Chemical characterization was performed using gas chromatography/mass spectroscopy (GC/MS) (Shimadzu, Japan). Gas chromatography with electron impact mass spectrometry (GC/EIMS) (70 eV) analysis was carried out using a Shimadzu GC/MS spectrometer (GC-2010). A Durabond-DB5 capillary column (30 m x 0.25 mm, 0.25 μm film thickness) (J&W Scientific) was operated at 60°C for 3 min and then programmed for 60-220°C at 5°C/min, after which it was kept under isothermal conditions at 220°C for 5 min. The carrier gas was helium (purity of 99.99%) (1 ml/min), and the injector temperature was 250°C. The analyses were performed in a split injector mode (1:30). The essential oil components were identified by comparing their retention indexes (relative to n-alkanes) and mass spectra with those found in the literature. 19, 20 (link) They were then stored in a spectrometer database. The analyses were performed in triplicate.
Gc ms
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The Shimadzu GC-MS is a gas chromatography-mass spectrometry system that combines the separation capabilities of gas chromatography with the analytical power of mass spectrometry. It is designed to identify and quantify a wide range of chemical compounds in complex mixtures.
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Lab products found in correlation
Qp2010, by Shimadzu (7 mentions)
N alkanes c8 c40, by Merck Group (5 mentions)
Qp 2010 system, by Shimadzu (5 mentions)
Rtx 5ms capillary column, by Restek (4 mentions)
Qp2010 plus, by Shimadzu (3 mentions)
Gcmssolution software, by Shimadzu (2 mentions)
Fatty acid methylation kit, by Nacalai Tesque (2 mentions)
Qp2010 ultra, by Shimadzu (2 mentions)
Ch2cl2, by Thermo Fisher Scientific (1 mentions)
Db 5 column, by Agilent Technologies (1 mentions)
Fluoview fv1000, by Olympus (1 mentions)
Dm1000 led, by Leica (1 mentions)
Silica gel f254, by Merck Group (1 mentions)
Penicillin streptomycin, by Thermo Fisher Scientific (1 mentions)
Rpmi 1640, by Merck Group (1 mentions)
Fetal bovine serum (fbs), by Thermo Fisher Scientific (1 mentions)
Hepes, by Thermo Fisher Scientific (1 mentions)
Sodium bicarbonate, by Thermo Fisher Scientific (1 mentions)
Methyl thiazolyl tetrazolium (mtt), by Merck Group (1 mentions)
Doxorubicin, by Merck Group (1 mentions)
75 protocols using gc ms
1
GC-MS Analysis of Essential Oil Composition
2
GC-MS Analysis of Rosemary and Licorice
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Acetone extracts of rosemary and licorice were concentrated in a desiccator and subjected to GC-MS analysis (Khalil et al., 2022a, b) . Gas chromatography coupled with mass spectroscopy (GC-MS, Shimadzu) was used to identify metabolic products. Temperatures were set at 270 °C for the injection port and 280 °C for the GC-MS interface, with a temperature flow rate of 10 °C/min. With 10 ml/min flow rate, helium was used as collision gas. The test samples' compound names and molecular formulas were determined using NIST library spectra databases.
3
GC-MS Analysis of Lignocellulosic Degradation
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The compositions of other lignocellulosic degradation products in samples were assessed using GCMS (Shimadzu) following the method of Chokwe et al. (9 (link)), with a detection limit for the peak area >2%. The liquid–liquid extraction pretreatment was conducted prior to the GCMS analysis using CH2Cl2 (chromatogram pure grade, Thermo Fisher Scientific, Waltham, MA, USA). A 20-mL pre-treated sample was freeze-dried prior to being dissolved in 2 mL of methanol. The sample was then filtered through a 0.22-μm nylon membrane before being analyzed. GCMS was equipped with a DB-5 column (Agilent, Santa Clara, CA, USA) with an internal diameter of 30 m×0.25 mm and film thickness of 0.25 μm. Conditions were set as follows: the initial oven temperature was held at 70°C for 2 min, increased at 20°C min−1 to 230°C, and then elevated to 270°C. Helium was used as the carrier gas at a flow rate of 1 mL min−1. The injector temperature was maintained at 250°C. A 1-μL sample was injected neat with a split ratio of 1:10. Mass spectra were recorded over the 50–650 amu range at 1 scan s−1 with an ionization energy of 70 eV and ion source temperature of 230°C. The compositions of samples were qualitatively identified through comparisons of their mass spectra in a library and published literature.
4
Spectroscopic Analysis of Oil Concentration
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The oil concentration was determined by ultraviolet spectrophotometry (Alpha-1860s, China) at 225 nm.23 (link) The positive correlation between the oil concentration and its absorbance was shown in Fig. S2.† The zeta potential were measured by using a Zeta Nanosizer instrument (Malvern Istruments, UK). The sediment and contaminant samples were imaged by optical microscopy (Leica DM1000 LED, Leica, Germany). Fluorescent images were obtained by a confocal laser scanning microscope (CLSM, Fluo View FV1000, Olympus Corporation, Japan). Petroleum hydrocarbon components in the extracts were analyzed using GC-FID (Agilent 7890A Series GC System, USA) and GC-MS (Shimadzu Kyoto, Japan). Parameters of GC-FID and GC-MS analysis are given in ESI.†
5
Antitumor Activity of Lansium domesticum
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Material L. domesticum fruit peel was collected from Purbalingga, Central Java, Indonesia and identified in Department of Biology, Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta, Indonesia. Solvents used were p.a grades from E Merck. Silica gel F254 were used for thinlayer chromatography dan Silica gel PF254 for preparative thin layer chromatography (Merck), Cerium (IV) sulfate tetrahydrate (E Merck), RPMI 1640, Fetal Bovine Serum, Penicillin-Streptomycin, Fungizon, Sodium bicarbonate (Gibco), HEPES (Invitrogen), Phosphate Buffered Saline, MTT, Doxorubicin (Sigma Aldrich). The T-47D and HepG2 cell lines were collection from Parasitology Laboratory, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia. Mass spectra were obtained from GC-MS (Shimadzu). Spectra of 1 H-and 13 C-NMR (CDCl3) were measured using JEOL JNM-ECZ 500R/S1 at 500 MHz. Infrared (KBr) spectrum was obtained from spectrophotometer (Shimadzu). Ultraviolet spectrum (CHCl3) was obtained from UV spectrophotometer (Hitachi UH 5300).
6
Bacterial Nitrogen Fixation Assay
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BNF was measured by acetylene reduction/ethylene production assay (ARA) as described previously by Majeed et al. (2015 (link)). Briefly, pure bacterial cultures were inoculated in 20 ml airtight vials containing 5 ml semisolid nitrogen free NFb medium and grown for 48 h at 28°C. Following pellicle formation, 10% (v/v) acetylene gas was injected into the vials, which were incubated for 16 h at 30°C. Samples were then analyzed by gas chromatography (GC) (Shimadzu, Japan) using RTX5 column (Restek, USA) and a H2-flame ionization detector (FID). The peaks of acetylene and ethylene were also confirmed by GC-MS (Shimadzu, Japan). All the experiments were performed in triplicates.
7
Anammox Species Respiration Kinetics
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The selected anammox species (“Ca. B. sinica”, “Ca. K. stuttgartiensis” and “Ca. Scalindua sp.”) were transferred into 30 mL of the inorganic medium in 100 mL serum vials containing 70 mL headspace. The residual DO was removed and the headspace was exchanged with highly pure helium gas (99.9999% He) at 1.5 atm as described above. O2 gas (99%, 200 µL) was injected into the headspace with a gas tight syringe 3 h before the addition of 15NH4Cl and Na14NO2 (final concentration of 3 mM each). Thereafter, the vials were incubated at room temperature (ca. 25 °C). The air samples were taken from the headspace over the course of the incubation time, and 14+15N2 and O2 concentrations were measured by a gas chromatography and mass spectrometry (GC-MS, SHIMADZU). The O2 concentrations (%) were converted to DO concentration using the standard curves of the measured DO concentrations vs. the headspace O2 concentrations (%, v/v) (Fig. S1 ) as described above. The O2 reduction rates were determined by dividing the slope of linear regression of DO concentration as a function of time by the protein concentration and are expressed as µmole DO per g-protein per hour.
8
Quantifying Short-Chain Fatty Acids in Feces
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The concentrations of SCFAs (acetate, propionate, butyrate, isobutyrate, valerate, and isovalerate) in feces were determined according to the previous method [40 (link)]. Samples (20 mg) were resuspended into 500 μL saturated NaCl solution, and then 20 μL sulfuric acid (10%) was added for acidification. SCFAs were extracted by adding 1000 μL diethyl ether. The mixture was centrifuged (12,000× g, 4 °C, 15 min), and the aqueous content was removed by adding 0.25 g Na2SO4. SCFAs were quantified by gas chromatography–mass spectrometry (GC-MS) (Shimadzu Corporation, Tokyo, Japan) using the external standard method.
9
Volatile Profiling of A. hygrophila Infestation
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After 24 h of mechanical damage treatment, volatiles were collected. The above A. hygrophila-infested plant was put into a new vial and kept for 24 h, respectively. Volatiles from healthy plants, mechanically damaged plants and A. hygrophila-infested plants were collected. After 24 h, the sample in the vial was equilibrated at 40 °C for 10 min in a water bath, respectively. After equilibration, the solid phase microextraction (SPME) was exposed to the headspace of the vial for 30 min, after which the SPME was inserted into a GC-MS (Shimadzu Corporation, Kyoto, Japan) desorption for 2 min for analysis.
10
Quantification of Limonene in Microalgae
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Limonene was collected with HayeSep porous polymer (Sigma) absorbent traps and eluted by 1 mL hexane supplemented with 50 µg/mL cedrene (Sigma) as the internal standard. The concentration of limonene was quantified by gas chromatography–mass spectrometry (GC-MS) (Shimadzu Scientific Instruments, Inc.) with a standard curve and normalized with recovery rates, which was determined by spiking different concentrations of limonene in 500 mL of UTEX 2973 wild-type cells (Supplementary Fig. 8 ). The total limonene yield was calculated by adding yields of each day together.
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