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7890b 5977a gc ms system

Manufactured by Agilent Technologies

The 7890B-5977A GC-MS system is a gas chromatography-mass spectrometry (GC-MS) instrument manufactured by Agilent Technologies. It is designed to perform qualitative and quantitative analysis of complex chemical samples. The system combines a 7890B gas chromatograph with a 5977A mass spectrometer, providing high-performance separation and detection capabilities for a wide range of applications.

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4 protocols using 7890b 5977a gc ms system

1

Metabolite Analysis using GC-MS

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We used an Agilent 7890B-5977A GC-MS system equipped with 7650 ALS, HT-5
MS 30 m capillary column and EI source for the metabolite analysis. 1 L of
sample was automatically injected in splitless mode and analyzed under the
following conditions: initial oven temperature was set to 70°C and held
for 1 minute, then ramped to 120°C by 5°C/min, then to
280°C by 12°C/min, and then to 300°C by 20°C/min and
held for 1 minute. A full scan from 60–600 m/z was performed. The single
run time was ~26 minutes.
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2

Lignin Quantification and Characterization

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Five mg of CWR were digested with 2.6 mL of 25% acetyl bromide in glacial acetic acid for 2 h at 50 °C using a HACH LT200 system. Samples were cooled on ice and transferred into 10 mL of 2 M NaOH plus 12 mL glacial acetic acid. The reaction tube was rinsed with glacial acetic acid and 1.75 mL of 0.5 M hydroxylammonium chloride was added. Each volume was adjusted to 30 mL with glacial acetic acid, centrifuged (3000 g, 15 min) and lignin content was measured spectrophotometrically (280 nm, extinction coefficient ε = 22.9 g− 1 L cm− 1).
Lignin was characterized following the nitrobenzene oxidation method previously described [69 (link), 78 (link)]. The products after nitrobenzene oxidation of ten mg of CWR were derivatized with Bis(trimethylsilyl)trifluoroacetamide and analysed by gas chromatography coupled to mass spectrometry (GC-MS). A HP-5MS column (30 m × 0.25 mm, 0.25 μm, Agilent) was used on a 7890B-5977A GC-MS system (Agilent). Salicylic acid-D4 was used as internal standard.
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3

Lignin Characterization by Nitrobenzene Oxidation

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Lignin was characterised on 3 or 4 biological replicates using the nitrobenzene oxidation method [64 (link)]. 10 mg of CWR were digested with 2 mL of 2 M NaOH and 30 μL nitrobenzene at 165 °C for one hour (Hach LT200 system). After centrifugation, ca. 1500 μL of supernatant was collected and 10 μl of vanillin-D3 (Sigma-Aldrich) at 10 mg/mL in 1,4-dioxan were added as a surrogate standard. Nitrobenzene was removed by four washing steps with ethyl acetate (1 mL, vortexing/centrifugation cycle). The pH of the solution was adjusted to 2–3 by adding approximately 200 μL of 6 N HCl solution. The oxidation products were recovered by two successive extractions with 1 mL ethyl acetate (vortexing/centrifugation cycle) followed by cleaning with 500 μl of saturated NaCl solution and drying with Na2SO4. The GC-MS analysis was performed after trimethylsilylation, realized by addition of 50 μl of Bis(trimethylsilyl)trifluoroacetamide (BSTFA) to 50 μL of dried extract and derivatization at 60 °C for 30 min. Quantitative analyses were performed using a HP-5MS column (30 m × 0.25 mm, 0.25 μm, Agilent) installed in a 7890B-5977A GC-MS system (Agilent). Injection was done at 250 °C in splitless mode. The oven program started at 40 °C for 5 min, increased to 230 °C at 10 °C/min, then to 320 °C at 40 °C/min and was kept at 320 °C for 10 min. Salicylic acid-D4 was used as internal standard.
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4

GC-MS Analysis of Metabolite Profiling

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For GC-MS analysis, 150 µl of the aqueous phase was dried down in a vial insert, before washing twice with 40 µl MeOH and drying again. Samples were methoximated (20 µl of 20 mg/ml methoxyamine in pyridine, RT overnight) before derivatising with 20 µl of N,Obis(trimetylsilyl)trifluoroacetamide + 1% trimethylchlorosilane (Sigma, 33148) for ≥1 h. An Agilent 7890B-5977A GC-MS system was use to perform metabolite analysis. Splitless injection (injection temperature 270 °C) onto a 30 m + 10 m × 0.25 mm DB-5MS + DG column (Agilent J&W) was used, using helium carrier gas, in electron-impact ionization (EI) mode. Initial oven temperature was 70 °C (2 min) with a subsequent increase to 295 °C at 12.5 °C/min, then to 320 °C at 25 °C/min (before holding for 3 min). Metabolite identification and quantification was performed using MassHunter Workstation software (B.06.00 SP01, Agilent Technologies) by comparison to the retention times, mass spectra and responses of known amounts of authentic standards. Fractional labelling of individual metabolites is reported after correction for natural abundance.
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