoprecipitation stage 2 with TALON Cobalt Resin, saved for on-bead digestion</p>
Spectra from "Contribution of MALDI-TOF mass spectrometry and Machine Learning including Deep Learning techniques for the detection of virulence factors of Clostridioides difficile strains"
<p><strong>This database includes spectra from 201 <em>C. difficile </em> (CD) strains :</strong></p> <ul> <li>50 non-toxigenic strains (tcdA- tcdB-) (designated ToxA-B-) belonging to 19 different PR,</li> <li>151 toxigenic strains harbouring toxins A and B genes (ToxA+B+). Among the 151 ToxA+B+ strains, 46 corresponding to 8 different PR also harboured the binary toxin genes (ToxA+B+CDT+) and 105 (23 different PR) did not (ToxA+B+CDT-).</li> <li>Among the 46 ToxA+B+CDT+ strains, 22 belonged to the Hv strains i.e. PR 027 (n=13), PR 176 (n=5) and PR 181 (n=4) strains (ToxA+B+CDT+Hv) (Table S1). </li> </ul> <p><strong>Sample preparation.</strong> Each isolate stored at −80°C (Microbank; Pro-Lab Diagnostics) was thawed and cultivated on Columbia Blood Agar (CBA, bioMérieux) incubated in anaerobic atmosphere at 37°C for 48 hours. A subculture was performed in the same conditions. A chemical protein extraction was then carried out. Briefly, a single colony was suspended in 200 µl water and vortexed. After adding 900 µl ethanol, samples were vortexed and centrifuged at 13,000 × g for 2 minutes. The supernatant was removed, and the remaining ethanol was evaporated at room temperature. Next, 25 µl of 70% formic acid was added and mixed with the pellet, then 25 µl of acetonitrile was added. After centrifugation at 13,000 × g for 2 minutes, the supernatant was ready for analysis. <strong>Eight deposits were performed for each isolate.</strong> The dried spots were coated with 1 µl of α-cyano-4-hydroxycinnamic acid (a-HCCA) in 50% acetonitrile-2.5% trifluoroacetic acid and <strong>each spot was analysed three times by MALDI-TOF MS</strong>.</p> <p><br> <strong>MALDI-TOF MS acquisition and analysis.</strong> Mass spectra were acquired using a Microflex LT instrument (Bruker Daltonics). The standard parameters of the CE-IVD method recommended by the manufacturer were used. This instrument was equipped with an N2 laser (377 nm) using the following parameters: mass range, 2,000 to 20,000 Da; ion source 1, 20 kV; ion source 2, 18.15 kV; lens, 6 kV; pulsed ion extraction, 150 ns; laser frequency, 20 Hz. A manual external calibration standard (Bacterial Test Standard; Bruker Daltonics) was used for calibration. Data acquisition was performed using FlexControl (version 3.0; Bruker Daltonics).</p> <p><br> <strong>A total of 4659 spectra were produced. </strong></p> <p><strong>Fore more details: please contact alexandre.godmer@aphp.fr</strong><br> </p>
RNA-seq and Mass spectrometry analysis reveals the roles of YTHDF1 in aging
GEO Series GSE149883. Mus musculus. 8 samples. Type: Methylation profiling by high throughput sequencing.
Chromatin proteins linked to dosage compensation in Drosophila captured by ChIP-mass spectrometry
GEO Series GSE42025. Drosophila melanogaster. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Supplementary material for "Identification of Protein Networks and Biological Pathways Driving the Progression of Atherosclerosis in Human Carotid Arteries through Mass Spectrometry-Based Proteomics"
Open the record for dataset details and reuse information.
Mass spectrometry analysis of DENV-2 Infected HeLa Supernatant
<p>II.15 Supernatant harvest for HeLa stimulation experiments</p> <p>HeLa were seeded at a density of 1x10<sup>6</sup> cells in a 75 cm<sup>3</sup> vented flask in complete media and incubated for 24 hr at 37 °C, 5% CO<sub>2</sub>. Following incubation, cells had media removed and were either inoculated with DENV-2 prepared (MOI=1) in 5 mL DMEM or received 5 mL DMEM only, rocking every 15 min for 90 min. Inoculum was then removed and cells received 20 mL of complete media. Cells were left to incubate for 48 hr at 37 °C, 5% CO<sub>2</sub>. Following incubation, cell culture media was harvested, and cells lysed in TRIzol for RT-qPCR to confirm DENV infection. Harvested supernatant was clarified by centrifugation at 2,600 x <em>g </em>for 5 minutes before storing at -80°C. Conditioned media is the term given to the supernatant of cells generated in the absence of DENV-infection.</p> <p>II.16 Sized based fractionation of DENV-infected HeLa supernatant</p> <p>Supernatants were either unfiltered or fractionated into large (>50 kDa) and small (<50 kDa) proteins by Ultra-15, MWCO 50 kDa centrifugal filters (Amicon) for 15 min at RT, at 2,600 x <em>g</em>. Supernatant fractions were then reconstituted to the starting volume (20 mL) in DMEM.</p> <p>II.18 Serum free fractionated supernatant generation and mass spectrometry analysis</p> <p>For mass spectrometry analysis, HeLa were infected in a 75 cm<sup>3</sup> vented flask in the absence of FCS and then had supernatant protein quantitated by BioRad protein assay. 10 μg of protein from supernatants was prepared by Sera-Mag Carboxylate SpeedBeads (Cytiva) clean up as per manufacturer’s instructions to remove contaminating salts and detergents. Protein was then digested using 0.5 μg trypsin gold (Promega Corporation, Alexandria, NSW, Australia) overnight at 37 °C. Peptide clean-up was performed for further salt removal using Sera-Mag Carboxylate SpeedBeads which were then dissociated from peptides as per manufacturer’s instructions in preparation for analysis. Peptides were analysed by the Flinders Proteomics Facility, performed by Dr Alex Colella using Mass spectrometry (TSQ Altis™ Triple Quadrupole Mass Spectrometer, Thermo Scientific) as previously described by Sharma et. al (2009).<sup>223</sup> </p>
On-line Solid Phase Extraction High Performance Liquid Chromatography Method Coupled with Tandem Mass Spectrometry for the Therapeutic Monitoring of Cannabidiol and 7-Hydroxy-cannabidiol in Human Serum and Saliva
<p>This database includes the raw data linked with the paper “On-line Solid Phase Extraction High Performance Liquid Chromatography Method Coupled with Tandem Mass Spectrometry for the Therapeutic Monitoring of Cannabidiol and 7-Hydroxy-cannabidiol in Human Serum and Saliva".</p> <p>Cannabidiol is a novel antiseizure medication approved in Europe and the US for the treatment of seizures associated with Lennox-Gastaut syndrome, Dravet syndrome and tuberous sclerosis complex. We describe in this article a new and simple liquid chromatography-mass spectrometry method (LC-MS/MS) for the determination of cannabidiol and its active metabolite 7-hydroxy-cannabidiol in microvolumes of serum and saliva (50 μL), to be used as a tool for therapeutic drug monitoring (TDM) and pharmacokinetic studies. After on-line solid phase extraction cannabidiol, 7-hydroxy-cannabidiol and the internal standard cannabidiol-d3 are separated on a monolithic C18 column under gradient conditions. Calibration curves are linear within the validated concentration range (10-1000 ng/mL for cannabidiol and 5-500 ng/mL for 7-hydroxy-cannabidiol).</p> <p>The method is accurate (intraday and interday accuracy within 94-112% for cannabidiol, 91-109% for 7-hydroxy-cannabidiol), precise (intraday and interday precision <11.6% for cannabidiol and <11.7% for 7- hydroxy-cannabidiol) and sensitive, with a LOQ of 2.5 ng/mL for cannabidiol and 5 ng/mL for 7-hydroxy-cannabidiol. The stability of the analytes was confirmed under different storage conditions. Extraction recoveries were in the range of 81-129% for cannabidiol and 100-113% for 7-hydroxy-cannabidiol.</p> <p>The applicability of the method to TDM was demonstrated by analysis of human serum and saliva samples obtained from patients with epilepsy treated with cannabidiol.</p>
NeurIPS_Mass_Spectrometry_data
Open the record for dataset details and reuse information.
Spectral database of Streptococcus pneumoniae, S. mitis and S. pseudopneumoniae (MALDI-TOF Mass Spectrometry)
<p>A total of 80 strains, including 60 <strong>pneumococca</strong>l strains, 8 <strong><em>S. pseudopneumoniae</em> </strong>strains, and 12 <strong><em>S. mitis</em></strong> strains, were molecularly characterized and obtained from the National Reference Center for Pneumococci for the creation of the database. Each strain was tested a minimum of 20 and a maximum of 24 times using MALDI-TOF MS.</p> <p><br> MALDI-TOF MS acquisition and analysis. Mass spectra were acquired using a Microflex LT instrument (Bruker Daltonics). The standard parameters of the CE-IVD method recommended by the manufacturer were used. This instrument was equipped with an N2 laser (377 nm) using the following parameters: mass range, 2,000 to 20,000 Da; ion source 1, 20 kV; ion source 2, 18.15 kV; lens, 6 kV; pulsed ion extraction, 150 ns; laser frequency, 20 Hz. A manual external calibration standard (Bacterial Test Standard; Bruker Daltonics) was used for calibration. Data acquisition was performed using FlexControl (version 3.0; Bruker Daltonics). <strong>Eight deposits were performed for each isolate.</strong> The dried spots were coated with 1 µl of α-cyano-4-hydroxycinnamic acid (a-HCCA) in 50% acetonitrile-2.5% trifluoroacetic acid and <strong>each spot was analysed three times by MALDI-TOF MS</strong>.</p> <p><strong>A total of 1890 spectra were produced :</strong></p> <ul> <li><em>S. mitis</em> (n=264),</li> <li><em>S.pneumoniae</em> (n= 1434),</li> <li><em>S. pseudopneumoniae </em>(n=192)</li> </ul> <p><strong>Fore more details:</strong> please contact alexandre.godmer@aphp.fr</p>
Table S1. Extended Mass Spectrometry data table
<p>Table S1. Extended Mass Spectrometry data table </p>
Dataset - Dissolved organic matter sources and processing in the endorheic Lake Nam Co catchment (Tibet) as assessed by ultra-high resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS)
<p> </p> <p>Disclaimer 2022-01-04: Associated full text in preparation</p>
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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.