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6538 q tof

Manufactured by Agilent Technologies

The 6538 Q-TOF is a high-resolution quadrupole time-of-flight mass spectrometer designed for accurate mass measurements and detailed structural analysis. It provides precise mass determination and fragmentation data for complex biomolecules and small molecules.

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6 protocols using 6538 q tof

1

Compound Analysis and Extrusion

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Example 3

Compounds were dissolved in acetonitrile at 1 mg/ml and used directly for analysis on an Agilent 6538 QTOF, using ESI MS+ as ion source.

A compound of the disclosure was formed into a rod in the glassy state by heat extrusion. The conjugate compound was initially melted at a temperature up to 140° C. The resulting material was then loaded into a heat extruder with a 30 G die head, heated between 70° C. to 125° C., and pressure was applied to a piston to form extrudate from the extruder. The extrudate was cut to different lengths.

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2

High-Resolution Mass Spectrometry Protocol

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High-resolution mass spectrometry (HRMS) was performed with an Agilent 6538 QTOF with an ESI MS+ ion source with high resolution, accurate mass capability. HRMS data are reported in the figure captions for Supplementary Figs. 1 and 1418.
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3

Untargeted Metabolomic Profiling of Cellular Activity

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The changes in cellular activity were studied using untargeted metabolomic profiling by HPLC–MS (high-performance liquid chromatography coupled to mass spectrometry). Chromatography was performed in the normal phase with established protocols using a Cogent Diamond Hydride HILIC 150 × 2.1 mm column in an Agilent 1290 UPLC system [28 (link)]. Mass spectrometry was performed using an Agilent 6538 Q-TOF. Metabolites with a median intensity of zero across all experimental groups were excluded from the analysis. Undetected remaining metabolites (i.e., intensity of zero) were replaced with a value of one half of the minimum peak intensity for statistical analyses. Statistical analysis was performed in Metaboanalyst. The data were first log-transformed and standardized. The metabolomic profiles between the experimental groups were compared using principal components analysis (PCA), hierarchical clustering, volcano plot analysis, and pathway enrichment analysis. Significance was assessed with false discovery rate corrections using a significance level of 0.05 selected a priori.
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4

UPLC-QTOF-MS Metabolomic Analysis

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In this experiment, chromatographic separation was performed using an ACQUITY UPLC HSS T3 column (2.1 × 100 mm I.D., 1.8 μm, Waters, USA). The column was maintained at a temperature of 35 °C, and the mobile phases consisted of water (Phase A) and acetonitrile (Phase B) with the addition of 0.1% formic acid. The gradient program involved the application of a 5% solution of Phase B for the first 3 min, followed by a linear increase from 5 to 95% solution B over the next 12 min (3–15 min), and then maintaining the 95% solution B for an additional 2 min (15–17 min). A 5-minute post-treatment period was conducted with a flow rate of 350 µL/min. The sample injection volume was approximately 2 µL.
The data in this study were collected using Agilent 1290 LC and 6538 Q-TOF mass spectrometers, employing electrospray ionization in both positive and negative ionization modes. The drying gas N2 was delivered at a rate of 9 L/min, while the temperature was maintained at 360 °C. The nebulizer pressure was set at 39 psi, and the capillary voltage was adjusted to 4000 V and 3900 V for positive and negative ionization modes, respectively. The scan range for the mass spectra was set from 50 to 1000 m/z. To ensure accuracy and reproducibility, a reference solution was utilized for real-time correction of the mass spectra, with the lock mass (m/z 922.009798, 121.050873) serving as a reference point.
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5

Mass Spectrometry Analysis of NDR1 Kinase

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The integrity and phosphorylation status of wild-type NDR1KD employed for crystallization studies was determined using ESI-LC/MS at the AIMS Mass Spectrometry Laboratory in the Department of Chemistry at the University of Toronto. 20 μl of 200 μM protein sample in 25 mM HEPES-NaOH pH 7.5, 100 mM NaCl, and 2 mM DTT was submitted for analysis. Sample was diluted in water 1000-fold prior to analysis using an Agilent 6538 Q-TOF interfaced to a 1290 ultrahigh pressure HPLC. A list of the ionic formulae was generated by the Molecular Formula Generation Algorithm as implemented in the MassHunter data processing software. The Molecular Formulae Generation Score takes into account the best match for the mass accuracies and relative abundances of the isotopomers identified for the target isotopic envelope. The standard m/z acquisition range for biomolecule analysis was set between 200–2000 Da; however, the mass spectrum was expanded to highlight the appropriate regions of interest. The reconstructed mass spectrum was generated by the Maximum Entropy algorithm in a plot of neutral mass (Da) versus intensity. Selected peaks were labeled with mass values rounded to one decimal place. Data processing was performed with the MassHunter BioConfirm software package.
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6

Spectroscopic Characterization of 1,3-Diketones

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NMR and HRMS graphs are reported in the supporting information. Where otherwise noted, all chemicals purchased were from a commercial supplier and were used without further purification. The THF solvent used for the synthesis of 1,3-diketones were first dried with a molecular sieve 4 Å and was stored under a nitrogen atmosphere for 72 h before being used. All the reactions were carried out under an inert atmosphere of argon. The progress of the reaction was monitored by TLC analysis. High-resolution mass spectra were recorded with a mass spectrometer (Agilent 6538 Q-TOF with dual ESI source). 1H and 13C NMR spectra were recorded on a Bruker Advance spectrometer [400 MHz (1H) and 100 MHz (13C) in CDCl3 (first de-acidified by passing it through calcium carbonate before testing) and with DMSO. The solvent peaks were referenced according to the literature56 (link). UV–visible absorption spectra were recorded on Eppendorf UV–Vis spectrophotometer. The fluorescence spectra were measured on Varian carry fluorescence spectrophotometer. The fluorescence lifetime was determined using Fluoromax-4 fluorimeter (Horiba) in a quartz cuvette (Starna). Excitation was carried out using a 293-nm delta diode (Horiba) in Fluoromax-4C-TCSPC configuration. The diode was pulsed at a 2 MHz repetition rate, the decay was measured until 10,000 counts were reached in the peak channel.
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