The concentrations of the remaining fatty acids and accumulating carboxylic acids in the medium (e.g., 9-hydroxynonanoic acid (6), 1,9-nonanedioic acid (8)) were determined as described previously [13 (link),19 (link),20 (link)]). The reaction medium was mixed with an equal volume of ethyl acetate containing 0.5 g/L methyl palmitate as an internal standard. The organic phase was harvested after vigorous vortexing and subjected to derivatization with N-methyl-N-(trimethylsilyl) trifluoroacetamide. The trimethylsilyl derivatives were analyzed using a Thermo Ultra Trace GC system connected to an ion trap mass detector (Thermo ITQ1100 GC-ion Trap MS, Thermo Scientific, Indianapolis, IN, USA). The derivatives were separated on a nonpolar capillary column (30 m length, 0.25 mm film thickness, HP-5MS, Agilent Technologies, Palo Alto, CA, USA). A linear temperature gradient was programmed as 160 °C, 25 °C/min to 235 °C, and 3 °C/min to 253 °C. The injection port temperature was 230 °C. Mass spectra were obtained within the range of 100–600 m/z. Selected ion monitoring was used for detection and the fragmentation analysis of the reaction products.
Trace gc ultra system
Manufactured by Thermo Fisher Scientific
Sourced in United States
The Trace GC Ultra system is a gas chromatography instrument designed for analytical laboratories. It provides precise and reliable separation, detection, and quantification of complex chemical mixtures. The system features advanced technology for optimized performance and efficient sample analysis.
Automatically generated - may contain errors
Lab products found in correlation
Hp 5ms, by Agilent Technologies (2 mentions)
Thermo itq1100 gc ion trap ms, by Thermo Fisher Scientific (2 mentions)
Dsq 2 ms detector, by Thermo Fisher Scientific (1 mentions)
Carbopac pa20 column, by Thermo Fisher Scientific (1 mentions)
Hpaec pad ics 5000 system, by Thermo Fisher Scientific (1 mentions)
Tr 5ms capillary column, by Thermo Fisher Scientific (1 mentions)
Tr fame column, by Thermo Fisher Scientific (1 mentions)
Trace tr 1ms fused silica capillary column, by Thermo Fisher Scientific (1 mentions)
Sephadex g 50, by GE Healthcare (1 mentions)
Bio gel p 2, by Bio-Rad (1 mentions)
15 protocols using trace gc ultra system
1
Quantitative Analysis of Fatty Acid Metabolites
2
Quantitative Analysis of Carboxylic Acids
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The concentrations of remaining carboxylic acids in the medium such as ricinoleic acid, n-heptanoic acid, and ω-hydroxyundec-9-enoic acid were determined as described previously [5 (link)]. The reaction medium was mixed with an equal volume of ethyl acetate containing palmitic acid as an internal standard. The organic phase was harvested after vigorous vortexing and was then subjected to derivatization by adding N-methyl-N-(trimethylsilyl) trifluoroacetamide (TMS). The TMS derivatives were analyzed using a Thermo Ultra Trace GC system connected to an ion trap mass detector (Thermo ITQ1100GC-ion Trap MS, Thermo Scientific, and Indianapolis, IN, USA). The derivatives were separated on a non-polar capillary column (30 m length, 0.25 μm film thickness, HP-5MS, Agilent Technologies, Palo Alto, CA, USA). A linear temperature gradient was programmed as 90°C, 5°C/min to 280°C. The injection port temperature was 230°C. Mass spectra were obtained by electron impact ionization at -70 eV. Scan spectra were obtained within the range of 100–600m/z. Selected ion monitoring (SIM) was used for the detection and fragmentation analysis of the reaction products.
3
GC-MS Analysis of Cinnamon Oil Composition
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GC–MS was used to analyze chemical compositions of cinnamon oil in nutrient broth (NB) of C1 at 0 and 180 min. GC–MS analysis was performed using a Thermo Trace GC Ultra system equipped with a Thermo TR-5MS capillary column (dimensions: 30 m × 250 mm × 0.25 mm; Thermo Scientific, Runcorn, UK) operating with helium as a carrier gas, coupled to a Thermo ITQ 1100 mass spectrometer (MS) through a heated transfer line (230 °C). The GC injector (230 °C) was operated in a pulsed split mode (50:1); 1 μL aliquots were injected using an autosampler. The initial oven temperature of GC was 100 °C, and programmed to 130 °C at a rate of 20 °C/min, then programmed to 170 °C at a rate of 5 °C/min, after then, programmed to 230 °C at a rate of 25 °C/min and then kept constant at 230 °C for 5 min. The MS was operated with the ion source at 230 °C and a damping flow of 1 mL/min. MS was taken at 70 eV and a mass range of 35–425 amu. The solvent delay time was 3 min. A library search was carried out using NIST98.L database. Relative percentage amount was calculated from TIC by the computer (Ooi et al. 2006 (link)).
4
Quantitative Analysis of Cell Wall Teichoic Acids
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After 24 h incubation period at 30°C in TSBYe medium with shaking rotator (200 tr/min), planktonic cultures were centrifuged at room temperature (10.000 x g, 10 min). The cell pellets were washed three times with 5 ml of sterile distilled water and lyophilized. WTA were depolymerized in situ by treatment of lyophilized cells with 48% HF, essentially as described in [14 (link)]. Two milligrams of lyophilized cells were treated with 48% hydrofluoric acid (Acros Organics, NJ, USA) for 48 h at 4°C. HF was evaporated at room temperature under a stream of nitrogen, 90 μg of internal standard (myo-Inositol) and 2 ml of 4 M trifluoracetic acid were added. The insoluble cell debris were removed by centrifugation, and the supernatant, containing WTA, was hydrolyzed at 110°C for 3 h. Monosaccharides were converted to reduced and acetylated derivatives (alditol acetates) by conventional methods and analyzed by GC-MS on a Trace GC ULTRA system (Thermo Scientific) with a DSQ II MS detector, equipped with a capillary column NMTR-5MS (30 m x 0.25 mm) using a temperature gradient of 170°C (3 min) to 250°C at 5°C/min.
5
Monosaccharide Analysis by GC-MS and HPAEC-PAD
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Monosaccharides were identified as reduced and acetylated derivatives (alditol acetates) by gas chromatography coupled to mass spectrometry (GC-MS) as described previously (34 (link)). The absolute configuration of the monosaccharides was determined by GC-MS analysis of acetylated (R)-2-butylglycoside derivatives as described previously (34 (link)). The products were analyzed by GC-MS and identified with standards prepared from monosaccharides with known configurations with (R)- and (S)-2-butanol. GC-MS was performed with a Trace GC ULTRA system (Thermo Scientific) equipped with an NMTR-5MS capillary column (30 m by 0.25 mm) by using a temperature gradient of 170°C (3 min) to 250°C at 5°C/min with a DSQ II MS detector.
The amount of CWPS extracted by HF from cell walls was determined by quantification of monosaccharides after acid hydrolysis with 4 M trifluoroacetic acid (TFA) for 3 h at 110°C. Monosaccharides were separated on a CarboPac PA20 column (Dionex) by HPAEC-PAD (ICS 5000 system; Thermo Fisher Scientific). Quantification was performed by comparison with standard amounts of each monosaccharide.
The amount of CWPS extracted by HF from cell walls was determined by quantification of monosaccharides after acid hydrolysis with 4 M trifluoroacetic acid (TFA) for 3 h at 110°C. Monosaccharides were separated on a CarboPac PA20 column (Dionex) by HPAEC-PAD (ICS 5000 system; Thermo Fisher Scientific). Quantification was performed by comparison with standard amounts of each monosaccharide.
6
GC-MS Analysis of Compound Mixtures
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The GC-MS analysis was conducted on a Trace GC Ultra system equipped with an AS 3000 auto-sampler, a split/splitless injector, and TSQ Quantum XLS MS detector with triple quadrupole (Thermo Fisher Scientific, Waltham, MA, USA). The TR-5 MS capillary column (30 m × 0.25 mm, 0.25 μm film thickness) was purchased from Thermo Fisher Scientific (Waltham, MA, USA).
The injection temperature and ion source temperature were 250 °C. The oven temperature program was maintained at 50 °C for 1 min, increased to 200 °C (rate: 8 °C/min), maintained at 200 °C for 5 min, increased to 280 °C (rate: 10 °C/min), and maintained for 5 min. Helium was used as the carrier gas (flow rate: 1 mL/min). Sample injection volume and split ratio were 1 μL and 50:1, respectively. The ionizing energy was 70 eV. The chromatograms were obtained by collecting the total ion currents in the scan range of m/z 50–550. Data were acquired using the Xcalibur 2.2 software.
The injection temperature and ion source temperature were 250 °C. The oven temperature program was maintained at 50 °C for 1 min, increased to 200 °C (rate: 8 °C/min), maintained at 200 °C for 5 min, increased to 280 °C (rate: 10 °C/min), and maintained for 5 min. Helium was used as the carrier gas (flow rate: 1 mL/min). Sample injection volume and split ratio were 1 μL and 50:1, respectively. The ionizing energy was 70 eV. The chromatograms were obtained by collecting the total ion currents in the scan range of m/z 50–550. Data were acquired using the Xcalibur 2.2 software.
7
GC-MS Analysis of Benzene
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For GC–MS
analysis,
a Thermo Scientific Trace GC Ultra System coupled with a triple quadrupole
spectrometer was used, equipped with Xcalibur software. The SPME fiber
was desorbed in split mode (1:25) for 1 min at 290 °C. Benzene
was detected using a DB-5MS:5%-phenyl-methylpolysiloxane capillary
column (30 m, 0.25 mm, 0.25 μm) with helium as a carrier gas
at a constant flow rate of 1 mL/min. The temperature program was set
at 40 °C and held for 1 min, increased to 50 °C at a rate
of 5 °C/min, then increased to 100 °C at a rate of 15 °C/min
and held for 0.5 min, and then the temperature increased at a rate
of 20 °C/min until reaching 250 °C, which was held for 1
min. The total run time was 14.83 min. The mass spectrometer was operated
in full scan mode (m/z range from
35 to 600). The ion source was set at 250 °C in the electron
impact ionization mode (70 eV). Benzene compound was identified based
on its retention time and its mass spectrum, while its quantification
was performed using the m/z 78.
analysis,
a Thermo Scientific Trace GC Ultra System coupled with a triple quadrupole
spectrometer was used, equipped with Xcalibur software. The SPME fiber
was desorbed in split mode (1:25) for 1 min at 290 °C. Benzene
was detected using a DB-5MS:5%-phenyl-methylpolysiloxane capillary
column (30 m, 0.25 mm, 0.25 μm) with helium as a carrier gas
at a constant flow rate of 1 mL/min. The temperature program was set
at 40 °C and held for 1 min, increased to 50 °C at a rate
of 5 °C/min, then increased to 100 °C at a rate of 15 °C/min
and held for 0.5 min, and then the temperature increased at a rate
of 20 °C/min until reaching 250 °C, which was held for 1
min. The total run time was 14.83 min. The mass spectrometer was operated
in full scan mode (m/z range from
35 to 600). The ion source was set at 250 °C in the electron
impact ionization mode (70 eV). Benzene compound was identified based
on its retention time and its mass spectrum, while its quantification
was performed using the m/z 78.
8
Steam Distilled Essential Oil Analysis
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The essential oil was obtained from the plant by steam distillation method in the Clevenger apparatus. The samples (35 g) were transferred to the Clevenger flask and 400 mL of water was added. The system was operated continuously for 3 h and the essential oil sample was separated (40 mg), dried over sodium sulfate and stored in the refrigerator. GC–MS analyses were performed with an SQ Quantum XLS mass spectrometer and a Thermo Scientific-Trace GC Ultra system. TG-5MS (30 m × 0.25 mm inner diameter × 0.25 μm film thickness) was used as the capillary column, and 1.0 mL/min high purity Helium (He) was used as the carrier gas. The injection temperature was set at 250 °C. Capillary column was fixed from 50 to 120 °C (rate: 3 °C/min), 120 to 220 °C (rate:3 °C/min, held for 0.67 min), 220 to 250 (rate: 5 °C/ min, held for 5.0 min). Split/non-split (25:1 split) mode was used for 1.0 μL samples (diluted 1/10 in acetone, v/v). Mass spectra of molecules were determined using relative peak areas through WILEY and NIST libraries18 . GC–MS analyses were performed at Hitit University HUBTUAM.
9
Fatty Acid Profiling of Avocado Oil
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Two grams of avocado oil were saponified with 5% methanolic KOH to obtain potassium salt of fatty acids. After acidification with 6N HCl, fatty acids were extracted several times with diethyl ether and later methylated using methanol/H2SO4 under reflux. After cooling, fatty acids methyl esters (FAMEs) were recovered with diethyl ether and subsequently analyzed using Trace GC Ultra system (Thermo Fisher Scientific Co., USA) equipped with Thermo TR-FAME column (70% Cyanopropyl Polysilphenylene Siloxane, 30 m × 0.25 mm i.d) with 0.25 µm film thickness using N2 at 30 mL/min and a flame ionization detector operating at a flow rate of 350 mL/min (H2). The injector temperature was set at 200 °C with an initial temperature of 140 °C, which was increased to 200 °C by five °C/min, then kept isothermal for 3 min. FAMEs were identified by comparing their relative retention times with external standards analyzed under the same conditions.
10
Glycan Identification by Chromatography and GC-MS
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Gel filtration chromatography was performed on a Sephacryl S-300 column (Pharmacia, 1 × 80 cm) and a Bio-Gel P2 column (1.6 × 80 cm) eluted with 0.1% acetic acid. Aliquots of each fraction were assayed for neutral sugars81 (link). Monosaccharides were identified by GC-MS with a Trace GC ULTRA system (Thermo Scientific) equipped with an NMTR-5MS capillary column (30 m × 0.25 mm) with a temperature gradient of 170 °C (3 min) to 250 °C at 5 °C min−1 and with a DSQ II MS detector. Prior to analysis, carbohydrate samples were hydrolyzed with 4 M trifluoroacetic acid (110 °C, 3 h) and converted to alditol acetates by conventional methods. For the identification of QuiNAc and FucNAc, authentic standards of P. aeruginosa PA14 and PAO1 O-antigens were used.
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