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3 protocols using tris 2 carboxyethyl phosphine hydrochloride tcep

1

Comprehensive Proteomics Workflow

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The following materials were from Sigma-Aldrich (St. Louis, MO): guanidine hydrochloride (GdmCl), S-methylmethanesulfonate (MMTS), dimethyl sulfoxide (DMSO), urea, centrifugal filter units (Amicon Ultra-0.5, 10k), tris(hydroxymethyl)aminomethane hydrochloride (Tris•HCl), thermolysin from geobacillus stearothermophilus, proteinase K from tritirachium album, phenylmethylsulfonyl fluoride (PMSF), trifluoroacetic acid (TFA), triethylammonium bicarbonate buffer (TEAB, 1 M, pH 8.5), methacrylic acid N-hydroxysuccinimide(NHS) ester, cytochrome c from equine heart. The following materials were from Thermo-Scientific (Waltham, MA): acetonitrile (ACN, LC-MS grade), 4-(2-aminoethyl)benzenesulfonyl fluoride hydrochloride (AEBSF), Bestatin, E-64, Leupeptin, Pepstatin A, EDTA solution (Corning, 0.5M, pH 8.0), TMT10plex isobaric label reagent set, N-hydroxysuccinimide(NHS)-activated agarose dry resin (Pierce), trypsin protease MS grade (Pierce). Tris(2-carboxyethyl)phosphine hydrochloride (TCEP) was from Santa Cruz Biotechnology (Dallas, TX). Phosphate-buffered saline (PBS, pH 7.4, 1X) was from Gibco (Gaithersburg, MD). Geldanamycin (≥98 wt%) was from Chem-Impex International, Inc. (Wood Dale, IL). Cyclosporin A (CsA) was from LKT Laboratories, Inc. MacroSpin columns (silica C4 and C18) were from Nest Group (Southborough, MA).
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2

Thermolysin-assisted Protein Digestion

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The following materials were from Sigma-Aldrich (St. Louis,MO): guanidine hydrochloride (GdmCl), S-methylmethanethiosulfonate (MMTS), dimethyl sulfoxide (DMSO), urea, centrifugal filter units (Amicon Ultra-0.5 mL, 10 K MWCO), tris(hydroxymethyl)aminomethane hydrochloride (Tris-HCl), thermolysin from geobacillus stearothermophilus, trifluoroacetic acid (TFA), triethylammonium bicarbonate buffer (TEAB, 1 M, pH 8.5), hydrogen peroxide (H2O2) (30% w/w), acetic acid, and 2-mercaptoethanol. The following materials were from ThermoScientific (Waltham, MA): acetonitrile (ACN, LC-MS grade), 4-(2-aminoethyl)benzenesulfonyl fluoride hydrochloride (AEBSF), bestatin, E-64, leupeptin, pepstatin A, EDTA solution (Corning, 0.5M, pH 8.0), TMT10-Plex isobaric label reagent set, NHS-activated agarose dry resin (Pierce), and porcine pancreas trypsin (proteomics grade). Methanol (gradient grade OmniSolv®) was from EMD Millipore. Both Tris(2-carboxyethyl)phosphine hydrochloride (TCEP) and Cyclosporine A (CsA) were from Santa Cruz Biotechnology (Dallas, TX). Phosphate-buffered saline (PBS, pH 7.4) was from Gibco (Gaithersburg, MD). MacroSpin columns (silica C18) and Pi3™ Methionine reagent kit were from Nest Group (Southborough, MA).
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3

Quantitative Proteomic Analysis Protocol

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The following materials were from Sigma Aldrich (St. Louis, MO): glucose, guanidine hydrochloride GdmCl , S-methylmethanethiosulfonate (MMTS), urea, centrifugal filter units (Amicon Ultra, 0.5 mL, 10 K MWCO), tris(hydroxymethyl)aminomethane hydrochloride (Tris-HCl), trifluoroacetic acid (TFA), triethylammonium bicarbonate buffer (TEAB, 1 M, pH 8.5), hydrogen peroxide (H2O2) (30% w/w), acetic acid, 2-mercaptoethanol, myoglobin from equine heart, proteinase K from Tritirachium album, and phenylmethylsulfonyl fluoride (PMSF). The following materials were from ThermoScientific (Waltham, MA): acetonitrile (ACN, LC-MS grade), 4-(2-aminoethyl)-benzenesulfonyl fluoride hydrochloride (AEBSF), bestatin, E-64, leupeptin, pepstatin A, TMT10-Plex isobaric label reagent set and porcine pancreas trypsin (proteomics grade). Tris(2-carboxyethyl)phosphine hydrochloride (TCEP) was from Santa Cruz Biotechnology (Dallas, TX). Phosphate-buffered saline 10X, Molecular Biology Grade (PBS, pH 7.4) was from Corning (Corning, NY). Yeast extract and peptone were from HiMedia (Mumbai, India). Adenine hemisulfate dihydrate was from MP Biomedicals (Santa Ana, CA). Macrospin columns (silica C18) and Pi3 Methionine reagent kit were from Nest Group (Southborough, MA). Research-grade xenon was from Airgas (Randor, PA). Screw top GC vials and caps were from Agilent Technologies (Santa Clara, CA).
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