An Agilent 7890B gas chromatography system combined with a 5977 AMSD system (Agilent Technologies Inc., Santa Clara, CA, USA) was used for GC-MS. The samples were separated using an ADB-5MS fused-silica capillary column (Agilent J&W Scientific, Folsom, CA, USA). Helium (>99.999%) was passed through the column at a rate of 1 mL/min. The injection volume was 1 μL, and the injector was operated in a splitless mode at 260 °C. The initial temperature of the oven was 60 °C, which was maintained for 0.5 min, and then it was gradually increased to 125 °C at a rate of 8 °C/min; to 210 °C/min at 5 °C/min; to 270 °C at 10 °C/min; and to 305 °C at 20/min, which was maintained for 5 min. The MS quadrupole and ion source (electron impact) temperatures were set to 150 °C and 230 °C, respectively. The collision energy was 70 eV. Mass spectral data were collected in full-scan mode (m/z 50–500) with the solvent delay time set to 5 min. The QC samples were injected at regular intervals (every 10 samples) during the run to assess reproducibility.
5977a msd system
Manufactured by Agilent Technologies
Sourced in United States
The 5977A MSD system is a mass spectrometer designed for analytical applications. It provides accurate mass measurements and targeted compound identification. The system is capable of performing electron ionization (EI) and chemical ionization (CI) techniques. The 5977A MSD system is a versatile tool for a range of analytical workflows.
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4 protocols using 5977a msd system
1
GC-MS Analysis of Complex Samples
2
GC-MS Analysis of Volatile Organic Compounds
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An Agilent 7890B GC coupled to a 5977A MSD system was used for analysis. The GC–MS contained an Agilent 5190-2293: 900 μL (single taper, ultra-inert) liner. Solvent injection volumes were calculated based upon the inlet liner volume, the inlet temperature, the inlet pressure, and the solvents properties [boiling point (°C), density (g cm−3) and molecular weight (amu)]. Vapour volumes were kept below 75% of the inlet maximum capacity and were as follows: n-hexane (2.7 μL), methanol (0.8 μL), ethanol (1.2 μL) and 2-propanol (1.4 μL). The GC–MS operational parameters are summarised in Table 2 .
Operating conditions for GC–MS used in this study.
| Operating parameters for GC/MS | |
|---|---|
| Column dimensions | 30 m × 0.25 mm × 0.25 μm |
| Carrier gas | Hydrogen |
| Oven temperature programme | 50 °C (held for 2 min), 10 °C/min to 280 °C (held for 1 min) |
| Column flow | 1.6 mL min−1 |
| Injection mode | Splitless |
| Inlet pressure | 5.04 psi |
| Inlet temperature | 280 °C |
| Ionisation | Electron ionisation (EI) |
| Ionisation energy | 70 eV |
| Auxiliary temperature | 280 °C |
| Source Temperature | 230 °C |
| Solvent delay | 3.0 min |
| Scan range | 50–500 |
| SIM | 95 m/z (quant.), 107 m/z (qual.) for 2-MIB, 112 m/z (quant.), 125 m/z (qual.) for geosmin, 136 m/z for cis-decahydro-1-naphthol |
3
GC-MS Analysis of Ammi visnaga Extracts
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The methanol extracts of A. visnaga L. roots and seeds were subjected to analysis using a Chromatography-mass spectrometry (GC–MS) system manufactured by Agilent Technologies Inc. Stevens Creek Blvd, Santa Clara, CA, USA. The GC–MS system was equipped with an Agilent 5977A MSD system. The volatile compounds present in the methanol extract were purified using a capillary column with dimensions of 30 m × 0.25 mm and a 0.25 μm film thickness. Helium gas was employed as the carrier gas, with a flow rate of 0.5 mL/min. During the analysis, the injector temperature was maintained at 250 °C. The oven temperature was programmed as follows: initially, it was held at 70 °C for 3 min, then increased by 3 °C/min to reach 100 °C, and held for 3 min. Subsequently, the temperature was further increased to 120 °C at a rate of 10 °C/min and maintained for 3 min. Finally, the temperature was raised to 220 °C at a rate of 10 °C/min. The mass spectrum settings included an electron impact (EI) source, with the ionization temperature set at 230 °C and the electron energy at 70 eV. The quadrupole temperature was maintained at 150 °C, and the interface temperature was set to 280 °C. The quantity scanning range for the mass spectrum analysis ranged from 20 amu to 500 amu.
4
Metabolomic Analysis of Cecal Content by GC-MS
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All samples were measured using the Agilent Technologies 7890B Gas chromatography system coupled with the Agilent Technologies 5977A MSD system (Agilent Technologies, Santa Clara, CA, USA). 60 mg cecal content sample was added to Eppendorf tube. Samples were homogenized with cold methanol (360 μL) and internal standard (40 μL, 0.3 mg/mL 2-chlorophenylalanine) and were sonicated for 30 min. After the samples were rotated for 2 min and sonicated with 300 μL chloroform and 600 μL water for 30 min, and the mixture was centrifuged at 13,000 rpm for 10 min at 4 °C. Finally, the supernatant was dried under vacuum, mixed with 80 μL of methoxyamine, and oximated for 90 min in the dry supernatant; then 80 μL BSTFA and 20 μL n-hexane solution were added for 60 min at 70 °C. Metabonomics analysis was performed by gas chromatography-mass spectrometry (GC-MS).
The peak recognition, peak alignment, waveform filtering and missing interpolation of the original data were analyzed by using MS-DIAL software and metabolite modeling was based on the Lug database. The data matrix sample information, the peak name of each substance, the retention time, the mass-to-charge ratio and the signal strength were acquired. Results were analyzed using the OE biotechnology cloud platform (https://cloud.oebiotech.com/task/ ) (accessed on 22 January 2023).
The peak recognition, peak alignment, waveform filtering and missing interpolation of the original data were analyzed by using MS-DIAL software and metabolite modeling was based on the Lug database. The data matrix sample information, the peak name of each substance, the retention time, the mass-to-charge ratio and the signal strength were acquired. Results were analyzed using the OE biotechnology cloud platform (
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