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Synapt g2 si mass spectrometer

Manufactured by Waters Corporation
Sourced in United States, United Kingdom, Germany

The Synapt G2-Si mass spectrometer is a high-performance analytical instrument designed for various applications in scientific research and industry. It utilizes advanced ion mobility separation technology to provide enhanced analytical capabilities. The Synapt G2-Si enables the separation, identification, and quantification of complex molecular samples, offering a powerful tool for various analytical workflows.

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97 protocols using synapt g2 si mass spectrometer

1

LC-MS Analysis of ShHTL7 Enzymatic Reactions

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For LC-MS analysis: a 200 μL reaction solution (100 mM HEPES, 150 mM NaCl, pH 7.0) containing 10, or 400 μM of tested samples 4a, (R)- and (S)-4a, and 4g-i, and 100 μg of recombinant ShHTL7 or its mutants was incubated at 25 °C for 30 min. Subsequently, the solution was filtered and analyzed by a nanoACQUITY UPLC system, which was directly interfaced with an SYNAPT-G2-Si mass spectrometer produced by Waters Company. For LC-MS/MS analysis, the above chemicals treated ShHTL7 reaction solution was subjected to the SDS-PAGE analysis. The corresponding protein band around 30 KDa was excised, respectively, then digested with trypsin (Promega) in NH4HCO3 solution (50 mM) at 37 °C for 24 h23 (link),26 (link)–28 (link). The covalent modification of C5H5O2/C6H6O on the peptide was analyzed by a Thermo-Dionex Ultimate 3000 HPLC system, which was directly interfaced with a Thermo Orbitrap Fusion Lumos mass spectrometer. MS-MS spectra are generated by pLabel software53 (link),54 (link).
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2

Stability Evaluation of Organic Compounds

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Stability studies were performed as described previously with some modifications for the specific compounds.18 (link), 38 (link) Pooled human plasma was diluted to 50% with phosphate buffered saline at pH 7.5 and compounds were added to a final concentration of 100 μM in a volume of 100 μL. These solutions were incubated for the indicated times at room temperature in the dark. Compounds were incubated then extracted with 300 μL of LCMS grade acetonitrile. Debris was pelleted by centrifugation at 10,000 x g for 2 minutes. Extracts were evaluated by LCMS with a Waters Synapt G2-Si Mass Spectrometer in positive mode using a gradient starting at 25% acetonitrile then increasing to 80% acetonitrile over 8 minutes. Masses corresponding to the molecular ion [M+H]+, the sodium adduct [M + Na]+, and the dehydration product [M - OH]+ were generally observed, though this data varied by compound. The allylic acetate containing compounds were additionally examined for the presence of the de-acetylated form, which was detectable as described in the text at the retention time and mass of the corresponding pure standard. The integrated peak values for all three ions of the test compound, and its deacetylated form when applicable, were summed and compared to those of t = 0 minutes for each compound.
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3

Deuterium Exchange Kinetics of PDK1

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The experiments were performed essentially as previously described for studies on the catalytic domain of PDK1 (84 (link)). In short, His-PDK11-556 and His-PDK150-359 were diluted in buffer containing deuterium oxide ([2H]2O) at 30°C for the indicated times. The exchange was stopped by quenching with acid ((0.5% TFA, 5 M GnCl) to achieve a final pH of 2.5) and cooling to 0°C. Each sample was immediately injected into nanoUPLC HDX Sample Manager (Waters) for online pepsin digestion using Poroszyme pre-packed pepsin column (Thermo Fisher Scientific), using 0.1% formic acid in LC-MS water at 100 μl/min, then trapped and desalted using a VanGuard C-18 column (Waters), followed by reverse-phase separation using ACQUITY™ 2.1 X 5 mm BEH C-18 column (Waters) using a 0.1% formic acid in acetonitrile gradient. The labelled derivative peptides were analyzed by Synapt G2 Si mass spectrometer (Waters) operating in positive ion mode using an MSE acquisition method. The mass spectrometer was continuously calibrated using 200 fmol/μl Glu-fibrinopeptide B standard flowing at 1 μl/min. The graphics represent the number of deuterium atoms incorporated into each peptide during the incubation.
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4

Hydrogen-Deuterium Exchange Mass Spectrometry

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After quenching, samples were injected onto a Waters nanoAcquity with HDX technology for online pepsin digestion at 15 °C and UPLC peptide separation at 0 °C. Samples were digested on a 2.1 × 50 mm stainless steel column packed with POROS 20AL resin coupled to porcine pepsin (Sigma). Peptides were trapped and desalted on a VanGuard Pre-Column trap (2.1 × 5mm, Acquity UPLC BEH C18, 1.7 μm) for 3 min. Peptides were eluted from the trap and separated using an Acquity UPLC HSS T3 1.8 μm 1.0 × 50 mm column with a 5–35% gradient of acetonitrile over 6 min at a flow rate of 65 μl/min. Mass spectra were acquired using a Waters Synapt G2Si mass spectrometer. Peptides were identified from triplicate undeuterated samples of each protein alone and in complexes using Waters MSE and Waters Protein Lynx Global Server (PLGS) 3.0. Peptide maps were generated and deuterium incorporation analyzed using Waters DynamX 3.0 software.
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5

Brucella melitensis Proteome Profiling

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Protein digestion has been performed according to the Filter-Aided Sample Preparation (FASP) protocol [19 (link)] as described in detail by Piras et al. [20 (link)].
Label-free proteomic analysis was performed on an ACQUITY MClass System (Waters Corporation) directly coupled to a high-definition Synapt G2-Si mass spectrometer (Waters Corp). according to Greco et al. [21 (link)].
Differential protein abundance was assessed by High-Definition expression configuration mode (HDMSE) as described by Marini et al. [22 (link)]. Each sample was run in four technical replicates.
Progenesis QI for Proteomics v4.0.6403.35451 (Waters Ltd., Newcastle upon Tyne) software was used for protein quantification [23 (link)]. Database search was performed by the ion accounting method against the UniProtKB database (Brucella melitensis biotype 1, UniProtKB UP000000419). Differentially expressed proteins were established according to the following criteria: proteins identified in at least three out of four runs of the same sample; fold change of regulation > ± 30%; p-value <0.05, according to the analysis of variance (ANOVA).
The data presented in this study are made publicly available in the PRIDE data repository (https://www.ebi.ac.uk/pride/), reference number PXD022472.
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6

Synthesis and Phosphorylation of Potassium Phosphoramidate

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Potassium phosphoramidate was synthesised from phosphoryl chloride and ammonia according to the procedure described by Wei and Matthews (Wei & Matthews, 1991; Hohenester et al, 2013; Gonzalez‐Sanchez et al, 2014). In brief, phosphoryl chloride was reacted with ammonium hydroxide for 15 min on ice producing ammonium hydroxide phosphate, which was added to potassium hydroxide at 50°C for 10 min. Potassium phosphoramidate (PPA) was precipitated with ethanol and collected by vacuum filtration. Equine myoglobin was phosphorylated by dissolution in 1 M aqueous PPA (150 nmol/ml) overnight at room temperature. Phosphorylation was evaluated by intact mass analysis of the resulting phosphorylated protein (5 μM in 20 mM ammonium acetate) by direct infusion via electrospray ionisation (ESI) into a Synapt G2‐Si mass spectrometer (Waters, UK).
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7

Nano-UPLC-MS/MS Workflow for Protein Identification

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The LC system used for sample separation and elution was a nanoACQUITY UPLC® (Waters, Milford, MA, USA) equipped with a trapping column nanoACQUITY UPLC® 2 G-V/M Symmetry® C18 Trap Column, 100 Å, 5 μm, 180 μm × 20 mm (Waters, Milford, MA, USA) and an analytical column ACQUITY UPLC® BEH130 C18, 130 Å, 1.7 μm, 100 μm × 100 mm Column (Waters, Milford, MA, USA). Trapping conditions were isocratic delivery of aqueous 0.1% formic acid, at 15 μL/min for two minutes at 40 °C. Sample separation was achieved on an analytical column at 1 μL/min by gradient elution (0.1–99% solvent B in 75 min) of channel A and B (aqueous 0.1% formic acid and 0.1% formic acid in 95% acetonitrile). Sample injection volume was 4 μL. The MS system used for protein identification was a SYNAPT G2-Si mass spectrometer (Waters, Milford, MA, USA) at a mass range of 50–4000 m/z. MSE data were acquired in positive ion mode for all samples and with the collision cell energy alternating between low energy (4 eV) to collect peptide precursor (MS) data, and elevated energy (rising gradient from 20 to 40 eV) to obtain peptide fragmentation (MSE) data (standard MSE procedure).
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8

Comprehensive Analytical Characterization

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Optical rotation data were obtained on a Rudolph Research AUTOPOL® III automatic polarimeter. ECD data were obtained on a JASCO J-715 CD instrument. NMR data were collected on Varian 500 and 600 MHz NMR spectrometers. Intensity data were collected using a D8 Quest κ-geometry diffractometer with a Bruker Photon II cmos area detector and an Incoatec Iμs microfocus Mo Kα source (λ = 0.71073 Å). LC-MS data were obtained on a Shimadzu LC-MS 2020 system (ESI quadrupole) coupled to a photodiode array detector, with a Phenomenex Kintex 2.6 μm C18 column (100 Å, 75 × 3.0 mm, 0.4 mL/min). The preparative HPLC system utilized SCL-10A VP pumps and system controller with Phenomenex Gemini 5 μm C18 column (110 Å, 250 × 21.2 mm, 10 mL/min), the analytical and semi-preparative HPLC system utilized Waters 1525 binary pumps with Waters 2998 photodiode array detectors, and Phenomenex Gemini 5 μm Gemini C18, Phenomenex Kinetex 5 μm biphenyl, Phenomenex Kinetex 5 μm pentafluorophenyl (250 × 4.6 mm, 1 mL/min and 250 × 10 mm, 4 mL/min). Accurate mass data were collected on a Waters SYNAPT G2-Si mass spectrometer. All solvents were of ACS grade or better.
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9

Synthesis of Novel Thiourea Derivatives

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All reactions were performed under a nitrogen atmosphere. All reagents and starting materials were purchased from commercial suppliers and used without further purification. The dichloromethane was dried over calcium hydride. 1H NMR (400 MHz) and 13C NMR (100 MHz) spectra were recorded on a Bruker Avance III multinuclear instrument. High resolution mass spectrometry measurements were performed using a Synapt G2-Si mass spectrometer (Waters) equipped with a quadrupole-Time-of-flight mass analyser. The mass spectrometer was operated in the positive ion detection mode. The results of the measurements were processed using the MassLynx 4.1 software (Waters) incorporated with the instrument. Melting points were determined in open glass capillaries and are uncorrected. Analytical TLC was performed using Macherey-Nagel Polygram Sil G/UV254 0.2 mm plates. 2,2-Diethyl malonyl dichloride and appropriate thioureas were commercial materials (Merck).
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10

UPLC-UDMS^E Proteomics Analysis

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UPLC-UDMSE was performed as previously described [16 (link), 17 (link)]. In summary, 4 μl of each sample (around 1.4 μg protein) was injected into a nanoACQUITY UPLC-system (Waters Corporation, MA, USA). For separation, TRIZAIC nanoTile 85 μm x 100 mm HSS-T3u wTRAP was used. The samples were loaded, trapped and washed for two minutes with 8.0 μL/min 1% B (0.1% formic acid in acetonitrile). The analytical gradient used was 0–1 min 1% B, at 2 min 5% B, at 65 min 30% B, at 78 min 50% B, at 80 min 85% B, at 83 min 85% B, at 84 min 1% B and at 90 min 1% B with 450 nL/min. Buffer A was 0.1% formic acid in water. Data were acquired in data-independent acquisition fashion with UDMSE mode using a Synapt G2-Si mass spectrometer (Waters Corporation, MA, USA). The collected data range was 100–2000 m/z, scan time one‐second, IMS wave velocity 650 m/s, and collision energy was ramped in trap between 20 and 60 V. Calibration was performed using Glu1‐Fibrinopeptide B MS2 fragments and Glu1‐Fibrinopeptide B precursor ion was used as a lock mass during the runs. All samples were run in triplicates and the coefficient of variation for the dataset was 4.1%.
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