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Lc qtof ms

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The LC-QTOF-MS is a liquid chromatography-quadrupole time-of-flight mass spectrometry system designed for high-resolution, accurate-mass analysis. It combines liquid chromatography for sample separation and quadrupole time-of-flight mass spectrometry for precise mass measurement and structural identification of analytes.

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16 protocols using lc qtof ms

1

Oxidative Regulation of Peroxiredoxin and PTP1B

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Recombinant hPrx2 (12 μM) was incubated with or without 100 μM Na2S2 for 10 min and then 1 mM H2O2 for 10 min at 25°C. Samples were desalted with PD SpinTrap G-25 desalting column and then treated with or without TrxR1 (250 nM), TRP14 (4 μM), and NADPH (1 mM) for 1 hour at 37°C. Samples were alkylated with 1 mM iodoacetamide for 30 min, followed by digestion with Trypsin Gold at 37°C for 10 hours. The digested samples were subjected to LC-Q-TOF MS (Agilent Technologies).
Recombinant human PTP1B (hPTP1B) containing 10 mM DTT was desalted by PD SpinTrap G-25 desalting column to remove DTT. Recombinant DTT-free hPTP1B (20 μM) was incubated with or without 50 μM Na2S2 for 10 min and then 100 μM H2O2 for 10 min at 25°C. Samples were treated with or without TrxR1 (250 nM), Trx1 (15 μM), TRP14 (15 μM), TRP32 (15 μM), and NADPH (1 mM) for 30 or 60 min at 37°C. Samples were alkylated with 1 mM iodoacetamide for 30 min, followed by digestion with Trypsin Gold at 37°C for 10 hours. The digested samples were subjected to LC-Q-TOF MS (Agilent Technologies), and the data were narrowed to the active-site peptide by Mascot search.
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2

Complementation Assay for tRNA Methyltransferase

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For the complementation assay, expression plasmids with an inducible promotor (T5) for E. coli were constructed by inserting trmR gene between BamHI and SmaI sites on pQE30a. The pQE30a-trmR was used to transform ΔcmoB cell; empty pQE30a plasmids were used to transform ΔcmoB cell as a control. Transformed cells were typically grown in 50 ml LB media at 37°C, which were harvested by centrifugation at 3214 g for 20 min. Total RNA was extracted by treating with one unit of P1 nuclease at 65°C for 30 min and one unit of Antarctic Phosphatase at 37°C for 1 h. The nucleoside samples were analysed using LC-MS (Agilent C18 column, 100 Å, 3.5 μm, 4.6 mm × 150 mm coupled to a 6545XT AdvancedBio Agilent LC-QTOF-MS) in positive mode. A linear gradient of 5 to 25% acetonitrile and 0.1% FA was used over 15 min.
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3

Plasma and Urine Metabolite Extraction and Analysis

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An aliquot of 200 µL plasma or 100 µL urine sample from each patient was separately transferred into the Eppendorf tubes. Before extraction of the metabolites, the urine samples were treated with 100 µL of urease enzyme at 37°C for 30 min.
The plasma and urine metabolites were extracted using methanol:water (9:1, v/v) mixture containing 1 µg/mL myristic acid as internal standard. Then, the extracts were centrifuged at 15,000 rpm for 5 min (at +4 °C) and 200 µL aliquots of each sample supernatant were transferred to three Eppendorf tubes and completely dried by a vacuum centrifuge for GC-MS, LC-qTOF-MS, and LC-MS/MS-based metabolomics analysis.
The extracted samples were analyzed using a gas chromatography-mass spectrometry system (GC-MS-QP-2010 Ultra system, Shimadzu, Kyoto, Japan) and LC-qTOF-MS (Agilent, California, USA). The representative chromatograms of GC-MS and LC-qTOF-MS based metabolomics analysis for plasma and urine samples are given in Figure S2.2 and Figure S2.3, respectively. The detailed protocols for GC-MS and LC-qTOF-MS analysis are given in Supplementary Materials File S2 (Sections S1.1.1–S1.1.4).
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4

Bioactive Compound Characterization by LC-QTOF-MS

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The characterization of bioactive compounds present in EECS was carried out by LC-QTOF-MS (Agilent Technologies, Santa Clara, CA, USA, Model no: 6545 QTOF).
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5

Metabolomic Analysis of FTR Samples

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For metabolome analysis, cells were lysed and metabolites were extracted from sediments in the FTRs in a methanol:chloroform mixture (1:2, v:v; -20C°) for 30 min under sonication. The metabolites in the supernatants were analysed by GC-QTOF-MS and LC-QTOF-MS (both Agilent Technologies) following Godzien, et al. 51 (link) and Kind, et al. 52 (link) with slight modifications. Volatile fatty acid concentration in FTR effluent was determined using SPME GC-MS. A HP-5MS non polar column (Agilent Technologies, Mount Waverley, Australia) of dimensions 30 m x 0.25 mm ID x 0.25 μm film thickness was used for separation in conjunction with splitless injection mode and H2 carrier gas. The method was optimized by exposing Carboxen/Polydimethylsiloxane SPME fibre to 10 mL of sample seawater headspace at 50°C for 60 min with 2g NaCl and acid addition prior to injection.
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6

Characterization of Phytochemicals in Fr. 3

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The characterization of bioactive phytochemicals present in the Fr. 3 was investigated using LC-QTOF-MS (Agilent Technologies, Santa Clara, CA, United States, Model no: 6545 QTOF) (Sasidharan et al., 2022c ).
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7

HPLC-Based AFB1 Degradation Assay

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The AFB1 degradation ability was confirmed using an HPLC system with an ultraviolet (UV) diode array detector at 360 nm; the specific detection conditions are listed in Table 1. LC-Q-TOF/MS (Agilent) was applied to analyze the AFB1 degradation products. All samples were filtered through a sterile 0.22 μM pore filter (Agilent) before testing.
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8

Enzymatic Glucosylation of Glycyrrhetinic Acid

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Enzyme reactions were performed in 100 µl of buffer (50 mM Tris-HCl pH 8.0) containing 50 µg purified protein, 1 mM UDP-Glc (electronic supplementary material, figure S1, Yuanye Biotech, Shanghai, China) and 100 µM glycyrrhetinic acid (Sigma-Aldrich, Shanghai, China). After 6 h of incubation at 37°C, the reactions were stopped by the addition of 100 µl methanol. The conversion rates were calculated by HPLC peak area (Aproduct/Asubstrate + Aproduct × 100%). The supernatants obtained by centrifugation (13 500 r.p.m. for 5 min) were analysed by Agilent 1260 HPLC (Agilent Technologies, Santa Clara, CA, USA) and LC-QTOF-MS (Agilent Technologies, Santa Clara, CA, USA), and internal standards (GA-3-O-monoglucose and GA-30-O-monoglucose) were supplied by Prof. Ye Min's laboratory (State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University).
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9

Identification of Phenolic and Flavonoid Compounds in BsE Fraction by LC-QTOF MS

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Phenolic and flavonoid compounds in BsE fraction were identified by liquid chromatograph–quadrupole time-of-flight mass spectrometer (LC-QTOF MS, Agilent Technology, Santa Clara, CA, USA). The chromatographic separation was run on a Zorbax Eclipse Plus C18 column (150 × 2.1 mm, particle size 1.8 µm) at 25 °C. The injection volume was 2 µL, and the flow rate was kept at 0.2 mL/min. Elution was carried out by using two mobile phases: eluent A (0.1% formic acid in water) and eluent B (acetonitrile). The gradient program was as follows: 5% B (3 min), 23% B (22 min), 35% B (10 min), and 5% B (10 min).
MS was operated with Dual AJS source, and the instrument parameters were as follows: gas temperature, 325 °C; gas flow, 13 L/min; nebulizer, 35 psi; sheath gas temperature, 275 °C; sheath gas flow, 12 L/min; VCap, 4000 V; nozzle, 2000 V; fragmentor, 175 V; skimmer, 65 V; and octopole RF peak, 750. The scan range of the ion trap was 100–1500 m/z for MS and 50–1500 m/z for MS/MS. The mass spectra were recorded in both negative and positive ion modes. The reference mass ions purine at 112.9856 (for negative mode) and 121.0508 (for positive mode), as well as the HP921 at 1033.9881 (for negative mode) and 922.0098 (for negative mode), were used for continuously correcting any mass drift. All data were analyzed by LC/MS Data Acquisition and Qualitative Analysis Workflows software.
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10

Plasma Proteomic Profiling Workflow

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Proteomic profiling in all the study groups was performed via shotgun proteomic analysis after the depletion of the 12 most abundant proteins using immuno-affinity kits from a 10 µL plasma sample. Then, the proteins were reduced and alkylated, and trypsin-based digestion was carried out to generate peptides using LC-qTOF-MS (Agilent, California, USA) analysis (Figure S2.4). The detailed protocol is given in Supplementary Materials File S2 (Section S1.1.3).
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