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13 results for “Native MS”
Native MS dataset for: "Insights into the pathogenesis of primary hyperoxaluria type I from the structural dynamics of alanine:glyoxylate aminotransferase variants"
<p>Native mass spectrometry dataset used in: <strong>Insights into the pathogenesis of primary hyperoxaluria type I from the structural dynamics of alanine:glyoxylate aminotransferase variants.</strong> Pavla Vankova, Juan Luis Pacheco-Garcia, Dmitry S. Loginov, Atanasio Gómez-Mulas, Alan Kádek, José Manuel Martín-Garcia, Eduardo Salido, Petr Man and Angel L. Pey. FEBS Letters (2024)</p> <p><strong>Description:</strong></p> <p>Native mass spectrometry (MS) analysis verifying the oligomeric state of alanine:glyoxylate aminotransferase (AGT) protein and its P11L and I340M (LM) polymorphism and LM G170R mutation variants in primary hyperoxaluria type I.</p> <p><strong>Sample processing:</strong></p> <p>AGT protein as well as its LM and LM G130R mutants were buffer exchanged into 150 mM aqueous ammonium acetate solution (pH 7.5, MS-grade, Sigma-Aldrich) through six cycles of tenfold dilution and re-concentration using centrifugal concentrators Vivaspin 500 (30 kDa cut-off, <em>Sartorius</em>). Desalted proteins were introduced into a Synapt G2Si mass spectrometer (Waters) via static nanoelectrospray ionization from in-house prepared gold-coated borosilicate glass capillaries Kwik-Fil 1B120F-4 (<em>World Precision Instruments</em>). Protein concentration in samples was determined by 280 nm absorbance measurements using DeNovix DS-11 spectrophotometer. Samples were diluted in ammonium acetate and electrosprayed at 1 and 2 µM concentration. The mass spectrometer was carefully tuned for best signal quality and intensity, while keeping ion activation and unfolding minimal. Namely, electrospray voltage was kept at 1.3 kV, source desolvation temperature 80°C, sampling cone 80 V and 10 V collision voltage with 6 ml/min flow of argon in the trap region for thermalization of ions. Quadrupole was operated in a broadband transmission mode up to 8000 m/z while the spectra were acquired in mass range 500 – 20000 m/z. Spectra were externally mass recalibrated using known masses of caesium iodide clusters.</p> <p><strong>Data processing:</strong></p> <p>Raw mass spectra were averaged over 75 scans and further processed in Waters MassLynx 4.1. The averaged spectra were exported for ZENODO deposition as plain in plain m/z vs intensity .txt files as well uploaded as part of the .raw file format of the whole analysis (including initial metadata) with scan descriptions and parameter changes described in a stand-alone .txt descriptor file.</p>
Native MS dataset for: "Caldendrin and myosin V regulate synaptic spine apparatus localization via ER stabilization in dendritic spines."
<p>Native mass spectrometry dataset used in: <strong>Caldendrin and myosin V regulate synaptic spine apparatus localization via ER stabilization in dendritic spines.</strong> Anja Konietzny, Jasper Grendel, Alan Kadek, Michael Bucher, Yuhao Han, Nathalie Hertrich, Dick H. W. Dekkers, Jeroen A. A. Demmers, Kay Grünewald, Charlotte Uetrecht and Marina Mikhaylova. <i>The EMBO Journal</i> (2021) e106523. doi:<a href="https://doi.org/10.15252/embj.2020106523">10.15252/embj.2020106523</a></p><p> </p><p><strong>Description:</strong></p><p>Native mass spectrometry (MS) analysis of the stoichiometry and ion occupancy of recombinant human calmodulin (CaM) and recombinant rat caldendrin (CaD) complex with synthetic mouse myosinV IQ1 (myoIQ) motif in the presence / absence of excess Ca2+ and Mg2+ ions.</p><p><strong>Sample processing:</strong></p><p>Full-length CaD and CaM as well as the synthetic myoVa peptide were buffer exchanged into 150 mM aqueous ammonium acetate solution (pH 7.4). CaM was twice passed through a Bio-Spin P-6 gel filtration spin column (6 kDa cut-off, <i>Bio-Rad</i>), CaD and the myoVa peptide were buffer exchanged through five cycles of tenfold dilution and re-concentration using centrifugal concentrators Vivaspin 500 (10 kDa cut-off, <i>Sartorius</i>) or Amicon Ultra 0.5mL (3 kDa cut-off, <i>Merck/Millipore</i>), respectively. Desalted proteins were introduced into an Orbitrap Q Exactive UHMR mass spectrometer (<i>Thermo Scientific</i>) via static nanoelectrospray ionization from in-house prepared gold-coated borosilicate glass capillaries Kwik-Fil 1B120F-4 (<i>World Precision Instruments</i>). Proteins were sprayed and analysed at 8.5 µM concentration in ammonium acetate alone or supplemented with 200 µM calcium acetate and 100 µM magnesium acetate (both for trace metal analysis, <i>Sigma-Aldrich</i>). For interaction analysis, CaM and/or caldendrin were mixed with myoVa peptide which had final concentration of 8.5 µM (low concentration) or 34 µM (high concentration). The mass spectrometer was tuned for best signal quality and intensity, keeping ion activation and unfolding minimal. Namely, electrospray voltage was kept at 1.3 kV, source desolvation temperature 250°C, in-source desolvation -50 V, ion transfer profile "high m/z", analyzer profile "low m/z", analyzer target resolution 12500 acquiring in mass range 500 – 9000 m/z. Nitrogen was used as collision gas in HCD cell at relative gas pressure setting 7.0 with gentle collisional activation by 10 V HCD voltage gradient.</p><p><strong>Data processing:</strong></p><p>Raw spectra were averaged over at least 50 scans for mass deconvolution and peak assignment in UniDec 4.4.1 package (<i>Marty et al., 2015</i>). The averaged spectra were exported for ZENODO deposition using <i>Thermo Scientific</i> FreeStyle 1.5.93.34 as single-scan Thermo .raw files (including instrumental parameters metadata) as well as in plain m/z vs intensity .txt files.</p>
Oligomeric state and ATP binding to <em>E. coli</em> Rho measured by native MS
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Supplementary material 1 from: Ollivier M, Kazakou E, Corbin M, Sartori K, Gooden B, Lesieur V, Thomann T, Martin J-F, Tixier MS (2020) Trait differentiation between native and introduced populations of the invasive plant Sonchus oleraceus L. (Asteraceae). NeoBiota 55: 85-115. https://doi.org/10.3897/neobiota.55.49158
Table S1. Location and climatic data for the 14 Sonchus oleraceus populations used for offspring comparisons under standardised conditions
Supplementary material 2 from: Ollivier M, Kazakou E, Corbin M, Sartori K, Gooden B, Lesieur V, Thomann T, Martin J-F, Tixier MS (2020) Trait differentiation between native and introduced populations of the invasive plant Sonchus oleraceus L. (Asteraceae). NeoBiota 55: 85-115. https://doi.org/10.3897/neobiota.55.49158
Table S2. Mean (± standard error) values for 20 traits assessed for native (Europe and North Africa) and invasive (Australia and New Zealand) populations of Sonchus oleraceus under standardised conditions
Supplementary material 3 from: Ollivier M, Kazakou E, Corbin M, Sartori K, Gooden B, Lesieur V, Thomann T, Martin J-F, Tixier MS (2020) Trait differentiation between native and introduced populations of the invasive plant Sonchus oleraceus L. (Asteraceae). NeoBiota 55: 85-115. https://doi.org/10.3897/neobiota.55.49158
Table S3. Results of mixed models assessing the effect of range (native: Europe and North Africa, introduced: Australia and New Zealand), population within range being considered as a random factor, for 20 plants traits measured on Sonchus oleraceus under standardised conditions
20211223 CutA directinfusion native MS first try
<p>E.coli CutA was measured with Native MS. First test run to test integrity of the protein under different conditions. </p>
Supplemntary tables S1-S6 related with the article entitled: LC-MS-Based Plasma Proteome Analysis in Nursery Pigs Fed Diets Enriched with Native Chicory Inulin
<p><span>Table S1: Composition of the pig diet: control diet (C) and diets supplemented with 1% (T1) or 3% (T2) of native chicory inulin.; Table S2: Nutrient contents of the control diet (C) and the diets supplemented with 1% (T1) or 3% (T2) of native chicory inulin.; Table S3: Chemical composition (%) of inulin (IN) used as a feed supplement.; Table S4: Porcine plasma proteins submitted for further analysis.; Table S5: Proteins significantly altered in response to the T1 diet.; Table S6: Proteins significantly altered in response to the T2 diet.</span></p>
Native MS of MIGA2
<p>Native MS analysis datasheet of human MIGA2 soluble portion (purified from bacteria).</p>
Figures 2-9 from: Silva GL, Metzelthin MH, Da-Costa T, Rocha MS, Silva DE, Ferla NJ, Silva OS (2017) Responses of water mite assemblages (Acari) to environmental parameters at irrigated rice cultivation fields and native lakes. Zoologia 34: 1-8. https://doi.org/10.3897/zoologia.34.e19988
Figures 2-9 View of the study sites: (2) Detailed view of the rice-water samples, (3) Rice area 1 – R1, (4) Rice area 2 – R2, (5) Rice area 3 – R3, (6) Rice area 4 – R4, (7) Lake 1 – L1, (8) Lake 2 – L2, (9) Lake 3 – L3.
Figures 12-13 from: Silva GL, Metzelthin MH, Da-Costa T, Rocha MS, Silva DE, Ferla NJ, Silva OS (2017) Responses of water mite assemblages (Acari) to environmental parameters at irrigated rice cultivation fields and native lakes. Zoologia 34: 1-8. https://doi.org/10.3897/zoologia.34.e19988
Figures 12-13 Ordination diagram (first two axes) of Non-Metric Multidimensional Scaling (NMDS) using (12) Bray-Curtis and (13) Jaccard indexes with Envfit function for the evaluated environments. (▲ Lake 1, ■ Lake 2 and 3, ● Rice Area). Stress: 0.15.
Figures 10-11 from: Silva GL, Metzelthin MH, Da-Costa T, Rocha MS, Silva DE, Ferla NJ, Silva OS (2017) Responses of water mite assemblages (Acari) to environmental parameters at irrigated rice cultivation fields and native lakes. Zoologia 34: 1-8. https://doi.org/10.3897/zoologia.34.e19988
Figures 10-11 Abundance and richness of mites in rice areas cultivation and native lakes: (10) abundance adults (± SD) (Log10 X+1); (11) richness (± SD) (Log10 X+1). Different letters indicate significant differences, Tukey test, p < 0.05.
Figure 1 from: Silva GL, Metzelthin MH, Da-Costa T, Rocha MS, Silva DE, Ferla NJ, Silva OS (2017) Responses of water mite assemblages (Acari) to environmental parameters at irrigated rice cultivation fields and native lakes. Zoologia 34: 1-8. https://doi.org/10.3897/zoologia.34.e19988
Figure 1 - Schematic map of Brazil and Rio Grande do Sul State illustrating the study area.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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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.