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17 protocols using 3200 q trap lc ms ms system

1

Biochemical Assays for Neurotransmitter Metabolites

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For LPO, MDA, GSH, and GSSG assay, SN-VTA or Hip tissue block was weighed and homogenized with 10 times (w/v) ice-cold 0.1 M phosphate buffer, PH 7.4. The homogenates were used to assess LPO, MDA, GSH, and GSSG spectrophotometrically using detection kits following the manufacturer's instruction (Nanjing Jiancheng Bioengineering Institute, China).
For dopamine (DA) and metabolites assay, CPu or Hip tissue block was weighed and homogenized in 80% acetonitrile containing 0.1% formic acid (5 μL/mg). The homogenates were centrifuged at 14,000 rpm for 10 min at 4°C. The supernatants were collected and stored at −80°C. DA, 3,4-dihydroxyphenylacetic acid (DOPAC), and homovanillic acid (HVA) were determined by LC-MS/MS. The LC separation was performed on Agilent 1200 LC system (Agilent, Santa Clara, USA) using a Synergi Fusion-RP C18 column (50 mm × 3.0 mm, 4 μm) provided by Phenomenex. MS/MS detection was carried out using a 3200 QTRAP™ LC-MS/MS System (Applied Biosystems, Foster City, CA, USA). The multiple-reaction monitoring mode was used for the quantification. The principal validation parameters of the LC-MS/MS were set up as shown in Table 1, based on the previous study [33 (link)].
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2

Isolation and Characterization of Bioactive Compounds

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For column chromatography, silica gel G60-230 (Merck, Germany) and Sephadex LH-20 (Sigma–Aldrich, USA) were used. Analytical thin layer chromatography (TLC) was performed on a pre-coated silica gel 60 GF254 (Merck or Machery-Nagel, Germany). The 1D and 2D NMR spectra were performed on Bruker-400 AscendTM spectrometer using CDCl3 or dimethyl sulfoxide deuterated (DMSO-d6) as solvents. The electrospray mass spectrometry (ESMS) experiments were conducted with the 3200 Q-trap LC/MS/MS system (Applied Biosystems, Foster City, CA, USA) Analyst version 1.4.1 software (MDS Sciex; Toronto, CA, USA).
The TLC chromatogram of the obtained EtOAc extract [CH2Cl2–MeOH (95: 5 v/v)] revealed the presence of three major spots on visualization with 10% H2SO4 spray reagent and heating at 110°C for 1 min. The first spot (Rf 0.65) had no response both under UV254 and under UV366 lights; on visualization, however, it gave a pale orange color. The other two spots (Rf 0.25 and 0.39) quenched UV254 light and gave a brown color.
The EtOAc extract (700 mg) was applied to a silica gel chromatographic column (35 g), packed in CH2Cl2 100% and eluted with CH2Cl2–MeOH mixtures with different polarities to afford compounds 1 (Rf 0.65, 18 mg), 2 (Rf 0.39, 7 mg), and 3 (Rf 0.25, 10 mg). A detailed isolation procedure is presented in Supplementary Materials.
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3

Quantitative Proteomic Analysis of Myotubes

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Myotubes were rinsed twice using PBS then harvested and dissolved in water with methanol (1:1, vol/vol) at 4 °C for 30 min, followed by centrifuging at 10,000 × g for 10 min. The resulting supernatant was filtered through a glass wool column and stored at −80 °C until further analysis. After centrifuging to separate the soluble from insoluble material, 40 μL of the supernatant was labeled with iTRAQ reagents using an AA 45/32 kit (Applied Biosystems, Life Technology, Forrest City, CA, USA), according to the manufacturer's instructions. The supernatant was then analyzed using an Applied Biosystems 3200 Q TRAP LC/MS/MS system equipped with a RP-C18-column (150-mm length, 4.6-mm diameter, 5-μm particle size).
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4

Spectroscopic Analysis of Test Compounds

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Purity and stability of test compounds were checked by spectroscopic techniques. 1H and 13C NMR spectra were recorded at 400 and 100 MHz, respectively, in appropriate deuterated NMR solvents, using TMS as an internal standard, on a JEOL Eclipse ECS-400 NMR spectrometer (Peabody, MA, USA). The ESI-MS experiments were conducted using a 3200 Q-trap LC/MS/MS system (Applied Biosystems, Foster City, CA, USA) using Analyst version 1.4.1 software (MDS SCIEX, Foster City, CA, USA).
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5

Plasma Protein Precipitation for LC-MS/MS

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Plasma samples were prepared for analysis by the protein precipitation method. An aliquot of 15 µL from each plasma sample was transferred to a PCR tube (Axygen, Union City, CA, USA). Four volumes of acetonitrile containing the analytical internal standard (IS) 4-methylumbelliferone were added and the resulting mixture was vortexed for 10 min on a Multi-Tube vortexer (VWR International, West Chester, PA, USA), and sonicated for 30 min at room temperature. The tube was centrifuged at 12,000× g for 10 min and the supernatant was analyzed for the test substance. Sample analysis was performed by 3200 Q TRAP LC-MS/MS system (Applied Biosystems, Concord, ON, Canada) in a negative MRM mode. The analytical methods are described below.
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6

Muscle and Serum Pretreatment for Amino Acid Analysis

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About 100 mg samples of longissimus thoracis muscle were dissolved in 50% methanol solution at 4°C for 30 min and centrifuged at 10, 000 × g for 10 min, then the supernatant was filtered through glass wool for further analysis (Li et al., 2015 (link)). Serum for free amino acid analysis was pretreatment as previously described (Kong et al., 2009 (link)). Briefly, 1 mL of serum and 2.5 mL of 7.5% trichloracetic acid were mixed thoroughly, then centrifuged at 12, 000 × g at 4°C for 15 min and the supernatant was filtered through a 0.45 μm membrane. Then a volume of 40 μL supernatant for each samples were labeled with iTRAQ reagents (AA 45/32 kit; Applied Biosystems) as recommended by the manufacturer, and analyzed on an Applied Biosystems 3200 Q TRAP LC/MS/MS system equipped with a RP-C18 column.
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7

HPLC-MS/MS Analysis of Compounds

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HPLC analysis was conducted using a 1260 series HPLC system (Agilent Technologies, Inc.) with a multiple wavelength detector set at 254, 280, 320 or 360 nm. A Prontosil C18 column (length, 250 mm; inner diameter, 4.6 mm; particle size, 5 µm; Phenomenex Co., Ltd.); Bischoff Chromatography) set at 30°C was used. The binary mobile phase system consisted of 0.1% formic acid in water (solvent A) and 0.1% formic acid in acetonitrile (solvent B). The gradient conditions were 0–10 min at 10% B, 10–60 min at 10–40% B, 60–70 min at 40–50% B, 70–80 min at 50–10% B and 80–90 min at 10% B. The flow rate was maintained at 1 ml/min and a sample injection volume of 10 µl was used in each experiment. The electrospray ionization MS/MS analysis was conducted using a 3200 QTrap LC/MS/MS system (Applied Biosystems, Fortser, CA, USA) operated in negative ion mode (spray voltage set at −4.5 kV) and nitrogen at a pressure of 45 psi was used as nebulizing agent and drying gas was supplied. The mass spectra were recorded in the range of m/z 100–1000. The obtained data were analyzed using BioAnalystTM software (version 1.4.2; SCIEX).
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8

Measuring P-glycoprotein Activity in hIOs

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To determine P-glycoprotein transporter activity, at least 20 hIOs per group were used in triplicate. hIOs were placed into 4-well plates, washed three times with Hank’s balanced salt solution (HBSS with calcium and magnesium, pH = 7.4; Invitrogen) containing 25 mM HEPES and incubated at 37 °C for 30 min. The P-gp substrate paclitaxel, in DMSO (10 μM, Sigma-Aldrich), was added to hIO cultures and incubated for 2 h on a shaker at 50 r.p.m. in the presence or absence of verapamil, a P-gp inhibitor, in phosphate-buffered saline (PBS; 50 μM, Sigma-Aldrich). After incubation, hIOs were washed three times with HBSS and ruptured with an ultrasonic cell disruptor. The homogenate was centrifuged at 13,000×g for 10 min at 4 °C, and the resulting supernatant was collected for analysis. The concentration of paclitaxel in each sample was quantitated by an LC-ESI/MS/MS analysis using a 3200 QTRAP LC-MS/MS system (Applied Biosystems, Foster City, CA, USA) equipped with a Turbo VTM Ion Spray source and an Agilent 1200 series HPLC system (Agilent Technologies).
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9

LC-MS/MS Quantification of Neurotransmitters

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Tissue block containing CPu was weighed and homogenized in 80% acetonitrile containing 0.1% formic acid (5 μL) and then processed following a previous study [24 (link)]. The homogenates were centrifuged at 14,000g for 10 min at 4°C. The supernatants were collected and used to determine dopamine (DA), 3,4-dihydroxyphenylacetic acid (DOPAC), and homovanillic acid (HVA) levels as previously described [24 (link)]. LC separation was performed on an Agilent 1200 LC system (Agilent, Santa Clara, USA) using a Synergi Fusion-RP C18 column (50 mm × 3.0 mm, 4 μm) provided by Phenomenex. MS/MS detection was carried out using a 3200 QTRAP™ LC-MS/MS System (Applied Biosystems, Foster City, CA, USA). The multiple-reaction monitoring mode was used for quantification. The principal validation parameters of the LC-MS/MS are described in a previous study [24 (link)].
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10

Plasma Sample Preparation for LC-MS/MS

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Plasma samples were prepared for analysis by the protein precipitation method [28 (link)]. A simple protein precipitation is to remove proteins in plasma samples with organic solvents. Briefly, 15 µL of each plasma sample was transferred to a PCR tube (Axygen, Union City, CA, USA). Four volumes of acetonitrile containing the analytical internal standard, 4-methylumbelliferone, were added, and the resulting mixture was vortexed for 10 min on a multi-tube vortexer (VWR International, Radnor, PA, USA). The samples were sonicated for 30 min at room temperature. The tubes were centrifuged at 12,000× g for 10 min, and the supernatant was analyzed for the test substance. Sample analysis was performed with a 3200 Q TRAP LC/MS/MS system (Applied Biosystems, Foster City, CA, USA) in negative MRM mode. The analytical methods are described in the following sections.
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