The C. beijerinckii NCIMB 8052 strain was grown anaerobically at 37 °C in the modified MP2 medium containing 5 g/L of glucose and 1 g/L of 13C-labeled sodium formate as the carbon sources. The 2 mL grown cells were harvested when they reached OD600 of 2.5 and then hydrolyzed with 6 M HCl for 12 h at 105 °C. The samples were dried in a vacuum centrifuge and then derivatized with 100 μL of pyridine and 50 μL of N-methyl-N-[tert-butyldimethylsilyl]trifluoroacetamide (MTBSTFA, M − 108) for 1 h at 85 °C. Following filtration (0.22-μm pore size; Millipore), 1 μL of samples were injected into the GC-MS system (Agilent 7890B–5977B, Agilent, USA) equipped with a HP-5MS column (19091S–433UI, 30 m × 0.25 mm × 0.25 μm), the carrier gas was Helium. The mass spectrometer (Agilent MS-5977B) was operated in the electron impact (EI) mode at 70 eV. GC-MS data were analyzed as described previously [33 (link)].
Ms5977b
Manufactured by Agilent Technologies
Sourced in United Kingdom
The MS5977B is a gas chromatograph-mass spectrometer (GC-MS) system manufactured by Agilent Technologies. It is designed for the separation, identification, and quantification of chemical compounds in complex samples. The MS5977B combines a high-performance gas chromatograph with a sensitive and selective mass spectrometer, providing users with a powerful analytical tool for a wide range of applications.
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Lab products found in correlation
Agilent 7890b gc, by Agilent Technologies (4 mentions)
Gc 7890b, by Agilent Technologies (3 mentions)
Agilent 7890b 5977b, by Agilent Technologies (1 mentions)
Db 1ms column, by Agilent Technologies (1 mentions)
Rxi 5sil, by Restek (1 mentions)
Masshunter workstation software, by Agilent Technologies (1 mentions)
Masshunter qualitative analysis software, by Agilent Technologies (1 mentions)
10 protocols using ms5977b
1
Metabolic Profiling of C. beijerinckii
2
GC-MS Analysis of PAH Degradation Metabolites
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Samples with reaction time of 0, 24, and 48 h were taken for intermediate metabolite detection. The intermediate metabolites from various degradation samples (neutral and acidic samples) were extracted by ethyl acetate, dehydrated by anhydrous Na2SO4, concentrated with a rotary evaporator, and dried with high‐purity N2. The dried samples were dissolved in 500 μl of chromatographic‐grade DMF. The re‐dissolved samples were detected by GC‐MS (Agilent & GC‐7890B; MS‐5977B), while the BSTFA‐derived redissolved samples were detected in the same way. A GC‐MS system equipped with an HP‐5MS column (30 m × 0.25 mm, 0.25 μM) was used to detect the intermediate metabolites of PAHs with the following oven heating program: maintained at 75°C for 3 min, increased to 250°C at a rate of 12°C/min and maintained for 1 min, then increased to 300°C at a rate of 10°C/min and maintained for 10 min. The indigo sample was detected using the previous method
64 (link).
64 (link).
3
Profiling VOCs by TD-GCMS Analysis
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VOCs sampled by Tenax TA tubes were analyzed by thermal desorption-gas chromatography mass spectrometry (TD-GCMS) (TD: TD 100-xr, Markes International; GC: 7890B, MS: 5977B, Agilent Technology). The determination conditions of TD-GCMS are shown in Table S1.† All the VOCs with the retention time between n-hexane and n-hexadecane were identified automatically using NIST library.33 (link) The concentrations were quantified using peak areas with the response coefficient of toluene,34 as seen in eqn (1) and (2) . Six consecutive samples were collected at the condition of RH 50% and ACR 1.0 h−1, and the relative standard deviation (RSD) of the VOCs concentrations was calculated to evaluate the precision of the measurement. The main components were selected to analyze the relationships of emission characteristics with RH and ACR. where ma is the mass of VOCs sampled in Tenax TA tube, μg; A is the peak area of the compound; k is the response coefficient of toluene; ca is the concentration of VOCs in the chamber, mg m−3; ma0 is the mass of VOCs in the background, μg; and V is the sampling volume, L.
4
GC-MS analysis of sterane and hopane biomarkers
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Saturate samples (1 µl) were injected (splitless) into an Agilent GC 7890B fitted with a DB‐1MS column (Agilent), coupled to an Agilent MS 5977B. The temperature was initially held at 40 °C for 1 min before being increased at a ramp of 6 °C/min to 320 °C and then held isothermally for 28 min.
Sterane and hopane biomarkers were analyzed by GC‐MS selected ion monitoring analysis (m/z 123, 191, 205, 217, 218, 358, 370, 372, 384, 386, 398, 400, 412, 414, 426, 428, 440, 442, 454, 456). Bicyclanes were analyzed by GC‐MS full‐scan extracted ion chromatography (EIC; m/z 179, 193, 208).
Data were analyzed by Agilent ChemStation software, with compound identification using National Institute of Standards and Technology library searches. Kovats retention indices (temperature programmed) were calculated using ASTM International Method D6730 (ASTM International, 2021 ). All confidence intervals provided are 2× standard error (2SE).
Sterane and hopane biomarkers were analyzed by GC‐MS selected ion monitoring analysis (m/z 123, 191, 205, 217, 218, 358, 370, 372, 384, 386, 398, 400, 412, 414, 426, 428, 440, 442, 454, 456). Bicyclanes were analyzed by GC‐MS full‐scan extracted ion chromatography (EIC; m/z 179, 193, 208).
Data were analyzed by Agilent ChemStation software, with compound identification using National Institute of Standards and Technology library searches. Kovats retention indices (temperature programmed) were calculated using ASTM International Method D6730 (ASTM International, 2021 ). All confidence intervals provided are 2× standard error (2SE).
5
Analytical Determination of Wine Aroma Compounds
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The main volatile substances related to the fermentation bouquet or secondary wine aroma compounds (esters, higher alcohols, fatty acids, etc.) were analyzed using headspace solid phase microextraction (HS-SPME), together with gas chromatography and mass spectrometry (GC-MS; (7890A and MS 5977B, Agilent)) using the multipurpose sampler MPS2 (Gerstel GmbH & Co. KG) for HS-SPME injection [23 (link)]. The determination followed the analytical method [28 (link)] according to the reported approach [26 (link),29 ], which was correspondingly adjusted and adapted [30 ]. A model wine (10% (v/v) solution of ethanol in water, 3 g/L of tartaric acid, adjusted to pH 3) was used for the calibration. SPME extraction was performed with a 65 µm polydimethylsiloxane and divinylbenzene fiber (Supelco). The gas chromatography column of 60 m × 0.25 mm × 1 µm (Rxi-5Sil, Restek, Bellefonte, PA, USA), together with particular GC-MS software and technical settings, was utilized for the aroma compound separation. The Agilent MassHunter workstation software provided by the GC-MS instrumentation was used for the instrumental control, acquisition of data and analysis of qualitative and quantitative data.
6
GC-MS Method Validation for Analytes
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GC-MS method validation was performed using an Agilent 7890B GC and a MS5977B mass selective detector (Agilent Technologies, Wokingham, UK) employing the parameters detailed in Section (2.4).
Mass spectra were obtained under selected ion monitoring (SIM) mode, using three specific fragment ions for each analyte (Supplementary Information, Table S3 andS5). The GC-MS method was validated in accordance with the ICH guidelines 42 using the following parameters: linearity, accuracy, precision (repeatability), limit of detection (LOD), and limit of quantification (LOQ). Linearity, precision: six replicate injections of the calibration standards were performed and the data analyzed under the same conditions. The LOQ respectively. 42 Signal-to-noise ratios were measured over six injections in the lower end of the concentration range (2.5 μg/mL for most analytes; 5.0 μg/mL for morphine) using the auto-rootmean-squared (Auto-RMS) algorithm from the Agilent MassHunter Qualitative Analysis software.
Mass spectra were obtained under selected ion monitoring (SIM) mode, using three specific fragment ions for each analyte (Supplementary Information, Table S3 andS5). The GC-MS method was validated in accordance with the ICH guidelines 42 using the following parameters: linearity, accuracy, precision (repeatability), limit of detection (LOD), and limit of quantification (LOQ). Linearity, precision: six replicate injections of the calibration standards were performed and the data analyzed under the same conditions. The LOQ respectively. 42 Signal-to-noise ratios were measured over six injections in the lower end of the concentration range (2.5 μg/mL for most analytes; 5.0 μg/mL for morphine) using the auto-rootmean-squared (Auto-RMS) algorithm from the Agilent MassHunter Qualitative Analysis software.
7
Biodegradation of Crude Oil using EXS14
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The strain (EXS14) with the maximum growth and the highest biosurfactant-production capacity was used to apply and demonstrate the biodegradation of crude oil in laboratory conditions. The experimental chamber containing 250 mL of MSM media was inoculated with 300 ppm of crude oil and 1 mL of EXS14 culture that contained approximately 1.5 × 108 cells/mL. Nitrogen (as ammonium nitrate) was added at 1400 ppm, salinity at 4%, and pH was kept at 7. Test bottles were agitated at 110 rpm at 30 °C for up to 14 days. The test bottles were closed by using sterile cotton which allowed the passage of air through them to maintain aerobic conditions inside the bottles. Experiments were performed in duplicates and individual flasks were analyzed at the beginning of the study (T0) and at 4 (T4), 7(T7), 10 (T10), and 14 days (T14). At the end of the experiments, the WAF (water-accommodated fraction of the oil) was separated from the rest of the crude oil using a separating funnel. 3 mL of methylene chloride (DCM) was then added to the WAF to extract the soluble fraction of hydrocarbons. Samples were then analyzed by Gas Chromatography-Mass Spectrometry (GC–MS) (Agilent – USA, Models: GC-7890B & MS-5977 B).
8
GC-MS Method Validation Protocol
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GC-MS method validation was performed using an Agilent 7890B GC and a MS5977B mass selective detector (Agilent Technologies, Wokingham, UK) employing the parameters detailed in Section 2.4. Mass spectra were obtained under Selected Ion Monitoring (SIM) mode, using three specific fragment ions for each analyte. The GC-MS method was validated in accordance with the ICH guidelines [30] using the following parameters: linearity, accuracy, precision, limit of detection (LOD) and limit of quantification (LOQ). Linearity, precision: six replicate injections of the calibration standards were performed and the data analysed under the same conditions. The RSD % was calculated for each replicate test sample. Accuracy (percentage recovery study): determined from spiked samples prepared in triplicate at three levels over a range of 80-120 % of the target concentration (15 μg mL -1 ). The percentage recovery and RSD % were calculated for each of the replicate samples. Limits of detection and quantification: six replicate injections of the calibration standards were performed and the data analysed under the same conditions. The limits of detection and quantification were determined based on the signal-to-noise (S/N) ratio, where a signal-to-noise ratio of 3:1 and 10:1 was used to calculate the LOD and LOQ respectively.
9
GC-EI-MS Analysis of Complex Samples
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GC-EI-MS analysis was performed using an Agilent 7890B GC and a MS5977B mass selective detector (Agilent Technologies, Wokingham, UK). The mass spectrometer was operated in the electron ionisation mode at 70 eV. Separation was achieved with a capillary column (HP-5MS,
10
GC-MS Analysis of Illicit Drugs
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GC-MS analysis was performed using an Agilent 7890B GC and a MS5977B mass selective detector (Agilent Technologies, Wokingham, UK). The mass spectrometer was operated in the electron ionization mode at 70 eV. Separation was achieved with a capillary column (HP-5MS, were dissolved at 1 mg/mL in methanol without derivatization, using eicosane (0.5 mg/mL) as an internal standard. Compounds were analyzed individually to acquire representative mass spectra, and in combination with fentanyl (18) (link), heroin (19) (link) and two adulterants, acetaminophen (20) (link) and caffeine (21) (link).
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