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6 protocols using mass spectrometry grade acetonitrile

1

Isolation and Proteomic Analysis of Valvular Interstitial Cells

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VICs were isolated from AVs removed for severe stenosis using tissue lysis with 2% collagenase (Sigma-Aldrich, St Louis, MO, USA). Protein extraction and proteolysis were performed with the methanol-chloroform method and trypsin [(Gold Grade; Promega, Wisconsin)/RapiGest procedure (Waters, Milford, MA, USA)], respectively, as previously published (18 (link)). Fifteen micrograms of protein was used per sample. The tryptic peptides were desalted using Oasis Hlb 1cc (10 mg) columns (Waters, Milford, MA, USA), and dried with a tabletop speed vacuum (SPD1010, Thermo Fisher Scientific, USA). After resuspension in 40 μl of 5% mass spectrometry grade acetonitrile (Thermo Fisher Scientific, USA) and 5% formic acid (Sigma-Aldrich, St Louis, MO, USA), the tryptic peptide samples were analyzed by liquid chromatography–mass spectrometry.
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2

Proteomic Sample Preparation Protocol

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MgT was purchased from Shanghai Yuanye Biotechnology Co., CAS number is 778571–57-6, molecular formula is C8H14MgO10, purity is more than 95%. Trypsin Golden (Promega, United States), dithiothreitol (DTT, Sigma, Germany), iodoacetamide (IAA, Sigma, Germany), ammonium bicarbonate NH4HCO3 (Sigma, Germany), urea (Sigma, Germany), pure water (China Wahaha Company), mass spectrometry grade methanol (Thermo Fisher Scientific, United States), mass spectrometry grade acetonitrile (Thermo Fisher Scientific, United States), mass spectrometry grade purified water (Thermo Fisher Scientific, United States), Tris-base (Promega, United States), thiosulfate (Sigma, Germany), thiamine (Sigma, Germany), thiophene (Promega, United States), and thiourea (Sigma, Germany) were obtained.
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3

Phenolic Profiling and Antioxidant Evaluation

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Leucine enkephalin was purchased from Waters Corporation (Milford, MA, USA). Chromatography-grade methanol, mass-spectrometry-grade acetonitrile, and formic acid were purchased from Thermo Fisher Scientific (Waltham, MA, USA). Folin & Ciocalteu phenol reagent was bought from Sigma-Aldrich, Co., Ltd. (St. Louis, MO, USA). Ferrous sulfate, ferric chloride, and analytical-grade ethyl alcohol were procured from Tianjin Xinbo Chemical Co., Ltd. (Tianjin, China). Analytical-grade anhydrous sodium carbonate (Na2CO3), aluminum chloride (AlCl3), potassium acetate, and gallic acid monohydrate (purity 99.0%) were obtained from Tianjin Yongsheng Fine Chemical Co., Ltd. (Tianjin, China). The phenolic standards such as rutin, quercetin, ferulic acid, caffeic acid, isorhamnetin, kaempferol 3-O-beta-rutinoside, p-coumaric acid, chlorogenic acid, and isoquercetin were purchased from Anpel Laboratory Technologies Inc. (Shanghai, China). Hydrochloric acid was purchased from Xi’an Chemical Reagent Factory (Xi’an, China). The 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), 1,1-diphenyl-2-picrylhydrazyl (DPPH), 2,4,6-tris (2-pyridyl)-s-triazine (TPTZ), and sodium acetate were provided by Beijing Solarbio Science & Technology Co., Ltd. (Beijing, China). Ultrapure water was purchased from Watsons Group Ltd. (Hong Kong, China).
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4

Proteomics Analysis of Mitral Valve

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A total of 27 samples were processed together for proteomics analysis. Out of those, 7 samples were not included in the final proteomic analysis due to the unavailability of the echocardiography measures and the tissue cryosections. Each piece of frozen MV was pulverized in liquid nitrogen, then sonicated in RIPA buffer (Pierce, 89900) complemented with 1% protease inhibitor cocktail. Protein precipitation was performed with chloroform:methanol (2:1) method and redissolve using a solution of urea 6M/thiourea 2M/TEAB 100 mM (pH 8). 15μg of protein were cleaved using trypsin/LysC cocktail at 37°C overnight. The peptides were desalted using Oasis HLB column (Waters, USA) and dried with a Speed Vacuum concentrator (SPD1010, Thermo Fisher Scientific, USA). After re-suspension in 40 μl of 5% mass spectrometry grade acetonitrile (Thermo Fisher Scientific, USA) and 5% formic acid (Sigma-Aldrich, USA).
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5

Purification and Analysis of Retinoids

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Kanamycin, sodium chloride, potassium chloride, Tris, Hepes, potassium phosphate, glycerol, benzonase, lysozyme, thrombin, protease inhibitor tablets, Coomasssie Brilliant Blue and atRA were purchased from Millipore-Sigma (St. Louis, MO, USA). The 4-oxo-atRA-d3 was purchased from Santa Cruz Biotechnology (Dallas, TX, USA) and 4-OH-atRA was purchased from Toronto Research Chemicals (North York, ON, Canada). Sodium hydroxide, PMSF, imidazole, Pierce BCA protein assay, DTT, EDTA, IPTG, tryptone, yeast extract, high-performance liquid chromatography (HPLC) and mass spectrometry grade acetonitrile, water, and ethyl acetate were purchased from Thermo Fisher Scientific (Waltham, MA, USA). Lipidex-5000 was purchased from Perkin Elmer Inc (Waltham, MA, USA). Mini-PROTEAN TGX protein gels were purchased from Bio-Rad (Hercules, CA, USA). NBD-stearate was purchased from Avanti Polar Lipids (Birmingham, AL, USA). Pooled human liver microsomes were purchased from Gibco (Thermo Fisher Scientific, Waltham, MA, USA). Recombinant CYP3A4 and CYP2C8 Supersomes co-expressed with cytochrome P450 reductase and cytochrome b5 were purchased from Corning (Glendale, AZ, USA). Recombinant CYP26A1 was expressed in Sf9 insect cells, as previously described [17 (link),20 (link)]. Rat P450 reductase was expressed in E. coli and purified, as previously described [33 (link)].
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6

Analytical Protocol for Kangfuxiaoyan Suppository

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Kangfuxiaoyan suppository (batch No. 20171225) was obtained from the Sunflower Pharmaceutical Group Co., Ltd. Sodium pentobarbital (batch No. 11011) was obtained from Merck. Mass spectrometry-grade acetonitrile and methanol, and HPLC-grade formic acid were obtained from Thermo Fisher Scientific. The water used for LC/MS analysis was purchased from Watsons.
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