CSF samples was mixed (5:1) with phosphate buffer solution containing 1.5 M KH2PO4, 580 µM TSP-d4, NaN3, D2O, pH 7.4 and transferred to 3 mm NMR tubes. The samples were analyzed at the Swedish Nuclear Magnetic Resonance (NMR) Centre in Gothenburg using an Oxford 800 Mhz magnet equipped with a Bruker Avance III HD console, 3 mm TCI cryoprobe and a cooled Sample Jet auto sampler (Bruker BioSpin, Fällanden, Switzerland), as described previously [16 (link)]. Generated data from NMR spectrometer were processed in TopSpin3.5pl7 (Bruker BioSpin, Fällanden, Switzerland). Chenomx 9.0 (Chenomx Inc., Edmonton, AB, Canada) and the Human Metabolite Database [24 (link)] were used for identification of the metabolite signals.
3 mm tci cryoprobe
Manufactured by Bruker
Sourced in Switzerland, Germany
The 3 mm TCI cryoprobe is a specialized lab equipment designed for nuclear magnetic resonance (NMR) spectroscopy. It features a 3 mm sample coil and is optimized for cryogenic operation to enhance signal-to-noise ratio. The core function of this probe is to detect and analyze molecular structures and properties using NMR technology.
Automatically generated - may contain errors
Lab products found in correlation
Avance 3 hd console, by Bruker (4 mentions)
Nmr suite 8, by Chenomx (3 mentions)
Topspin 3.5pl7, by Bruker (2 mentions)
Avance 3 hd spectrometer, by Bruker (2 mentions)
Samplejet autosampler, by Bruker (1 mentions)
Topspin 3.5pl6, by Bruker (1 mentions)
Topspin 3.2pl6, by Bruker (1 mentions)
Samplejet, by Bruker (1 mentions)
Advance 3 hd spectrometer, by Bruker (1 mentions)
Matlab, by MathWorks (1 mentions)
7 protocols using 3 mm tci cryoprobe
1
Metabolic Profiling of CSF Samples
2
NMR Spectroscopy of Biofluids
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1H-NMR spectra were measured at 800 MHz using Bruker Avance III HD spectrometer equipped with a 3 mm TCI cryoprobe and a cooled (6°C) SampleJet for sample handling. All 1H-NMR experiments were performed at 298 K. NMR data (1D perfect echo with excitation sculpting for water suppression) was recorded using the Bruker pulse sequence ’zgespe’ with (serum) or without (urine) a CPMG pulse train to suppress macromolecular resonances. The spectral width was 20 ppm, the relaxation delay 3 s, the acquisition time 2.04 s and a total of 128 scans were collected into 64k data points resulting in a measurement time for each sample of approximately 12 minutes. All data sets were zero filled to 128 k and an exponential line-broadening of 0.3 Hz was applied before Fourier transformation. All data processing was performed with TopSpin 3.2pl7 (Bruker BioSpin, Rheinstetten, Germany) and TSP-d4 was used for referencing.
Optimal buckets were performed using the MatLab function opt bucket [17 ] with size bucket = 0.04ppm and slackness = 0.5. The bucketed spectra were probabilistic quotient normalized [18 (link)] using an inhouse MatLab algorithm. Chenomx NMR suite 8.4 (Chenomx Inc., Edmonton, Canada) was used for annotation with the aid of the Human Metabolome Database (HMDB) [19 (link)] and an in-house implementation of the STOCSY routine [20 (link)].
Optimal buckets were performed using the MatLab function opt bucket [17 ] with size bucket = 0.04ppm and slackness = 0.5. The bucketed spectra were probabilistic quotient normalized [18 (link)] using an inhouse MatLab algorithm. Chenomx NMR suite 8.4 (Chenomx Inc., Edmonton, Canada) was used for annotation with the aid of the Human Metabolome Database (HMDB) [19 (link)] and an in-house implementation of the STOCSY routine [20 (link)].
3
NMR Profiling of Metabolite Samples
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NMR data were acquired on an Oxford 800 MHz magnet equipped with an Avance III HD console and 3 mm TCI cryoprobe (Bruker BioSpin). Samples were kept at 6 °C in the SampleJet before measurement at 25 °C. One-dimensional excitation sculpting with perfect echo pulse sequence (‘zgespe’) was used to acquire profiling data. With a sweep width of 20 ppm, 128 scans were acquired in 64 k points, using an acquisition time of 2.04 s and relaxation delay of 3 s. Data were zero-filled to 128 k and Fourier-transformed including 0.3 Hz exponential line-broadening. Spectra were phased and referenced to the TSP-d4 signal. All processing was performed in TopSpin 3.5 pl6 (Bruker BioSpin).
4
Metabolomic Profiling of Infant Serum
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Infant blood samples were collected at postnatal days (PND) 1, 7, 14, and 28, and at postmenstrual age (PMA) 32, 36, and 40 weeks. The blood was allowed to clot at 4°C for a minimum of 45 min and a maximum of 2 h before centrifugation at room temperature at 1500 g for 10 min. The serum was then transferred into cryovials and stored at −20°C for up to 1 week before long-term storage at −80°C until analysis. All samples had been subjected to at least one, but less than five, freeze-thaw cycle before NMR analysis.
Serum samples (50 μl) were prepared and then analyzed on an Oxford 800 MHz magnet equipped with an Avance III HD console and 3 mm TCI cryoprobe (Bruker BioSpin). Details of sample processing and the 1H NMR analysis have been published (Nilsson et al., 2020 (link)). Tentative annotations of peaks were made using ChenomX 8.3 (ChenomX Inc.) and the spectral data in the Human Metabolome Data Bank (Wishart et al., 2018 (link)). In total, 260 NMR features were detected in the serum samples. From these, 31 metabolites could be chemically and structurally annotated. In instances where multiple features represented a single metabolite, a strong well-separated peak was selected, or two or more peaks were summarized. All metabolite levels are reported as normalized NMR signals or as standardized values.
Serum samples (50 μl) were prepared and then analyzed on an Oxford 800 MHz magnet equipped with an Avance III HD console and 3 mm TCI cryoprobe (Bruker BioSpin). Details of sample processing and the 1H NMR analysis have been published (Nilsson et al., 2020 (link)). Tentative annotations of peaks were made using ChenomX 8.3 (ChenomX Inc.) and the spectral data in the Human Metabolome Data Bank (Wishart et al., 2018 (link)). In total, 260 NMR features were detected in the serum samples. From these, 31 metabolites could be chemically and structurally annotated. In instances where multiple features represented a single metabolite, a strong well-separated peak was selected, or two or more peaks were summarized. All metabolite levels are reported as normalized NMR signals or as standardized values.
5
NMR Analysis of Blood Plasma Metabolites
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The plasma samples were prepared by mixing the plasma 1:1 with phosphate buffer (75 mM Na2HPO4, 4% NaN3, 2.32 mM TSP-d4, 10% D2O, pH 7.4) to a total volume of 220 µl. The mixture was transferred to 3 mm NMR tubes using a SamplePro L liquid handling robot (Bruker BioSpin, Rheinstetten, Germany).
The samples were analyzed at Swedish Nuclear Magnetic Resonance (NMR) Centre in Gothenburg using an Oxford 800 MHz magnet (Bruker BioSpin, Germany) equipped with a Bruker Avance III HD console, 3 mm TCI cryoprobe and a cooled Sample Jet auto sampler. 1D CPMG-edited experiment (pulse sequence 'zgespe') as well as 2D J-resolved spectra (pulse sequence 'jresgpprqf') were acquired for each sample. Experimental details available upon request. Data acquisition and processing of raw data, including Fourier transformation, phasing, baseline correction and referencing to TSPd4 of the 1D CPMG data was performed in TopSpin 3.5pl7 (Bruker BioSpin). The data obtained from NMR were annotated with the use of Chenomx 8.4 (Chenomx Inc, Edmonton, Canada), the 2D J-resolved data and publicly available spectral databases such as HMDB22 (link). A criterion that a metabolite was present at detectable levels in at least 40% of the subjects in one group to be included in the statistical analysis was set.
The samples were analyzed at Swedish Nuclear Magnetic Resonance (NMR) Centre in Gothenburg using an Oxford 800 MHz magnet (Bruker BioSpin, Germany) equipped with a Bruker Avance III HD console, 3 mm TCI cryoprobe and a cooled Sample Jet auto sampler. 1D CPMG-edited experiment (pulse sequence 'zgespe') as well as 2D J-resolved spectra (pulse sequence 'jresgpprqf') were acquired for each sample. Experimental details available upon request. Data acquisition and processing of raw data, including Fourier transformation, phasing, baseline correction and referencing to TSPd4 of the 1D CPMG data was performed in TopSpin 3.5pl7 (Bruker BioSpin). The data obtained from NMR were annotated with the use of Chenomx 8.4 (Chenomx Inc, Edmonton, Canada), the 2D J-resolved data and publicly available spectral databases such as HMDB22 (link). A criterion that a metabolite was present at detectable levels in at least 40% of the subjects in one group to be included in the statistical analysis was set.
6
High-Resolution 1H-NMR Metabolite Profiling
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1H-NMR spectra were measured at 800 MHz using a Bruker Avance III HD spectrometer with a 3-mm TCI cryoprobe and a cooled (6°C) SampleJet for sample handling. All 1H-NMR experiments were performed at 25°C. NMR data (1D perfect echo with excitation sculpting for water suppression) were recorded using the Bruker pulse sequence “zgespe.” The spectral width was 20 ppm, the relaxation delay 3 s, the acquisition time 2.04 s, and a total of 128 scans were collected into 64k data points resulting in a measurement time for each sample of 12 min 4 s. All data sets were zero filled to 128k and an exponential line-broadening of 0.3 Hz was applied before Fourier transformation. All data processing was performed with TopSpin 3.2pl6 (Bruker BioSpin) and TSP-d4 was used for referencing.
Chenomx NMR suite 8.31 (Chenomx Inc.) was used for annotation with the aid of the Human Metabolome Database (8 (link)) and an in-house implementation of the statistical total correlation spectroscopy (STOCSY) routine (9 (link)). Metabolic pathway information was retrieved from the Kyoto Encyclopedia of Genes and Genomes pathway database (10 (link)).
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1H-NMR spectra were measured at 800 MHz using a Bruker Avance III HD spectrometer with a 3-mm TCI cryoprobe and a cooled (6°C) SampleJet for sample handling. All 1H-NMR experiments were performed at 25°C. NMR data (1D perfect echo with excitation sculpting for water suppression) were recorded using the Bruker pulse sequence “zgespe.” The spectral width was 20 ppm, the relaxation delay 3 s, the acquisition time 2.04 s, and a total of 128 scans were collected into 64k data points resulting in a measurement time for each sample of 12 min 4 s. All data sets were zero filled to 128k and an exponential line-broadening of 0.3 Hz was applied before Fourier transformation. All data processing was performed with TopSpin 3.2pl6 (Bruker BioSpin) and TSP-d4 was used for referencing.
Chenomx NMR suite 8.31 (Chenomx Inc.) was used for annotation with the aid of the Human Metabolome Database (8 (link)) and an in-house implementation of the statistical total correlation spectroscopy (STOCSY) routine (9 (link)). Metabolic pathway information was retrieved from the Kyoto Encyclopedia of Genes and Genomes pathway database (10 (link)).
7
Comprehensive NMR Metabolite Profiling
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1H-NMR analysis has been described in detail previously [31 (link)]. In short, spectra were recorded at 800 MHz with a Bruker Advance III HD spectrometer with a 3-mm TCI cryoprobe. NMR data were recoded using the Bruker pulse sequence “zgespe”. A total of 128 scans were collected into 64 k data points. Data processing was performed with TopSpin 3.2p16 (Bruker BioSpin) and MatLab (MathWorks Inc., Natick, MA, USA), using TSP-d4 for referencing. In total 237 peaks were manually aligned and integrated peak-by-peak, and these variables represent ∼70 metabolites. A variable could also reflect more than one metabolite. Only variables of interest were identified.
For annotation Chenomx NMR suite 8.31 (Chenomx Inc., Edmonton, AB, Canada), the Human Metabolome Database [37 (link)] and an in-house implementation of the statistical total correlation spectroscopy (STOCSY) routine [38 (link)] were used.
For annotation Chenomx NMR suite 8.31 (Chenomx Inc., Edmonton, AB, Canada), the Human Metabolome Database [37 (link)] and an in-house implementation of the statistical total correlation spectroscopy (STOCSY) routine [38 (link)] were used.
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