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17 protocols using g2 xs qtof

1

Peach Fruit Metabolic Analysis

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The obtained data manifested that respiration burst on D4 and D8, meanwhile ethylene production reached the peak on D8. We speculate that D4 and D8 is crucial time of peach fruit metabolism. Therefore, we choose peach materials of these two time point for further LC/MS analysis. The phenolic compounds extraction and LC/MS analysis were conducted followed by our previous report [22 (link)]. Briefly, approximately 10 g of peach tissue was ground with liquid nitrogen, then accurately weigh 5 g of ground sample and homogenized in 100 mL of 95% acidic (0.1 M HCl) methanol. After 4 h of extraction, the mixture was centrifuged at 10,000× g for 20 min. The supernatant was collected and evaporated to dryness. For LC/MS analysis, the residue was redissolved in 6 mL of methanol and filtered through a 0.22 μL membrane (Millipore) filter. LC/MS analysis system (G2-XS QTof, Waters) and liquid chromatography (UPLC) column (2.1 × 100 mm × 1.7 μm) was used in this study according to our previous research [22 (link)].
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2

Metabolomics Data Analysis Protocol

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Whole-scale metabolites were detected via mass spectrometer Xevo, G2-XS QTOF (Waters, UK) and identified based on the database KEGG. Software Progenesis QI (version 2.2) (Waters, UK) and R package metaX were used for statistical analysis of mass spectrometry data [54 (link)]. Variable Importance in the Projection (VIP) of the first two principal components in the multivariable PLS-DA model was used to screen differential metabolites by combining fold-change and q-value values. The VIP-score is a quantitative measure that indicates the strength and explanatory ability of each metabolite on the classification discrimination of samples in each group. Screening conditions are VIP≥1, fold-change ≥1.2 or ≤0.8333 and q-value<0.05. Metabolites satisfy the three conditions were identified as differential metabolites.
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3

Melanin and Bikaverin Production in F. verticillioides

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Melanin pigments from each F. verticillioides mutant were extracted using a previously reported method [28 ]. The extracted pigments and synthetic melanin (Sigma-Aldrich, MO, USA) were then analyzed by using Fourier transform infrared (FT-IR) spectroscopy (Thermo Fisher Scientific, Warsaw, Poland) following the protocols described by Drewnowska et al [29 (link)]. To detect the production of bikaverin, each F. verticillioides strain was cultured at 25°C in PDB medium for 10 d. A 100 mL culture of each strain was extracted three times with ethyl acetate acidified with 1 mL of 25% HCl [30 (link)]. The samples were then analyzed on an HPLC–MS system (G2-XS QTof, Waters) using a protocol previously described [30 (link)].
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4

Optimized UPLC-QTOF-MS Metabolomic Analysis

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Chromatographic separation was performed by a Waters ACQUITY I-Class UPLC system equipped with an ACQUITY UPLC HSS T3 column (2.1 × 100 mm, 1.8 μm, Waters). Parameters were set as follows: column temperature 40°C; flow rate of 0.4 ml/min; injection volume of 4 μl; mobile phase A was H2O containing 0.1% FA and B was ACN. The gradient elution condition was referenced by previous study (He et al., 2021 (link)): 0–1.00 min, 0% B; 1.01–4.00 min, 0–35% B; 4.01–15.50 min, 35–95% B; 15.51–18.00 min, maintaining at 95% B; 18.01–23.00 min, back to 0% B. MS detection and data acquisition were performed by a Q-TOF MS (Waters, Xevo, G2-XS QTof) in both positive and negative ion modes. MS parameters were set as follows: m/z range at 50–700 Da; capillary voltage at + 3.0 kV or −2.5 kV for positive or negative ion mode respectively; sampling cone at 40 V; source temperature at 110°C; desolvation temperature at 450°C; cone gas at 50 L/h, desolvation gas at 600 L/h. MassLynx (version 4.1, Waters) was used for data acquisition.
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5

UPLC-QTOF Analysis of RSV Identification

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The screening and identification of RSV was performed with a Waters Acquity I Class UPLC system with the Xevo G2-XS QTof equipped with an ACQUITY UPLC BEH C18 column (Water, Milford, CT, USA) (1.7 µm, 2.1 × 50 mm i.d.). The chromatographic conditions included 0.01% formic acid in water as solvent A, and 100% acetonitrile as solvent B. The established elution gradient was 1% B (1 min), 1 to 20% B (10 min), 20 to 25% B (10 min), 35 to 50% B (5 min), and a column rebalancing flow rate of 0.25 mL min−1. The analysis was carried out with an electrospray ionization (ESI) source, within a mass range of m/z 100 to 1200 Da, negative mode with a capillary voltage of 0.5 kV, cone gas flow of 30 L h−1, desolvation gas flow of 900 L h−1, source temperature of 140 °C, and a desolvation temperature of 450 °C, with a sample cone and source offset of 40 and 80, respectively. MS/MS experiments were carried out in conjunction with collision energy (CE) ramps: low CE off and high CE from 20 to 30 eV. All data were processed using UNIFI TM v1.8 software under the Mass Lynx NT 4.1 (Waters, Milford, USA) operating interface.
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6

Headspace Analysis of Flavored Dispersions

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The headspace concentrations were measured at equilibrium as independent triplicates with a G2-XS Q-TOF high-definition mass spectrometer (XEVO, Waters) coupled to a patented Venturi interface [16] . An automated PAL system sampled 5 mL of headspace air with a 5 mL headspace syringe and injected this into the mass spectrometer. Mass spectra were collected in centroid mode over the range m/z 20-400 every 1 s. APCI-MS was performed in positive ionization mode with a cone voltage of 4.0 kV, source temperature of 105°C, heated sample transfer line temperature of 130°C and auxiliary gas flow of 600 Lh−1. Lock spray (on-the-fly mass calibration) was used to apply a mass correction to measured m/z values during the analysis. All the signal intensities were corrected for the background addition. The relative headspace concentration (RHC) was calculated as: RHC%=Peak areaflavored dispersionPeak areaflavor in water100%
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7

Comprehensive Characterization of Novel Materials

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Nuclear magnetic resonance (1H and 13C NMR) spectra were collected using Bruker ARX400 Nuclear Magnetic Resonance. The chemical shift was relative to tetramethylsilane as the internal standard. Resonance patterns were reported with the notation of s (singlet), d (doublet), t (triplet), q (quartet), and m (multiplet). High-resolution mass spectrum was measured on Waters G2-XS QTOF in a positive ion mode. High-performance liquid chromatogram spectrum was recorded on Agilent 1290II. UV–Visible absorption spectra were obtained using Perkin Elmer Lambda 35. Steady-state PL spectra and excitation spectra were measured using Hitachi F-4600. The delayed PL spectra and lifetimes were measured on an Edinburgh FLSP 980 spectrophotometer equipped with a xenon arc lamp (Xe 900) and microsecond flash-lamp (μF900), respectively. The PLQYs were measured on an Edinburgh FLSP 980 spectrophotometer equipped with an integrating sphere. The variable temperature emission spectra were measured on OLYMPUS BX53M with the constant excitation wavelength of 360 nm under nitrogen atmosphere. Single-crystal x-ray diffraction experiments were carried out using a Bruker D8 QUEST x-ray single crystal diffractometer. Luminous patterns of information encryption and display under different UV excitation wavelengths were taken by cell phone in professional mode.
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8

Untargeted Acyl-CoA Metabolomics Analysis

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Samples were extracted using methanol:water:chloroform as previously described with slight modifications9 (link). Briefly, untargeted extractions were reconstituted with 400 µl tributylamine with no dilutions for analysis. Analysis was performed using a Xevo G2-XS QTOF attached to a Waters UPLC (Waters, Milford, MA) with negative-mode electrospray ionization run in MSE continuum mode. LC phases, gradient rates, and columns were used as previously published9 (link). For untargeted acyl-CoA analysis, MSE continuum data was processed with Progenesis QI (Waters) to align features, peaks, deconvolute, and annotate metabolite peaks. Metabolite annotations were scored based on a mass error < 12 ppm to Human metabolome Database entries85 (link), isotopic distribution similarity, and theoretical fragmentation comparisons to MSE high-energy mass spectra using the MetFrag option with each metric contributing a max of 20 points towards a max score of 60. Raw signals for each compound abundances were normalized to a correction factor calculated using a median and mean absolute deviation approach by Progenesis QI. Significance was determined by a one-way ANOVA adjusted for multiple comparisons with a Dunnett’s post-hoc test.
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9

Intact LC-MS Analysis of Biomolecules

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For intact LC-MS analyses, 25 μl of each sample was injected. LC separation was carried out using a Waters ACQUITY UPLC I-Class system including a sample manager with flow-through needle. The LC column used was a Thermo Scientific, MabPac RP (1 mm × 50 mm, 4 μm, 1500 Å) with a 0.25 ml/min flow rate. LC buffer A consisted of 0.1% formic acid and 0.02% TFA in water, and LC buffer B consisted of acetonitrile. The sample was loaded directly on the column by the following LC gradient with a total run time of 5 min at 80 • C. The gradient was as follows: hold 80% A for 2 min, flow to 20% A in 15 s, hold 20% A for 1.25 min, flow to 80% A in 30 s and hold 80% A for 1 min.
The MS instrument used for detection was a Waters G2-XS Q-TOF operating in TOF MS positive ESI mode with a Z-Spray electrospray source. The following instrument settings were used: source temperature at 150 • C, desolvation temperature at 500 • C, capillary voltage at 2.5 kV, sampling cone at 150 V, source offset at 150 V, cone gas at 0 l/h, desolvation gas at 700 l/h, analyzer mode set to sensitivity, dynamic range set to normal, sensitivity set to normal, detection range from 2500 to 4000 m/z, data type set to continuum, scan time at 0.4 s and trap and transfer collision energies were off.
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10

Enzymatic Synthesis of Anthocyanin Derivatives

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The reaction was performed in 200 mM potassium phosphate buffer (pH 8.0) containing 2.5 mM vinyl acetate, 0.5 mM cyanidin-3-O-glucoside, and 0.5 mg/mL purified enzymes. The reactions were incubated at 40 °C for 10 min. An ultrahigh-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS) system (G2-XS QTof, Waters Milford MA USA) was used to analyze the molecular mass of the product. Three microliters of the solution was injected into the UPLC column (2.1 × 100 mm ACQUITY UPLC BEH C18 column containing 1.7 μm particles) with a flow rate of 0.3 mL/min. Mobile phase A was water containing 0.5% formic acid, while mobile phase B was acetonitrile. The gradient program of the mobile phase was as follows: 0–1 min, 5% B; 1–5 min, 5–90% B; 5–6 min, 90% B; 6–6.1 min, 90–5% B; 6.1–8 min, 5% B. UPLC-ESI-MS/MS was performed with a collision energy of 20 eV employing an electrospray source in positive ion mode with a selected mass range of 50–600 m/z. The ionization parameters included the following: capillary voltage of 3.0 kV, cone voltage of 40 V, source temperature of 550 °C, and dissolution gas temperature of 400 °C. Data acquisition and processing were performed employing Masslynx 4.1 (Waters, Milford, MA, USA) software package.
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