Raw FID data were Fourier transformed after applying an exponential window function with 2 Hz line broadening and phase corrected using the TOPSPIN program (Bruker Biospin). Peak integration and fitting of signal intensities were performed with MATLAB (The MathWorks, Natick, MA). Before integration, a linear baseline correction was applied for each peak, defined by baseline points on either side of the peak.
Topspin program
Manufactured by Bruker
Sourced in Germany
TopSpin is a software program developed by Bruker for the acquisition, processing, and analysis of Nuclear Magnetic Resonance (NMR) data. It provides a comprehensive suite of tools for managing and manipulating NMR experiments, and is compatible with a range of Bruker NMR spectrometers.
Automatically generated - may contain errors
Lab products found in correlation
Matlab, by MathWorks (1 mentions)
Avance 3, by Bruker (1 mentions)
Avance 3 spectrometer, by Bruker (1 mentions)
Mnova 11, by Mestrelab Research (1 mentions)
Topspin, by Bruker (1 mentions)
800 mhz nmr spectrometer, by Bruker (1 mentions)
Avance 600 spectrometer, by Bruker (1 mentions)
Drx 600 mhz spectrometer, by Bruker (1 mentions)
12 protocols using topspin program
1
NMR Data Processing and Analysis
2
Sevelamer Chelation of Phosphate Measured by NMR
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Spectra were obtained with a 1D31P nuclear magnetic resonance (NMR) spectrometer (Avance III; Bruker, Billerica, MA, USA) operating at 14.1 Tesla (600 MHz for 1H and 242 MHz for 31P) equipped with a reverse pentanuclear observation probe of 5 mm field gradient z (QXI) axis. We evaluated the phosphate concentration in samples containing phosphate (4 mM), with or without 3% sevelamer, to validate in vitro the chelating effect of sevelamer to phosphate. The samples were solubilized in 600 μL of a solution of D2O:H2O (1:9 v/v) at 30°C. The 31P decoupled spectra were obtained with a 30° angle, with a magnetization window of 400 ppm and an acquisition time of 0.17 s. The relaxation time of 0.200 and 1024 transients was processed with the help of the TopSpin program (Bruker, Karlsruhe, Germany) applying exponential multiplication on the acquired free induction decays (FIDs). All analyses were performed in triplicate.
3
NMR Spectroscopic Analysis of Compounds
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The NMR spectra were recorded on a Bruker Avance III spectrometer at a 1H frequency of 400 MHz, 700 MHz, or 900 MHz equipped with a TCI cryoprobe. Lyophilized samples (varying from 1 to 7 mg) were dissolved in 280 µL DMSO-d6 (Cambridge Isotope) and all spectra were recorded at 25 °C (298 K). 1H and 13C resonances were assigned through the analysis of 1D–1H, 1D–13C, 2D 1H–1H rotating frame Overhauser effect spectroscopy (ROESY), 2D 1H–13C heteronuclear single quantum correlation (HSQC), and 2D 1H–13C heteronuclear multiple bond correlation (HMBC) (optimized for long-range heteronuclear couplings of 6 Hz). 1H and 13C chemical shifts were calibrated with reference to the DMSO solvent signal (2.50 and 39.5 p.p.m. for 1H and 13C, respectively). NMR experiments were processed with Bruker Topspin program (version 3.57) and analyzed with mnova software.
4
TMAO Quantification by NMR Spectroscopy
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TMAO concentrations were quantified in serum samples using Nuclear Magnetic Resonance (NMR) as previously described [62 (link)]. The NMR spectra were analyzed in a Bruker Avance IVDr 600 MHz spectrometer (Bruker Biospin, Rheinstetten, Germany) and processed using the TopSpin program (Bruker Biospin, Germany). Three NMR spectra were analyzed separately for each sample. The intensity of the TMAO peaks were measured for all spectra and the concentrations in each sample were calculated with fitted calibration curves.
5
Monitoring Peptide Dynamics by NMR
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NMR experiments were recorded on a Bruker Avance III spectrometer operating at a 1H frequency of 500 MHz and equipped with a TCI cryoprobe (temperature 20 °C) as previously described51 (link). Experiments were processed and analyzed with TopSpin program (Bruker). Measurements were carried out in 10 mM potassium phosphate buffer in D2O at pH 7.4. Peptide concentrations were 50 µM in the absence and in the presence of anle145c. The peptide film was dissolved in the phosphate buffer and immediately transferred in a Shigemi tube of 5 mm diameter, comprising a sample volume of 300 µL. The evolution in time of the peptide signal intensity was followed by recording one-dimensional 1H spectra until the peptide signal intensity decayed completely. Peptide 1H resonances (both in the aliphatic and in the amide/aromatic region) were then integrated and these values are plotted as a function of time, leading to a sigmoidal curve that can be fitted using R program by a Boltzmann sigmoidal equation.
6
STD NMR Characterization of SARM1 Proteins
7
NMR Data Processing Workflow
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All data was processed with zero‐filling, Gaussian line broadening, Fourier transformation, and phase and baseline correction using the TOPSPIN program (Bruker Biospin). Pure shift data was processed using the reconstruction macro pshift4f.
All experimental data, pulse program codes, macros and experimental parameters are freely available athttps://doi.org/10.48420/19583323 .
All experimental data, pulse program codes, macros and experimental parameters are freely available at
8
Structural Analysis of K1 Lyase Products
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Seven mg of the K1 lyase-digested products was dissolved in 300 μl D2O containing 33 μM DSS as an internal chemical shift standard, with the pH value of the sample being 4.65. The 2D DQF-COSY spectrum of the products was collected at 298 K on a Bruker 800 MHz NMR spectrometer equipped with a cryogenic probe. All experiments were carried out with the standard pulse sequences provided by Bruker software and the responsive data were processed with Bruker TopSpin program. The data acquisition parameters are as follow: 2048 (F2) by 512 (F1, increments) data matrix, 56 scans for each increment, 9 ppm spectral width in both dimensions. Data processing parameters are as follow: 4096 (F2) by 1024 (F1) data matrix. A 60-degree shifted sinebell window function was applied in both dimensions.
9
NMR Characterization of DNA Triple Helix
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NMR spectra of the triple helix were measured with an AVANCE 600 spectrometer (Bruker) at a probe temperature of 283 K. The 15N-labeled cyanuryl nucleoside DNA sample was dissolved in 300 μL of 20 mM potassium phosphate buffer (pH 5.9) with 5% D2O. The sample concentration was 0.2 mM for each strand. NMR data were processed with the TopSpin program (Bruker) and analyzed with the Sparky program.36 A NOESY spectrum measured with a mixing time of 150 ms was used to assign signals and measure NOE volumes.
10
Analyzing Frog Skin and Benzotop Extracts using 1H-NMR and R Studio
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The 1H-NMR spectra of extracts from frog’ skins and the Benzotop© product had both phase distortions and baselines adjusted in the TopSpin program (version 4.0.7, Bruker Biospin) where they were automatically converted to CSV files (Comma-separated values). Subsequently, the CSV files were analysed using the R Studio program (R Studio, version 3.3 [29 ]). We evaluated potential differences or similarities between the samples tested, selecting specific regions in the 1H-NMR spectra to be excluded from the analyses, to perform a comparison based on the chemical shifts of interest, and eliminate potential noise from the sample (Table 1 ). In this analysis, only the regions corresponding to the chemical shifts of benzocaine were maintained. In total, five regions were chosen for exclusion.
To highlight potential similarities or divergences between the different samples analysed, we used a Hierarchical Cluster Analysis (HCA) to assess whether there is the formation of groups between samples from Euclidean distances, the results of which are illustrated in a dendrogram. The analyzes were performed using the software R Studio.
To highlight potential similarities or divergences between the different samples analysed, we used a Hierarchical Cluster Analysis (HCA) to assess whether there is the formation of groups between samples from Euclidean distances, the results of which are illustrated in a dendrogram. The analyzes were performed using the software R Studio.
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