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15 results for “Orbitrap”
Amoxicillin degradation pathways and mass spectra raw data (using LC-MS orbitrap)
<p>The link provides five documents namely:</p> <p>File No.1 (Proposed Chemical Structures-tabulated)</p> <p>File No.2 (MS and MS2 images) support for File no.1</p> <p>File No.3 Transformation Products Pathway</p> <p>File No.4 Explanation + Justification of proposed chemical structures</p> <p>Raw Data obtained from compound discoverer</p>
Pure Electronic Noise of an Orbitrap Mass Spectrometer (36 replicates)
<p>The provided data was produced by performing measurements in an HPLC-ESI-Orbitrap instrument setup without the ESI being connected to an eluent flow, and consequently not producing a spray cone. We provide this data to allow researchers developing algorithms for data analysis in mass spectrometry to estimate the behaviour of their tools when confronted with real, non-chemical noise. </p> <p>As a consequence of the experimental setup, chromatographic information is included in the provided files. This does not reflect any condition of the system, as the HPLC was not connected to the MS. When using a (chromatographc) peak finding algorithm, consequently no peaks should be found. This property of the data was confirmed using the qAlgorithms program, with no peaks and at most single-digit numbers of EICs being detected.</p> <p>All data is provided in profile mode, both as the .raw file and converted to .mzML using msconvert. </p>
Online Aerosol Chemical Characterization by Extractive Electrospray Ionization − Ultrahigh-Resolution Mass Spectrometry (EESI-Orbitrap)
<p>These datasets are the raw data presented in the presented work of "Online Aerosol Chemical Characterization by Extractive Electrospray Ionization − Ultrahigh-Resolution Mass Spectrometry (EESI-Orbitrap)" in <em>Environmental Science & Technology Journal</em>, doi:10.1021/acs.est.9b07090.</p> <p>Abstract: Current mass spectrometry techniques for the online measurement of organic aerosol (OA) composition are subjected to either thermal/ionization-induced artifacts or limited mass resolving power, hindering accurate molecular characterization. Here, we combined the soft ionization capability of extractive electrospray ionization (EESI) and the ultrahigh mass resolution of Orbitrap for real-time, near-molecular characterization of OAs. Detection limits as low as tens of ng m<sup>−3</sup> with linearity up to hundreds of μg m<sup>−3</sup> at 0.2 Hz time resolution were observed for single- and mixed-component calibrations. The performance of the EESI-Orbitrap system was further evaluated with laboratory-generated secondary OAs (SOAs) and filter extracts of ambient particulate matter. The high mass accuracy and resolution (140 000 at <em>m/z</em> 200) of the EESI-Orbitrap system enable unambiguous identification of the aerosol components’ molecular composition and allow a clear separation between adjacent peaks, which would be significantly overlapping if a medium-resolution (20 000) mass analyzer was used. Furthermore, the tandem mass spectrometry (MS<sup>2</sup>) capability provides valuable insights into the compound structure. For instance, the MS<sup>2</sup> analysis of ambient OA samples and lab-generated biogenic SOAs points to specific SOA precursors in ambient air among a range of possible isomers based on fingerprint fragment ions. Overall, this newly developed and characterized EESI-Orbitrap system will advance our understanding of the formation and evolution of atmospheric aerosols.</p> <p>Structure of the datasets: The raw data are separated into individual file of excel format for the figures. Simulation data from Figure 4 can be generated using the matlab code named <em>Figure4PeakSimulation.m.</em> </p>
IDSL.UFA comparison for Orbitrap and QTOF instruments
<p>Molecular formula annotation results were compared for LC-HRMS data from orbitrap and qtof instruments for a biorec plasma sample. </p>
Orbitrap analysed non-volatile compound data from blue swimmer crab (Portunus armatus) flesh for manuscript: "Climate-driven changes to taste and aroma determining metabolites in an economically valuable portunid (Portunus armatus) have implications for future harvesting"
<p>Accurate mass measurements of non-volatile metabolites conducted on a Q-Exactive Orbitrap LC-MS (Thermo Scientific, Scoresby, VIC, Australia) equipped with a heated electrospray ionization (H-ESI) source. Source conditions were as follows: spray voltage (positive ion 3.9 kV), sheath gas 60 (arbitrary units), auxiliary gas 10 (arbitrary units) and sweep gas 1 (arbitrary units), capillary temperature of 350 °C and auxiliary gas heating temperature of 400 °C.</p>
Thermo Orbitrap IDX files (UPLC-DAD-HRMS-MS/MS)
<p>Raw data for metabolomics workflow validation. Known producer-strains and standard samples (see metadata).</p>
Orbitrap data: Arsenolipids are not uniformly distributed within two brown macroalgal species Saccharina latissima and Alaria esculenta.
<p>ESI-orbitrap-MS raw data from project SilhouetteOfSeaweed. Possible to look for e.g. other arsenolipid species that had not been discovered at the time of publication. Analysed on Thermo Orbitrap. .raw files. Full scan from 100-1400. Further details in paper: Arsenolipids are not uniformly distributed within two brown macroalgal species <em>Saccharina latissima</em> and <em>Alaria esculenta.</em> Published in Analytical and Bioanalytical Chemistry (2019) - <a href="https://doi.org/10.1007/s00216-019-01907-x">https://doi.org/10.1007/s00216-019-01907-x</a></p>
Quantitative high sensitivity proteomics with the Orbitrap ASTRAL platform
Open the record for dataset details and reuse information.
Figure 2 from: Voynikov Y, Gevrenova R, Zheleva-Dimitrova D, Balabanova V, Nikolova I, Marinov L, Benbassat I, Momekov G (2023) UHPLC-Orbitrap screening of oleraindoles in hydromethanolic extracts of Portulaca oleracea. Pharmacia 70(4): 1521-1527. https://doi.org/10.3897/pharmacia.70.e113577
Figure 2 MS2 spectra and fragmentation analysis of the three basic HCA-I conjugates in negative ionization mode. The characteristic difference of 149.048 Da, indicating a neutral loss of the 5,6-dihydroxyindole is indicated. The fragment ion corresponding to 5,6-dihydroxyindole is 148.04 m/z.
Figure 3 from: Voynikov Y, Gevrenova R, Zheleva-Dimitrova D, Balabanova V, Nikolova I, Marinov L, Benbassat I, Momekov G (2023) UHPLC-Orbitrap screening of oleraindoles in hydromethanolic extracts of Portulaca oleracea. Pharmacia 70(4): 1521-1527. https://doi.org/10.3897/pharmacia.70.e113577
Figure 3 Proposed fragmentation behavior and diagnostic fragment ions of the basic components of oleraindoles: 5,6-dihydroxyindole, and coumaroyl, caffeoyl, and feruloyl moieties. (A): negative ionization mode; (B): positive ionization mode.
Figure 1 from: Voynikov Y, Gevrenova R, Zheleva-Dimitrova D, Balabanova V, Nikolova I, Marinov L, Benbassat I, Momekov G (2023) UHPLC-Orbitrap screening of oleraindoles in hydromethanolic extracts of Portulaca oleracea. Pharmacia 70(4): 1521-1527. https://doi.org/10.3897/pharmacia.70.e113577
Figure 1 Workflow chart of the study. The hydromethanolic extract of purslane was subjected to UHPLC-HRMS with subsequent MS2 analysis. After the raw data files were transformed with MSconvert, the data filtering (DIF and DDF) were performed either with MS2Analyzer, MZmine and the in-house R script. The scans that fell within 1.5% retention time threshold and 15 ppm m/z treshold were grouped, as belonging to the same substance. Then, the obtained list of possible oleraindole structures were manually inspected with the Xcalibur software.
Supplementary material 2 from: Voynikov Y, Gevrenova R, Zheleva-Dimitrova D, Balabanova V, Nikolova I, Marinov L, Benbassat I, Momekov G (2023) UHPLC-Orbitrap screening of oleraindoles in hydromethanolic extracts of Portulaca oleracea. Pharmacia 70(4): 1521-1527. https://doi.org/10.3897/pharmacia.70.e113577
Scripts
Supplementary material 1 from: Voynikov Y, Gevrenova R, Zheleva-Dimitrova D, Balabanova V, Nikolova I, Marinov L, Benbassat I, Momekov G (2023) UHPLC-Orbitrap screening of oleraindoles in hydromethanolic extracts of Portulaca oleracea. Pharmacia 70(4): 1521-1527. https://doi.org/10.3897/pharmacia.70.e113577
MS/MS spectra of identified compounds
Orbitrap LC-MS/MS data for phage nucleosides
<p>These are files containing LC-MS/MS data for phage T4 and phage SPO1 nucleosides. Phage SPO1 data are in files prefixed ORB59709, and T4 data are in files prefixed with ORB59710. The .RAW files are Thermo .raw files obtained after tandem mass spectrometry, and were converted to .mgf format using MSConvert 3.0.22031 (a component of the Proteowizard open source mass spectrometry bioinformatics software package) under generic default presets for .mgf file extraction.</p> <p>Also included are our mass and charge lists for known nucleosides, known charged adducts, and known neutral adducts.</p> <p>File list: </p> <p>ORB59709.RAW = Raw SPO1 data<br> ORB59709.mgf = Processed SPO1 data<br> ORB59710.RAW = Raw T4 data<br> ORB59710.mgf = Processed T4 data</p> <p>Mass_lists_Nucleosides.csv = Masses and charges of known nucleosides<br> Mass_lists_Charged_adducts.csv = Masses and charges of common charged adducts<br> Mass_lists_Neutral_adducts.csv = Masses of common neutral adducts</p> <p> </p>
Scheme 1 from: Voynikov Y, Gevrenova R, Zheleva-Dimitrova D, Balabanova V, Nikolova I, Marinov L, Benbassat I, Momekov G (2023) UHPLC-Orbitrap screening of oleraindoles in hydromethanolic extracts of Portulaca oleracea. Pharmacia 70(4): 1521-1527. https://doi.org/10.3897/pharmacia.70.e113577
Scheme 1 Scheme 1. Common scaffold of an oleraindole.
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