GC was started with an initial temperature of 150 °C for 3 min, then increased with a rate of 3 °C per minute until 250 °C and from there with 25 °C per minute until 320 °C for 10 min. Following column was used: Restek Rxi 5Sil MS column in 30 m. OA constituent rhamnose, as well as core moieties were detected via reference substances and FucNAc was detected with the help of the Mass Spectra analyzed using the Xcalibur software from Bruker (Bremen, Germany).
Rxi 5sil ms column
Manufactured by Restek
Sourced in United States, Japan, United Kingdom
The Rxi-5Sil MS column is a fused silica capillary column designed for gas chromatography-mass spectrometry (GC-MS) applications. It features a 5% diphenyl, 95% dimethyl polysiloxane stationary phase, which provides good separation and inertness for a wide range of analytes.
Automatically generated - may contain errors
Lab products found in correlation
Thermo trace ultra chromatograph, by Thermo Fisher Scientific (3 mentions)
Thermo dsq mass spectrometer, by Thermo Fisher Scientific (3 mentions)
Trace 1310 gc, by Thermo Fisher Scientific (2 mentions)
Qp2010 ultra, by Shimadzu (2 mentions)
Model 6890, by Agilent Technologies (1 mentions)
Tof mass spectrometer, by Leco (1 mentions)
Tsq quantum xls triple quadrupole mass spectrometer, by Thermo Fisher Scientific (1 mentions)
Trace 1300 gc, by Thermo Fisher Scientific (1 mentions)
Pegasus 3 4d tof ms, by Leco (1 mentions)
Agilent 6890n, by Agilent Technologies (1 mentions)
Ethyl decanoate, by Merck Group (1 mentions)
Hplc grade hexane, by Thermo Fisher Scientific (1 mentions)
Qp5050a, by Shimadzu (1 mentions)
Gc fid, by Thermo Fisher Scientific (1 mentions)
Pegasus ht time of flight mass spectrometer, by Leco (1 mentions)
Scion 436 ms, by Bruker (1 mentions)
Alphagaz 2, by Air Liquide (1 mentions)
5973 inert, by Agilent Technologies (1 mentions)
Ms chemstation, by Agilent Technologies (1 mentions)
Qp2020 nx, by Shimadzu (1 mentions)
38 protocols using rxi 5sil ms column
1
GC Analysis of Polysaccharide Constituents
2
Metabolite Profiling of Soybean Organs
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Metabolites were extracted from five different organs (1st [L1], 2nd [L2], and 3rd [L3] trifoliate leaves; stems [S]; and roots [R]) of soybean plants at the V3 growth stage (25 mg/sample) using extraction medium (3:1:1 [v/v/v] methanol/chloroform/water). Extraction and derivatization were performed as described (Kusano et al., 2007 , 2011 ). Metabolites were detected using a GC instrument (Model 6890, Agilent Technologies, Palo Alto, CA, USA) fitted with an Rxi‐5Sil MS column (0.25‐mm i.d., 0.25‐ µm film; Restek) coupled to a TOF mass spectrometer (Leco, St. Joseph, MI, USA). Ten stable isotope reference compounds were used as internal standards (Kusano et al., 2007 ). All raw data in netCDF format were pre‐processed by hyphenated data analysis (Jonsson et al., 2005 , 2006 ). The obtained data matrix was normalized and summarized using the cross‐contribution‐compensating multiple standard normalization method (Redestig et al., 2009 ). For metabolite identification, we cross‐referenced the obtained mass spectra with GC‐EI‐MS mass spectral and RI libraries (Schauer et al., 2005 ) in the Golm Metabolome Database (Kopka et al., 2005 ) and our own in‐house libraries. The reproducibility of GC‐TOF‐MS analysis was assessed with three biological replicates per experiment.
3
Thermal Desorption-GC/MS Analysis of SOA
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SOA composition was analyzed using a thermal desorption–gas chromatography mass spectrometry, or TD-GC/MS (TDS3, Gerstel, Mülheim an der Ruhr, Germany; Model 7890B and 5977A, Agilent, Santa Clara, CA, USA). Briefly, a small punch of SOA filter (containing about 13 μg SOA) was placed into a thermal desorption system and heated from 40 to 320 °C at 60 °C/min and then held at 320 °C for 5 min. Carried by helium gas, the desorbed organic compounds were trapped and re-concentrated in a cooled liner at 20 °C. The liner was then heated to 320 °C and kept at 320 °C for 10 min to transfer all the organic components to the GC/MS. An Rxi-5sil MS column with dimensions of 29 m × 250 μm × 0.25 μm (Restek Corporation, Bellefonte, PA, USA) was used during the measurements. GC oven temperature was ramped from 50 to 300 °C at 10 °C/min, and held at 300 °C for 5 min.
For the analysis of the SOA extract, the remaining filter was extracted in methanol/water (1:3) solution. After sonication and filtration (to remove of quartz debris), 10 μL of the extract (containing about 7 μg SOA) was added onto a punch of a blank prebaked quartz filter. The filter punch was then analyzed by the same method mentioned previously.
For the analysis of the SOA extract, the remaining filter was extracted in methanol/water (1:3) solution. After sonication and filtration (to remove of quartz debris), 10 μL of the extract (containing about 7 μg SOA) was added onto a punch of a blank prebaked quartz filter. The filter punch was then analyzed by the same method mentioned previously.
4
GC-MS/MS Analysis of Compounds
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A Thermo Scientific TSQ Quantum XLS triple quadrupole mass spectrometer coupled with a Thermo Scientific Trace 1300 GC (San Jose, CA, USA) was used for GC–MS/MS analysis. An Rxi®-5SiL MS column (20 m × 0.18 mm I.D., 0.18 μm film thickness) from Restek Corporation (Bellefonte, PA, USA) was used for the chromatographic separation of the compounds. The column temperature program started from 40 °C (hold 0.6 min), increased to 180 °C at the rate of 30 °C/min, then increased to 280 °C at the rate of 10 °C/min, then increased to 290 °C at the rate of 20 °C/min, and held at this final temperature for 5 min. The temperature of the injector port was 250 °C, and a 1 μL volume was injected into the splitless mode with a split flow of 50 mL/min and a splitless time of 1.0 min. The helium carrier gas flow rate was 0.85 mL/min. The ion source and transfer line temperature were 280 °C. The MS was operated in the electron ionization mode at 70 eV with the selective reaction monitoring (SRM) data acquisition mode. The MS/MS parameters are shown in Supplementary Materials Table S3 .
5
GC-MS Analysis using Thermo Trace Ultra
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For GC-MS analysis, the Thermo Trace Ultra chromatograph was used, coupled with the Thermo DSQ mass spectrometer (Thermo Scientific, Waltham, MA, USA). The analyses were carried out with use of the Rxi ® -5Sil MS column (Restek, Bellefonte, PA, USA). The following working parameters were employed: injector temperature, 260 °C; oven temperatures, 100 °C for 2 min, ramp at 20 °C/min to 260 °C; the carrier gas (helium) flow rate, 1.2 mL min -1 ; MS transfer line temperature, 250 °C; MS source temperature, 250 °C; the injection volume, 1 μL, the splitless mode.
6
GC-TOF-MS Protocol for Compound Analysis
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The samples were injected into an Agilent 6890N (Agilent Technologies, Wilmington, DE, USA) gas chromatograph equipped with a Rxi-5Sil MS column (30 m × 0.25 mmID × 0.25 μm; RESTEK, Bellefonte, PA, USA). We used the splitless injection mode and helium as a carrier gas at a constant flow rate of 1 mL/min. The GC temperature program was as follows: the initial column temperature 55 °C was maintained for 3 min, then increased to 150 °C at the rate of 15 °C/min, then increased to 200 °C at the rate of 3 °C/min, and finally maintained at 200 °C for 2 min. The back-inlet temperature was kept at 250 °C. Mass spectral analysis was performed on a Pegasus III 4D TOF-MS (LECO, St. Joseph, MI, USA). The MS ionization energy (voltage) was set at 70 eV. The ionization source temperature was 200 °C; the MS scan range (m/z) was 29–500 amu; and the acquisition rate was 30 spectra/s.
7
Volatile Analysis of Rice Plants
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The collection of volatiles emitted from 3‐week‐old rice plants was performed using a previously described open headspace system (Sun et al., 2017 ). In brief, volatiles were collected for 24 h on 50 mg of 60/80 mesh Tenax‐TA (Shanghai ANPEL Scientific Instrument Company, Shanghai, China). The collected volatiles were extracted with 300 μL of HPLC‐grade hexane (Fisher Scientific, New Jersey), to which 25.95 ng ethyl decanoate (Sigma‐Aldrich, Oakville, ON) was added as an internal standard. One microlitre of each sample was analysed using a Shimadzu GC‐MS (GC‐MS‐QP2010 SE, Japan) on an Rxi‐5Sil MS column (30 m × 0.250 mm×0.25 μm, Restek, Bad Homburg, Germany). The GC oven temperature program was 40°C for 1 min followed by an increase to 130°C at a rate of 4°C/min (5‐min hold) and then to 250°C at a rate of 10°C/min (5‐min hold). Chiral GC‐MS analysis of limonene was performed using an Rt™‐β DEXsm column (Restek, Bad Homburg, Germany) and a temperature program of 40°C (1‐min hold) followed by an increase to 100°C at a rate of 1°C/min and then to 240°C at a rate of 10°C/min (2‐min hold). The flow rate of the carrier gas (helium) was 1 mL/min. Limonene standards were obtained from Sigma.
8
Volatile Profiling of Plasmodia
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On the 8th day and 18th day after the transfer of plasmodia to a fresh agar plate, volatiles were collected from the headspace of plasmodia on the agar plate using solid phase microextraction (SPME) (https://www.sigmaaldrich.com). After collection for one hour, the SPME fiber was withdrawn and then inserted into the injector port of a Shimadzu 17A gas chromatograph coupled to a Shimadzu QP5050A quadrupole mass selective detector for volatile identification and identification. Separation was performed on a Restek Rxi-5Sil MS column (30 m × 0.25 mm i.d. × 0.25 µm thickness; Restek) with helium as the carrier gas and a temperature program from 60 °C to 300 °C at 5 °C per minute rate. The experiment was performed with three biological replicates.
9
Octane and Dodecane Bioconversions Analysis
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Reactions in MWPs were first stopped by acidifying with 50 μl l−1 of 10 mol l−1 H3PO4, subsequently 100 μl ethyl acetate were added to the reaction mixture. After incubating on a thermomixer for 10 min at 50 °C and 1000 rpm the samples were centrifuged and the organic phase removed.
Organic samples were analyzed by GC-FID (Thermo Fisher Scientific, UK) equipped with a Rxi-5Sil MS column (30 m × 0.53 mm × 1.5 μm; Restek, USA) using helium as carrier gas (constant flow rate, 5 ml min−1). Octane bioconversions were analyzed with an injector and detector temperature of 250 and 280 °C respectively. The temperature program was set at 80 °C for 2 min, increased to 200 °C at 20 °C min−1 with a final hold of 3 min. Dodecane bioconversions were analyzed with an injector temperature of 270 °C. A temperature program of 100 °C for 1 min with an increase to 270 °C at 20 °C min−1 and a final hold of 1 min was used. Quantification was achieved using external standards. Reported concentrations are in relation to the aqueous reaction volume.
Organic samples were analyzed by GC-FID (Thermo Fisher Scientific, UK) equipped with a Rxi-5Sil MS column (30 m × 0.53 mm × 1.5 μm; Restek, USA) using helium as carrier gas (constant flow rate, 5 ml min−1). Octane bioconversions were analyzed with an injector and detector temperature of 250 and 280 °C respectively. The temperature program was set at 80 °C for 2 min, increased to 200 °C at 20 °C min−1 with a final hold of 3 min. Dodecane bioconversions were analyzed with an injector temperature of 270 °C. A temperature program of 100 °C for 1 min with an increase to 270 °C at 20 °C min−1 and a final hold of 1 min was used. Quantification was achieved using external standards. Reported concentrations are in relation to the aqueous reaction volume.
10
GC-TOF-MS Analysis of Metabolites
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The GC-TOF-MS analysis was performed using an Agilent 7890 gas chromatograph system (Agilent Technologies Inc., Santa Clara, California, USA) coupled with a Pegasus HT time-of-flight mass spectrometer (LECO Corp., St. Joseph, MI, USA) that included an Rxi-5Sil MS column (Restek, Bellefonte, USA), which was 30 m in length and 0.25 mm in inner diameter with a film thickness of 0.25 μm. We injected one microliter of sample in splitless mode. The carrier gas was helium with a 3 ml/min front inlet purge flow and a 2 ml/min gas flow rate through the column. The original temperature was maintained at 50°C for 1 min; the temperature was then increased to 330°C at a 10°C/min rate and maintained for 5 min. The ion source, transfer line and injection temperature were at 250°C, 280°C and 280°C, respectively. We performed the ionization with a voltage of -70 eV in the mode of electron impact during the mass spectrometry analysis process. The mass spectrometry data were acquired in the full-scan mode in the m/z range of 85–600 at a rate of 20 spectra per second after a solvent delay of 366 s.
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