For SPME‐GC‐MS data, processing was carried out with XCALIBUR™ 2.2 software provided by ThermoFisher Scientific (Waltham, MA, USA), while for CLSA‐GC‐MS data, processing was carried out with MSD ChemStation E.02.02.1431 (Agilent, Santa Clara, CA, USA). Identification of the volatile compounds was made by injecting pure reference standards, and quantifications were performed after calibration lines had been prepared with the same standards.
Msd chemstation e 02
Manufactured by Agilent Technologies
Sourced in United States, France
The MSD ChemStation E.02.02.1431 is a software application designed to control and manage Agilent Technologies' mass spectrometry instruments. It provides data acquisition, processing, and reporting capabilities for analytical workflows.
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Lab products found in correlation
Xcalibur 2, by Thermo Fisher Scientific (1 mentions)
5973 network mass selective detector, by Agilent Technologies (1 mentions)
Mps2 autosampler, by Gerstel (1 mentions)
5975c msd, by Agilent Technologies (1 mentions)
Db ffap, by Agilent Technologies (1 mentions)
Gc 7890a, by Agilent Technologies (1 mentions)
Cis 4 injection system, by Gerstel (1 mentions)
Ase 300, by Thermo Fisher Scientific (1 mentions)
Bio beads s x3, by Bio-Rad (1 mentions)
Hp6890n, by Agilent Technologies (1 mentions)
Agilent 6890a, by Agilent Technologies (1 mentions)
Agilent 5975b, by Agilent Technologies (1 mentions)
Agilent 6890n, by Agilent Technologies (1 mentions)
5973 inert mass selective detector, by Agilent Technologies (1 mentions)
7890 gas chromatography system, by Agilent Technologies (1 mentions)
Agilent 7693a autosampler, by Agilent Technologies (1 mentions)
5975c mass spectrometer, by Agilent Technologies (1 mentions)
13 protocols using msd chemstation e 02
1
Gas Chromatography-Mass Spectrometry Data Analysis
2
Thermal Desorption-GC-MS Analysis of MAT
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All sampled MAT are analyzed via TD-GC-MS: thermal desorption (nCx Instrumentation, Garlin, France, ‘nCx-TD’ thermodesorber prototype) coupled to gas chromatography (Agilent 6890A GC) and mass spectrometry detection with quadrupole mass filter (Agilent 5973Network Mass Selective Detector) programmed as in Table 4 using the MSD ChemStation E.02.02.1431 software (Agilent) and the NIST Mass Spectral Search Program version 2.0 d, 2005. Each MAT is placed in the thermodesorber in the reverse direction as compared to the gas sampling direction. The nCx-TD prototype was presented in previous work38 (link) and the chromatographic peak resolutions, limits of detection and repeatabilities obtained with this TD-GC-MS analytical chain have also been presented in (ref. 38 (link)). Note the 200 °C temperature programmed in the nCx-TD corresponds to an effective desorption temperature of 300 °C inside adsorbent tubes. The MAT desorption temperature is 300 °C since desorbing MAT at 330 °C (desorption temperature of CpX, Table 1 ) would induce thermal degradation of TA (desorption temperature 300 °C) with associated injection of its thermal degradation products in the GC-MS and falsification of the analytical results as well as irreversible TA damage.
3
Volatile Profiling of 'Sable' Berries
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Volatiles from mature berries of ‘Sable’ (51 and 70 d in GA, CPPU, and GA + CPPU after treatment) were extracted and analyzed according to the procedure described26 (link). Volatiles were extracted from 2 g of frozen powder in three replicates. Volatile compounds were analyzed using MSD Chemstation E.02.00.493, and their MS description was based on the NIST library, Version 05 (Agilent Technologies, USA). Volatile compounds were identified based on the Retention Index (RI) and mass spectra, specific compounds were also identified by authentic standards as described previously27 (link).
4
CCC Fraction Comparative Analysis
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For the selection of the most suitable CCC fraction used in further enrichment and cleanup steps, averaged GC/MS chromatograms of CCC fractions 25–37 (or less fractions) were created by exporting the data points (148 data points per minute) of the thirteen GC/MS chromatograms to Microsoft Excel 2019 (Microsoft, Redmond, WA, USA). The abundance data (y axis parameter) of each chromatogram was first normalized with the IS (14:0-EE) to level out run-to-run variations. Specifically, the area of the IS was determined in each fraction using MSD ChemStation E. 02.00.493 (Agilent, Waldbronn, Germany), and a correction factor CF1 was calculated for each fraction ( with as the peak area of IS in the ith CCC fraction and as the mean of the peak area of IS in all selected samples). In the next step, all data points (y axis value) from each fraction were multiplied with its determined CF1 and its dilution factor (DF). Then, the corrected abundance data points of the thirteen chromatograms were added for each retention time data point (x value). Afterwards, the sum was divided by the mean dilution factor ( ) of the thirteen fractions, and the final y axis values were plotted against the retention time (x axis value).
5
GC-MS Analysis of Eluting Compounds
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The characteristic mass spectra (EI, CI) of eluting compounds were obtained on an Agilent MSD quadrupole system (GC 7890A and MSD 5975C, Agilent Technologies, Waldbronn, Germany) equipped with a GERSTEL CIS 4 injection system and GERSTEL MPS 2 autosampler (GERSTEL, Duisburg, Germany). The software used to record the mass spectra and perform the data analysis was MSD ChemStation E.02.00.493 (Agilent Technologies). DB-FFAP and DB-5 (30 m × 0.25 mm, film thickness 0.25 µm, Agilent J&W Scientific, Santa Clara, USA) were used in the GC. An uncoated, deactivated fused silica capillary was used as a pre-column (2–3 m × 0.53 mm) and changed regularly to avoid accumulation of impurities. Helium was used as carrier gas and the total flow of the system was 1.0 mL/min, which was transferred into the MS using an uncoated, deactivated fused silica capillary (0.3–0.6 m × 0.25 mm) transfer line. EI mass spectra were generated in full scan mode (m/z 30–350) at 70 eV. The GC oven was held at 40 °C for 7 min, then raised to 240 °C and 250 °C for FFAP and DB-5, respectively, at a rate of 8 °C/min and held for 7 min.
6
Automated Extraction and Analysis of PAHs
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A pressurised liquid extractor ASE 300 (Dionex, Sunnyvale, CA, USA) was used for the extraction of the samples. An automated gel permeation chromatography (GPC) system of LCTech (Dorfen, Germany) equipped with a GCP column (25 mm id, 320 mm length) was filled with 50 g Bio-Beads S-X3 from Bio-Rad Laboratories (Hercules, CA, USA). A FW-20 UV detector (LCTech) operated at 254 nm and an automated concentrator CPC 2000-II Vacuumbrand (Wertheim, Germany) was used for the first step of the sample purification. Samples were evaporated after PLE on a Turbo Vap® workstation (Zymark, Hopkinton, MA, USA), respectively, after SPE on a Techne Sample Concentrator Dri-Block® DB-3D (Bibby Scientific, Staffordshire, UK).
A gas chromatograph (GC) HP 6890N (Agilent Technologies, Santa Clara, CA, USA) with programmable temperature vaporisation (PTV) injection port (septumless head) equipped with a J&W Select PAH GC column (15 m × 150 μm × 0.10 μm; Agilent Technologies) was used for the analysis of the target PAHs. The GC was coupled to an Agilent 5975B single quadrupole mass spectrometer (Agilent Technologies) operated in electron ionisation (EI) mode at 70 eV. Injection was carried out using an automated GC PAL injection system (CTC Analytics, Zwingen, Switzerland). Acquired data were evaluated by MSD ChemStation E.02.00.493 (Agilent Technologies).
A gas chromatograph (GC) HP 6890N (Agilent Technologies, Santa Clara, CA, USA) with programmable temperature vaporisation (PTV) injection port (septumless head) equipped with a J&W Select PAH GC column (15 m × 150 μm × 0.10 μm; Agilent Technologies) was used for the analysis of the target PAHs. The GC was coupled to an Agilent 5975B single quadrupole mass spectrometer (Agilent Technologies) operated in electron ionisation (EI) mode at 70 eV. Injection was carried out using an automated GC PAL injection system (CTC Analytics, Zwingen, Switzerland). Acquired data were evaluated by MSD ChemStation E.02.00.493 (Agilent Technologies).
7
Quantification of Short-Chain Fatty Acids
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Short-chain fatty acids (SCFAs) were determined in colonic-fermented digests of BSG (FBSG) and EBSG (FEBSG). Fecal inoculum SCFAs were also determined to establish the baseline. Four hundred µL of samples or standards were acidified with 200 µL of phosphoric acid (0.5%). One hundred µL of methyl valeric (8092 µM) was added as an internal standard and was extracted with 1000 µL of n-butanol. Identification and quantification of SCFAs was performed using a gas chromatograph (Agilent 6890A, Santa Clara, CA, USA) equipped with a flame ionization detector (260 °C), an automatic injector (G2613A, Santa Clara, CA, USA) and a DB-WAXtr column (60 m × 0.325 mm × 0.25 μm) (Agilent Technologies, Santa Clara, CA, USA). Two µL of samples or standards were injected using a splitless method at 250 °C. The carrier gas used was helium at a constant flow rate (1.5 mL/min). The initial column temperature was 50 °C held for 2 min, increased to 150 °C at a rate of 15 °C/min, to 200 °C at 5 °C/min and then increased to 240 °C at a rate of 15 °C/min and kept for 20 min. The control software used was MSD Chemstation E.02.00.493 Agilent (Santa Clara, CA, USA). Analyses were performed in triplicate.
8
Quantification of Fatty Acid Methyl Esters
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FAMEs were quantified in accordance with Tsogtbaatar et al. (2015) (link) using an Agilent 6890N gas chromatograph (Agilent Technologies, Santa Clara, CA) coupled to a Agilent 5975B mass selective detector. An Omegawax 250 capillary column (30 m × 0.25 mm × 0.25 μm; MilliporeSigma, Burlington, MA) was used to separate FAMEs at a constant flow rate of 1.4 ml min−1 using helium as the carrier gas. The initial temperature was 120°C and held for 30 s, followed by an increase to 245°C for the remaining 9.5 min at a rate of 100°C min−1. The injection temperature was set at 225°C, with the injection mode set to a split ratio of 10:1. Mass spectra were acquired using electron impact ionization in positive ion mode, with ion source and interface set to 240 and 150°C, respectively. Acquisition and integration of GC–MS data was carried out via MSD ChemStation E.02.02.1431 (Agilent Technologies, Santa Clara, CA).
9
GC-MS Analysis of Volatile Compounds
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The analysis of volatiles was performed by 6890 N gas chromatography and mass spectrometry (GC-MS), networked to a 59,73 Inert Mass Selective Detector (Agilent Technologies; Santa Clara, CA, USA). The analytical conditions were as follows: stationary phase HP-5MS J&W silica capillary column (30 m × 0.25 mm i.d. x 0.25 μm thickness film; 5%-phenyl-95% methylpolysiloxane); helium carried gas at a constant flow of 1 mL·min−1; transfer line was maintained at 220°C. Initial temperature (40°C) was maintained for 1 min, Ramp 1 from 5°C min−1 up to 200°C for 1 min−1, and Ramp 2 from 15°C min−1 up to 250°C for 3 min. The electron impact mode with ionization energy of 70 eV (source temperature 225°C) was used for detection by the mass spectrometer, and the acquisition was performed in scan mode (mass range m/z 35–350 amu). MSD ChemStation E.02.02.1431 (Agilent Technologies) was used to perform chromatograms and mass spectra. Fiber cleaning between samples was 5 min at 250°C.
10
GC-MS Metabolite Quantification
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