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18 protocols using nexera xr hplc system

1

Gel Filtration Chromatography for Molecular Mass

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Molecular mass distribution was determined using gel filtration chromatography by a Nexera XR HPLC system (Shimadzu, Tokyo, Japan) on a Superdex® Peptide PE 7.5/300 column (GE Healthcare, Uppsala, Sweden) as described by Dupas et al. (20 (link)). A volume of 50 µL from each sample, filtered through a 0.45-μm syringe filters, was injected into the column. Elution was achieved at a flow rate of 0.25 mL/min with 30% (V/V) of 0.1% (V/V) trifluoroacetic acid (TFA) in acetonitrile and 70% (V/V) of 0.1% (V/V) TFA in water during 120 min. The elution was controlled spectrophotometrically at 215 nm (Cecil CE 2041; Cecil Instruments Ltd, Cambridge, UK). The column was previously calibrated using standard proteins: cytochrome C (12 400 Da), aprotonin (6500 Da), substance P (1348 Da), glycine 6 (360 Da), glycine 3 (189 Da) and glycine (75 Da).
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2

Yeast Growth and Metabolite Analysis

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Strains in seed cultures were grown overnight to reach the late exponential phase. Then seed cultures were inoculated to 50 mL YPD medium with 10 mM CaCl2 and 0.6 mM ZnCl2 with an initial OD600 of 0.005. Samples were taken at different time points for analysis. The concentration of metabolites (glucose, ethanol, glycerol, etc.) in the culture was measured as described by Huang et al. [48 (link)]. 20μL supernatant was loaded to an Aminex HPX-87H column (Bio-Rad, USA) on a Nexera XR HPLC system (Shimadzu, Japan) and the mobile phase was 5 mM H2SO4 with a flow rate of 0.6 mL/min at 45 °C.
Intracellular ATP, NAD(H), NADP(H) and GSH were determined by using ATP assay kit (Cat No. BC0300, Solarbio, China), NAD(H) assay kit (Cat No. BC0310, Solarbio, China), NADP(H) assay kit (Cat No. BC1100, Solarbio, China) and GSH assay kit (Cat No. BC1170, Solarbio, China), respectively, according to the manufacturer’s protocols.
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3

Fractionation of Tryptic Peptides via Basic pH HPLC

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Basic pH HPLC fractionation of tryptic peptides was performed based on the protocol described by Lewandowska [59 (link)]. Separation was carried out using Nexera XR HPLC System with the PDA detector (Shimadzu, Kyoto, Japan) and Jupiter Proteo 90 Å column (4 μm, 250 × 2.6 mm, Phenomenex, Torrance, CA). Used buffers—A: 100 mM ammonium bicarbonate pH 8, and B: 100% ACN. The flow rate was 1 ml/min, and the gradient was 0–50% B. During a 2 h chromatographic run, 60 fractions of 2 ml each were manually collected. Chromatographic separation was repeated three times. All fractions from separate runs were combined at the same time points, and then they were evaporated to dryness in SpeedVac and dissolved in 100 µl of 60% ACN with the addition of 1% AA. Before LC–MS/MS measurements, samples were concentrated into 30 µl fractions ready for MS analysis.
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4

Targeted DIA-LC-MS/MS Analyses

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DIA-LC-MS/MS analyses were performed on the SCIEX QTOF 6600 mass spectrometer hyphenated to a Shimadzu Nexera XR HPLC system (Shimadzu, Kyoto, Japan) as described for the DDA-mode, with the exception that in DIA mode, the duty cycle included a single MS-scan (96 msec; m/z range 50-1000) followed by a series of product ion scans (41.2 msec each) across 28 isolation windows of m/z width 26.
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5

Human Liver Microsomal Metabolism Assay

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Microsomal incubations were performed three times in 0.1 M potassium phosphate buffer (pH 7.4) in 1.5 mL tube. NADPH-dependent metabolism was evaluated by PF-543, derivatives, or Verapamil (positive control) into pooled liver microsomes of human (HLM), dog (DLM), rat (RLM), and mouse (MLM) in the presence of NADPH regenerating system. The final mixtures contained 0.5 mg/mL HLM, 0.1 M potassium phosphate buffer (pH 7.4), and NADPH regenerating system (10 mM MgCl2, 1 mM NADPH). HLM was added and the mixture was preincubated at 37 °C in a shaking incubator at approximately 350 rpm for 5 min under Thermo mixer (Eppendorf., Hamburg, Germany). The reaction was started by adding 1 mM NADPH and was then terminated by adding 40 µL of ice-cold acetonitrile containing 10 µM chlorproamide as an internal standard at 0, 30 min. The incubation mixtures were centrifuged at 15,000× g for 5 min at 4 °C. A 2 µL of the supernatant was taken and directly injected into the LC-MS/MS system. The LC-MS/MS system is the Nexera XR HPLC system (Shimadzu Co., Kyoto, Japan) coupled to the TSQ Vantage triple quadrupole mass spectrometer equipped with Xcalibur version 1.1.1 (Thermo Fisher Scientific Inc., Waltham, MA, USA).
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6

DDA-LC-MS/MS Analysis of Compound Mixtures

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DDA-LC-MS/MS analyses were performed on a SCIEX QTOF 6600 mass spectrometer (SCIEX, Framingham, MA, USA) equipped with a DuoSpray ESI source (SCIEX, Framingham, MA, USA) hyphenated to a Shimadzu Nexera XR HPLC system (Shimadzu, Kyoto, Japan) and controlled by the SCIEX Analyst TF 1.7 software. For DDA experiments, each cycle included a 100 msec TOF-MS scan (m/z range 50-1000) followed by the acquisition of up to 20 MS/MS-spectra at an intensity threshold of 300 counts (collision energy set at 20V with a 10V spread in high sensitivity acquisition mode). The ESI source was operated with source gas 1 and 2 adjusted to a flow of 60 (arbitrary units), while the curtain gas was maintained at 25 (arbitrary units). The ion source temperature was maintained at 650 °C with a voltage of 5200 V in positive and −4500 V in negative mode. Chromatographic separation was performed using the LC-method described for the MRM-LC-MS/MS analysis; acquisitions were performed in positive and negative ionization mode.
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7

Amino Acid Quantification in Freeze-Dried FPH

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About 50 mg of freeze-dried FPH was weighed into glass tubes, 1 ml 6 M HCl was added. The glass tubes placed into a heating cupboard for 24 h, at 105 °C. Samples were diluted 50 times using distilled water before filtering through 0.22 μm.
For the derivatization, 300 μl of the sample were transferred to a glass tube, containing 600 μl 0.4 M borate buffer (pH 9). 600 μl FMOC (9-fluorenylmethoxycarbonyl chloride, 15 mM in acetonitrile) was added, mixed, and then allowed to stand at room temperature for 10 min on an orbital shaker. After amino acid derivatization with FMOC, 600 μl ADAM (12 mM in acetone:water 1:1) was added.
Amino acids were analyzed using a Shimadzu Nexera XR HPLC system, equipped with a PDA detector (Shimadzu, USA). Separation of amino acids were carried out on a Restec ARC-18 column (10 mm × 2.1 mm) at 30 °C. The mobile phase was 0.1% formic acid with 20 mM ammonium formate and 0.1% formic acid with 10 mM ammonium formate in 90:10 acetonitrile water in gradient mode, with a flowrate of 0.35 ml min−1.
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8

Pharmacokinetics of CA140 in Mice

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ICR mice (n = 3) were dosed with CA140 dissolved in DMSO/Tween-80/saline (10:5:85%) via a single intravenous administration (10 mg/kg). Blood was collected by cardiac puncture at 5 min and then centrifuged to isolate plasma. The brain was collected at 5 min and homogenized in PBS after washing with fresh PBS. The concentrations of CA140 in the plasma and brain were determined by LC-MS/MS. The LC-MS/MS system comprised a Nexera XR HPLC system (Shimadzu Co., Kyoto, Japan) coupled to a TSQ Vantage triple quadrupole mass spectrometer equipped with Xcalibur version 1.1.1 (Thermo Fisher Scientific Inc., Waltham, MA, USA).
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9

Astaxanthin Quantification via HPLC

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Acetone:methanol lipophilic extracts were analyzed via reverse-phase HPLC using a Kinetex 2.6 μm PS C18 100 Å (150 × 2.1 mm) column (Phenomenex; Torrance, CA) attached to a Shimadzu Nexera XR HPLC system. The mobile phase was a binary gradient of Solvent A (70% acetonitrile/30% water) and Solvent B (70% acetonitrile/30% isopropanol) flowing at 0.45 mL/min. Absorbance was measured between 200 and 600 nm using a Shimadzu SPD-M20A photodiode array detector. An astaxanthin commercial standard (Sigma-Aldrich) was used to identify and quantify astaxanthin in the extracts. astaxanthin eluted at a retention time of 12.6 min.
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10

HPLC-MS/MS Analysis of Phosphatidylcholines

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A Nexera XR HPLC system (Shimadzu, Tokyo, Japan) coupled to a 4500 Qtrap mass spectrometer (Sciex, Toronto, ON, Canada) equipped with a heated ESI source (V source) was used for the analysis, following Oliva et al. [47 (link)]. The different PCs were separated using an Excel 2 C18-PFP (10 cm × 2.1 mm ID) column from Advanced Chromatography Technologies (Aberdeen, UK) with 2 μm particles and safety protection. H2O with 1% acetic acid was used as mobile phase (A) and ACN as phase (B). The injection volume was set to 6 μL and the flow rate was set to 0.300 mL min−1. All analytes were detected in negative ionization with a capillary voltage of −4500, nebulizer gas (air) at 40 psi, and turbogas (nitrogen) at 40 psi and 500 °C. Data collection and processing were performed with Analyst 1.7.2 software and quantification with Multiquant 3.0 software (Sciex).
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