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21 protocols using icon nmr software

1

High-Resolution NMR Experiments Using Cryogenic Probe

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All NMR experiments are conducted at 298 K using a Bruker AVANCE III HD 700 MHz spectrometer equipped with a 5 mm quadruple resonance QCI-P cryoprobe (1H, 13C, 15N, and 31P) with z-axis gradients. An automatic tune and match system (ATM), and a SampleJet automated sample changer system with Bruker ICON-NMR software were used to automate the NMR data collection (seeFigure 5).
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2

NMR Spectroscopy Analysis of Metabolites

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All NMR spectra acquisition were performed at 300 K on a Bruker Avance III 600 MHz Ascend NMR Spectrometer (Bruker Italia, Milano, Italy), operating at 600.13 MHz, equipped with a TCI cryoprobe (inverse Triple Resonance Cryoprobe Prodigy), incorporating a z-axis gradient coil and automatic tuning-matching (ATM). Experiments were run in automation mode after loading samples on an integrated Bruker Automatic Sample Changer, interfaced with IconNMR software (Bruker). For each sample, a 1H NMR spectrum was acquired using water signal suppression (Bruker pulseprogram zgcppr), the spectral window of 20.0276 ppm (12,019.230 Hz), 90° pulse of 7.620 µs, and 64 scans. The standard FID processing procedures, such as the Fourier transform, phase and baseline correction, and 0.3 Hz line broadening, were carried out using TopSpin 3.5 (Bruker, Biospin, Italy). All the NMR spectra were calibrated to the internal standard TSP (δ = 0.00 ppm). The characterization of the metabolites was also supported by two-dimensional homo- and heteronuclear NMR spectra (2D 1H J-resolved, 1H COSY, 1H–13C HSQC, and HMBC) and comparison with the literature data2 (link),10 (link),11 (link),16 (link),35 .
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3

NMR Spectroscopy of Serum Metabolites

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Samples stored at −80 °C were thawed and 110 µL of serum transferred to a fresh 1.5 mL Eppendorf tube, and 450 µL of 1 x DPBS (Gibco Life Technologies), 50 µL of D2O (Cambridge Isotope Laboratories, Inc, MA, USA), and 10 µL of sodium 2,2-dimethyl-2-silapentane-5-sulfonate (DSS) (Cambridge Isotope Laboratories, Inc, MA, USA) (3.7 mg in 700 µL MilliQ water) added. Samples were centrifuged at 14,000 rpm for 10 min at 4 °C, and 550 µL transferred to an NMR tube. One-dimensional NMR spectra (128 scans) were recorded at 298 K using a standard CPMG sequence on a Bruker Avance III 600 MHz spectrometer equipped with a cryoprobe using automated data collection via IconNMR software (Bruker). Two-dimensional spectra were recorded on selected samples, including COSY, TOCSY, and 1H-13C-HSQC. Samples were processed randomly. Metabolite assignments were based on the Human Metabolome Database57 (link) and chemical shifts derived from standard samples. For the statistical analysis, spectra were normalized to total intensity.
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High-Resolution NMR Analysis of Compounds

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A Bruker Ascend 400 MHz high-resolution NMR with a sampleXpress autosampler was applied in this study and all the experiments were carried out using ICON-NMR software (Bruker Biospin) and controlled by ICON-NMR. All the experiments were carried out after 3D shimming and 1D shimming. A 1D NOESY experiment with water suppression (noesygppr1d) was carried out with 32k increments, 64 transients which took around 7 min. All the spectra were carefully phased and calibrated to TSP in Bruker Topspin 4.06 (Bruker Biospin).
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5

NMR Data Collection and Analysis Protocols

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1D and 2D NMR data collection and analysis were performed as described previously.13 (link), 14 (link) Briefly, all NMR spectra were collected on a Bruker Avance DRX 500 MHz spectrometer equipped with a 5-mm triple-resonance (1H, 13C, 15N), Z-axis gradient cryoprobe. Automated data collection utilized a Bruker ATM unit for automatic tuning and matching, a BACS-120 sample changer and Bruker Icon NMR software. The 1D 1H NMR spectra were collected using excitation sculpting for water suppression.15 (link) Six replicates were acquired at 298.15 K with 128 scans, 16K data points, 16 dummy scans, a relaxation delay of 1.5 s, a spectral width of 5000 Hz, and a total acquisition time of approximately 7 minutes. 2D 1H-13C HSQC NMR spectra were collected at 298.15 K with 128 scans and a relaxation delay of 1.5 s. The spectra were collected with 2K data points and a spectrum width of 5,000 Hz in the direct dimension, and 64 data points and a spectrum width of 17,605.6 Hz in the indirect dimension, and a total acquisition time of approximately 4 hours. The 2D 1H-13C HSQC NMR spectra were processed in NMRPipe and analyzed with NMRViewJ version 9.16 (link), 17 (link)
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High-Resolution NMR Characterization

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All NMR experiments are conducted at 298 K using a Bruker AVANCE III HD 700 MHz spectrometer equipped with a 5 mm quadruple resonance QCI-P cryoprobe (1H, 13C, 15N, and 31P) with z-axis gradients. An automatic tune and match system (ATM), and a SampleJet automated sample changer system with Bruker ICON-NMR software were used to automate the NMR data collection (seeFig. 5).
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7

NMR-based Metabolite Profiling of S. aureus

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The data collection and analysis of NMR was conducted as previously described [36 (link)]. A Bruker AVANCE IIIHD 700 MHz spectrometer equipped with a 5 mm quadruple resonance QCI-P cryoprobe (1H, 13C, 15N, and 31P), an automatic tune and match system (ATM), and a SampleJet automated sample changer system with Bruker ICON-NMR software were utilized. The 2D 1H−15N HSQC spectra collected for S. aureus cell lysates and culture media were assigned using a database of 2D 1H−15N HSQC reference spectra for known metabolites [36 (link)]. A chemical shift tolerance of 0.08 ppm for 1H and 0.25 ppm for 15N were used to match metabolites to our reference database.
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8

Automated Cryogenic NMR Acquisition

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Bruker AVANCE DRX 500 MHz spectrometer equipped with 5 mm triple-resonance cryogenic probe (1H, 13C and 15 N) with a Z-axis gradient was utilized to acquire the NMR data. The experiment was automated using BACS-120 sample changer, ATM (automatic tuning and matching) and Bruker IconNMR™ software. The one-dimensional (1D) proton nuclear magnetic resonance (1H NMR) data were collected at 300 K with 32 K data points, 128 scans, 16 dummy scans and a spectral width of 5,483 Hz using an excitation sculpting pulse sequence (Nguyen et al., 2007 (link)). The 2D 1H-13C hetero-nuclear single quantum coherence (HSQC) NMR spectra were collected with 2 K data points and a spectrum width of 4,735 Hz in the direct dimension and 64 data points and a spectrum width of 17,607 Hz in the indirect dimension at 300 K with 64 scans, 16 dummy scans and a 1.5 s relaxation delay.
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9

Serum Metabolic Profiling by NMR Spectroscopy

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Venous fasting blood samples were collected in serum-tubes with no additives. The serum samples were stored at − 80 °C, until the time of metabolic profiling. The serum samples were slowly thawed at 4 °C. Aliquots of 150 μL were mixed with equal amounts of buffer solution and transferred to high-quality 3 mm MR tubes as described elsewhere [30 (link)].
The MR spectra were acquired using a Bruker Avance III 600 MHz/54 mm US-Plus (Bruker Biospin, Rheinstetten, Germany) operating at 600 MHz for proton (1H), equipped with a QCI cryoprobe. All spectra were recorded in an automatic fashion using a Bruker SampleJet and the ICON-NMR software (Bruker Biospin). Proton spectra were obtained at a constant temperature of 310 K (37 °C) using [1 (link)] a standard nuclear overhauser effect spectroscopy (NOESY) pulse sequence (Bruker: noesygppr1d) and [2 (link)] a Carr-Purcell-Meiboom-Gill (CPMG) pulse sequence with presaturation during the relaxation delay (Bruker: cpmgpr1d) to achieve water suppression, and to facilitate the detection of low-molecular-weight species by avoiding the large overlapped signals derived from large molecules, such as proteins and lipids. Measurement and processing were done in full automation using Bruker standard automation programs controlled by ICON-NMR (along with TopSpin). Chemical shift was calibrated to the middle of the alanine peaks at 1.50 ppm.
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10

Metabolic Profiling of PDAC and CAF Cells

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S2-013 PDAC cells and CAF 09-11 human PSCs were cultured in complete DMEM supplemented with 10% FBS and 25 mM U-13C6 glucose (Cambridge Isotope Laboratories). U-13C6 glucose-labelled CAF 09-11 cells were cultured with and without unlabelled tumour cell-conditioned medium. 13C6-labelled polar metabolites secreted into the medium were extracted from the medium using 80% methanol extraction. All NMR experiments were conducted at 298 K using a Bruker AVANCE III-HD 700-MHz spectrometer equipped with a 5-mm quadruple resonance QCI-P cryoprobe (1H, 13C, 15N and 31P) with z-axis gradients. A SampleJet automated sample changer system with Bruker ICON-NMR software was used to automate the NMR data collection. Two-dimensional (2D) 1H-13C heteronuclear single quantum coherence (HSQC) spectra were collected and analysed as described previously55 (link).
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