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Synapt g2 si high definition mass spectrometer

Manufactured by Waters Corporation
Sourced in United States, United Kingdom

The SYNAPT G2-Si High Definition Mass Spectrometer is a laboratory instrument designed for high-resolution mass spectrometry analysis. It provides accurate mass measurements and detailed structural information about molecular compounds.

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14 protocols using synapt g2 si high definition mass spectrometer

1

High-Resolution Mass Spectrometry Analysis

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All complexes were analyzed using SYNAPT G2-Si High Definition Mass Spectrometer (Waters, Manchester, U.K.). For the analysis, all protein solutions were buffer exchanged into 200 mM ammonium acetate (pH 7.5) using Micro Bio-Spin chromatography columns (Bio-Rad). Aliquots (∼2 μL) were introduced into the mass spectrometer via nanoflow capillaries using the following conditions: capillary voltage 1.2 kV, sampling cone 120 V, source offset 20 V. The source temperature was set up for 25 °C. The collision voltage was adjusted for the optimal signal level. Maximum entropy (MaxEnt, Waters) deconvolution was applied to electrospray data to recalculate the gas phase existing masses.
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2

Ion Pairing Chromatography for Metabolite Analysis

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Ion pairing-reversed phase chromatography separations were run on an ultra high performance liquid chromatography system (UHPLC, Acquity H-Class® Waters, Manchester, UK), equipped with a BEH C18 column (100 mm × 2.1 mm, packed with 1.7 μm porosity particles) (Waters, Manchester, UK). The flow rate was of 0.150 mL min−1 and column was heated at 30 °C. A ternary gradient was used (A, pure water; B, pure acetonitrile; and C, 20 mM hexylammonium dissolved in water, and pH value adjusted to 6 by addition of acetic acid), from 16.6% to 35% of solvent B in 10 min, then up to 63.4% at 20 min and maintained at 73.4% for 4.5 min. Percentage of solvent C was kept constant at 25%.
MS measurements were done through a direct coupling with a Synapt G2Si high-definition mass spectrometer (Waters Corp., Manchester, UK) on a mass range of 300–2000 m/z. The instrument was operated in a negative ionization mode in the so-called sensitivity mode, with an ESI capillary voltage of 2.5 kV and a sampling cone voltage of 50 V. Data acquisition was carried out using MassLynx software (V4.1).
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3

Comprehensive Metabolite Profiling via UPLC-MS

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The samples were analysed by an ACQUITY UPLC system coupled to a SYNAPT-G2-Si high-definition mass spectrometer from Waters (Milford, USA). The HILIC method helped to separate highly polar metabolites whereas the traditional RPLC method provided efficient separation of nonpolar metabolites. These two methods were complementary and together, can provide enhanced coverage of metabolites.
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4

High-Resolution Mass Spectrometry for Compound Profiling

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All MS was performed using both 15 T FT-ICR (SolariX; Bruker Daltonics, Billerica, MA, USA) and Q-TOF (SYNAPT G2-Si High Definition Mass Spectrometer; Waters Co., Milford, MA, USA) mass spectrometers. UHR ESI/FT-ICR MS was used to profile compounds in fractions and determine the molecular formulae of compounds; UPLC/MS was employed to identify SAOx in mulberry extracts using high-resolution mass profiling and MSMS.
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5

Synthesis of Fluorescent Lactose Derivatives

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All reagents were obtained from commercial sources. D-lactose, acetic anhydride, N,N-dimethylformamide (DMF), trichloroacetonitrile, 1,8-diazabicyclo [5.4.0]undec-7-ene (DBU), boron trifluoride diethyl etherate (BF3·Et2O), propargyl alcohol, sodium metal, Dowex-50 resin (H+ form), 5-bromovaleryl chloride, 2,4-dimethyl pyrrole, triethylamine (TEA), N-iodosuccimide (NIS) were purchased from Sigma Aldrich (St. Louis, MO, USA). Sodium azide, sodium ascorbate, copper (II) sulfate pentahydrate, sodium hydroxide (NaOH), sulfuric acid (H2SO4), sodium hydrogen carbonate (NaHCO3), magnesium sulfate (MgSO4), and ammonium carbonate [(NH4)2CO3] were procured from Daejung Chemical (Gyeonggi-do, South Korea) and used without further purification. Ethyl acetate (EtOAc), dichloromethane (CH2Cl2), tetrahydrofuran (THF), methanol, and other solvents were of analytical grade and were dried under calcium hydride prior to use, except THF.
All compounds were characterized by 1H- and 13C-NMR spectroscopy on a Bruker AM 250 spectrometer (Billerica, MA, USA) and high-resolution electrospray ionization mass spectrometry (HR-ESI-MS) on a SYNAPT G2-Si high definition mass spectrometer (Waters, London, United Kingdom).
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6

Metabolic Profiling of Brown and Inguinal Adipose Tissues

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30 mg of accurately weighted BAT or iWAT were homogenized in 200 μL of methanol:water (3:1) mixture under cold conditions. The tissue homogenates were vortexed for 10 min at 4 °C and centrifuged at 13,000 rpm (Heraeus Fresco 21, Thermo Fisher Scientific, Hamburg, Germany) for 15 min at 4 °C. The supernatant was carefully collected and dried under nitrogen gas, resuspended with 100 μL of acetonitrile and centrifuged at 13,000 rpm for 10 min at 4 °C before UPLC–QTOF-MS/MS analysis at the pharmaceutical core facility of Capital Medical University. The chromatographic separation of different metabolites was performed on an Acclaim RSLC C18 column (ThermoFisher Scientific). Mass spectrometry analysis was conducted using the SYNAPT G2-Si high-definition mass spectrometer (Waters) equipped with an electrospray ionization source. The acquired data were imported into Progenesis QI software for data normalization using peak alignment and baseline correction. The processed data were then searched against compound databases (KEGG, HMDB) using ChemSpider to obtain accurate molecular weight and fragmentation information of the compounds. Differentially enriched metabolites (P < 0.05, fold change >1.2, variable importance in projection score >1, and those including mass spectrometry fragments) were selected.
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7

Metabolomics Analysis by UPLC-MS

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Mass spectrometry data were collected by a SYNAPT G2-Si High-Definition Mass Spectrometer with an electrospray ionization (ESI) source (Waters Ltd., Milford, MA, USA) in both positive and negative ion modes for the serum and the urine samples, whereas only negative ion mode was used for the liver and colon aqueous extracts due to the limited valuable compounds detected in the positive ion mode. Nitrogen gas was set as desolvation and cone gas. The capillary voltage was set at 2.5 kV, nebulizer gas at 6 bar, cone voltage at 35 kV, cone gas flow at 30 L/h, source temperature at 110°C, desolvation gas temperature at 350°C, and desolvation gas flow at 700 L/h. The eluted compounds were scanned from mass/charge (m/z) 50 to m/z 1,200 at a rate of 0.3 s per scan for both MS mode and MSE mode. The collision energy was set from 20 to 50 eV for MSE mode. To ensure mass accuracy and reproducibility, leucine enkephalin was used to correct data (m/z 556.2720 in positive mode and m/z 554.2615 in negative mode) at a concentration of 1 ng/μl and a flow rate of 5 μl/min continuously.
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8

Proteomics Analysis of Frozen Frontal Cortex

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Frozen frontal cortex samples were homogenised in 50 mM Ambic buffer with 2% ASB‐14 and pooled per disease group (three cases per pooled sample other than TREM2+ controls that only had 2). Proteins were extracted into two fractions; soluble supernatant and the insoluble pellet fraction. For each fraction Label‐free mass spectrometry was performed with a SYNAPT G2‐Si High Definition mass spectrometer (Waters, UK) with 2D fractionation as previously described (8, 40). There were four fractions run for each sample and 0.5 µg of protein were injected per fraction per run. The raw data were imported into Progenesis for proteomics software (Nonlinear dynamics, UK) and processed. Identifications were obtained by searching the data against the human reference proteome (2016). Data for identifications with more than 1 unique peptide were exported for downstream analysis.
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9

Mass Spectrometry Analysis of Amyloid-β Peptide

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Mass spectra of 20 μM Aβ40 peptide dissolved in 20 mM ammonium acetate buffer, pH 7.4, with and without addition of toluene and Pb(IV) acetate at 1:1 ratios were recorded three times each on a Synapt G2-Si high definition mass spectrometer (Waters corporation) equipped with a conventional ESI source operating in positive ion mode. Flow rate was 20 μl/min, capillary voltage 2.5 kV, cone voltage 40 V. Analysis was done in high-resolution mode (average resolution of 30 000) in the 500–4000 m/z range.
Data processing was done using the Proteowizard124 (link), UniDec125 (link), and mMass126 (link) softwares. Peaks were identified by comparison between raw experimental data and generated theoretical peak lists, and by analysis of isotopic patterns (Supp. Fig. S4). All data were normalized to the +4 charge state signal of the Aβ monomer, to account for small deviations in concentration and ionization efficacy across samples.
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10

Electrospray Mass Spectrometry of Proteins

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All samples were analyzed by using the SYNAPT G2-Si High-Definition Mass Spectrometer (Waters, Manchester, U.K.) [51 (link), 52 (link)]. For the analysis, all protein solutions were buffer-exchanged into 200 mM ammonium acetate (pH 7.5) using Micro Bio-Spin chromatography columns (Bio-Rad). Aliquots of ∼2 μL were introduced into the mass spectrometer via nanoflow capillaries under the following conditions: capillary voltage 1.2kV, sampling cone 120V, and source offset 20V. The source temperature was set to 25°C. The collision voltage was adjusted for optimal signal level. Maximum entropy (MaxEnt, Waters) deconvolution was applied to electrospray data to recalculate the gas phase existing masses.
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