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6 protocols using milli q integral 3 purification system

1

Biochemical Reagents for Protein Analysis

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Urea (99%) and formic acid (98%+, pure) were obtained from Acros Organics (Geel, Belgium). Trifluoroacetic acid (99%, Reagent Plus®), triethylammonium bicarbonate (1 M solution), 4-vinylpyridine (95%), sodium deoxycholic acid (>97% titration) were from Sigma (St. Louis, MO, USA). Acetonitrile (HPLC grade, filtered for 0.2 µm) was purchased from Fisher Chemical (Loughborough, UK). Acetic acid (EMSURE®, glacial, anhydrous for analysis) was from Merck (Darmstadt, Germany). TCEP (Tris(2-carboxyethyl)phosphine hydrochloride) was purchased from Pierce™ (Thermo Fisher, Rockford, IL, USA). Trypsin (sequencing grade modified) was supplied by Promega (Madison, WI, USA). Water (TOC<3 ppb) was obtained from Milli-Q Integral 3 purification system, Millipore S.A.S (France).
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2

Mass Spectrometry Sample Preparation Protocol

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Urea (99%) and formic acid (98%+, pure) were obtained from Acros Organics (Geel, Belgium). Trifluoroacetic acid (99%, Reagent Plus®), triethylammonium bicarbonate (1 M solution), 4-vinylpyridine (95%), and sodium deoxycholic acid (>97% titration) were from Sigma (St. Louis, MO, USA). Acetonitrile (HPLC grade, filtered for 0.2 µm) was purchased from Fisher Chemical (Loughborough, UK). Acetic acid (EMSURE®, glacial, anhydrous for analysis) was from Merck (Darmstadt, Germany). TCEP (Tris(2-carboxyethyl) phosphine hydrochloride) was purchased from Pierce™ (Thermo Fisher, Rockford, IL, USA). Trypsin (sequencing-grade-modified), 5 vials × 20 µg, lyophilized powder, were from Promega (Madison, WI, USA). β-glucuronidase from the Escherichia coli K12 strain, 5 mL falcon vial, specific activity ~140 U/mg at 37 °C, was from Roche Diagnostics GmbH (Mannheim, Germany). Water (TOC < 3 ppb) was obtained from the Milli-Q Integral 3 purification system, Millipore S.A.S (France). Oasis®, 3 cc (cubic centimeter) nominal volume, 60 mg resin, type of resin: WAX-weak anion exchange, was from Waters Corporation (Milford, MA, USA).
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3

Comprehensive Proteomics Workflow Reagents

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Urea (99%) and formic acid (98%+, pure) were obtained from Acros Organics (Geel, Belgium). Trifluoroacetic acid (99%, Reagent Plus®), triethylammonium bicarbonate (1 M solution), 4-vinylpyridine (95%), sodium deoxycholic acid (> 97% titration) were from Sigma (St. Louis, MO, USA). Acetonitrile (HPLC grade, filtered for 0.2 µm) was purchased from Fisher Chemical (Loughborough, UK). Acetic acid (EMSURE®, glacial, anhydrous for analysis) was from Merck (Darmstadt, Germany). TCEP (Tris(2-carboxyethyl) phosphine hydrochloride) was purchased from Pierce™ (Thermo Fisher, Rockford, IL, USA). Trypsin (sequencing grade modified), 5 vials × 20 µg, lyophilized powder (Promega; Madison, WI, USA). β‐glucuronidase from Escherichia coli K12 strain, 5 ml falcon vial, specific activity ~ 140 U/mg at 37 °C (Roche Diagnostics GmbH; Germany). Water (TOC < 3 ppb) was obtained from Milli-Q Integral 3 purification system, Millipore S.A.S (France). Oasis® 3 cc (cubic centimeter) nominal volume, 60 mg resin, type of resin: WAX—weak anion exchange (Waters Corporation; Milford, MA, USA). d5-betamethasone, 1 mg, powder (catalogue number: B327002; Toronto Research Chemicals; Toronto, ON, Canada). UPS-2—Universal Proteomics Dynamic Range Standard, 10.6 µg, dynamic range: 0.5 fmoles—50,000 fmoles; 48 different proteins (Sigma; Saint Louis, MO, USA).
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4

Lipid Extraction and Oxidative Stress Assay

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Sodium alginate, sodium chloride, calcium chloride, 2′,7′-Dichlorofluorescin diacetate (H2DCFDA), and methionine sulfone were purchased from Merck (Darmstadt, Germany). CellTiter-Blue® viability reagent was purchased from Promega Corporation (Madison, WI, USA). Lipid standards were from Avanti Polar Lipids (Alabaster, AL, USA). Isopropanol was obtained from Carlo Erba Reagents (Sabadell, Spain). Tert-butyl methyl ether (MTBE) was purchased from Scharlab (Barcelona, Spain). High-grade purity methanol and ACN, used as mobile phases, were obtained from Fisher Chemicals (Waltham, MA, USA). Ultrapure water was obtained from the Milli-Q Integral 3 purification system (Merck, Darmstadt, Germany).
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5

Grape Seed Extract Procyanidin Purification

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The starting material for this work was a concentrated, industrially produced crude grape seed extract (from Output Trade S.L., Villafranca del Penedés, Spain) with 288 NTU of turbidity and 26% of total soluble substances (TSSs).
For procyanidin purification by UF and SPE by diafiltration, demineralised particle-free water with electrical conductivity of 7–8 µS/cm was obtained inhouse by a Genius 300 reverse osmosis unit (Filtec Depuradoras, Girona, Spain). For HPLC analysis, Milli-Q grade water was produced inhouse by a Milli-Q® Integral 3 purification system (Merck Millipore, Burlington, MA, USA). HPLC grade methanol and acetonitrile were purchased from Scharlab (Barcelona, Spain). Glacial acetic acid (p.a.) was obtained from Sigma-Aldrich (Madrid, Spain) and technical grade acetone and ethanol (96%) from PanReac AppliChem ITW Reagents (Barcelona, Spain).
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6

HPLC Analysis Setup and Materials

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For HPLC analysis, milli-Q grade water was produced in-house by a Milli-Q® Integral 3 purification system (Merck Millipore, MA, USA). Methanol (HPLC grade) was purchased from Scharlab (Barcelona, Spain) and glacial acetic acid, from Sigma-Aldrich (Madrid, Spain). Demineralized water with electrical conductivity of 7-8 µS/cm was obtained in-house by a reverse osmosis unit (Genius 300, Filtec Depuradoras, Girona, Cell culture dishes were obtained from Sarstedt (Barcelona, Spain).
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