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811 protocols using ammonium hydroxide

1

Peptide Fractionation and Mass Spectrometry

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Peptides were fractionated using a Dionex 3000 Ultimate loading pump equipped with a 2.1*150 mm 3.5-μm Xbridge C18 column (Waters). Solvent A consisted of 10 mM ammonium hydroxide (Sigma-Aldrich) in water (pH 10), and solvent B consisted of 10 mM ammonium hydroxide and 90% acetonitrile in water (pH 10). Peptides were separated across a 60-min gradient, and 96 fractions were collected and concatenated for a total of 24 fractions. Fractions were analyzed using a Fusion Lumos mass spectrometer with SPS-MS3 acquisition. Data were analyzed using Proteome Discoverer v.2.3. Spectra were queried against the human proteome with a 1% FDR. Eighty percent of SPS matches were required for a hit to be included.
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2

Peptide Fractionation Using Reversed-Phase HPLC

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Peptides were pre-fractionated using a Dionex 3000 Ultimate loading pump equipped with a 2.1 × 150 mm  3.5 µm Xbridge C18 column (Waters). Solvent A consisted of 10 mM ammonium hydroxide (Sigma-Aldrich) in water, pH 10 and solvent B consisted of 10 mM ammonium hydroxide, 90% acetonitrile (ACN) in water, pH 10. Peptides were fractionated across a 60-min gradient, and collected fractions were concatenated to yield a total of 21 fractions.
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3

Bioinspired Green Synthesis of Nanocomposites

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APTES (3-Aminopropyltriethoxysilane, 98%), Glutaraldehyde (25 % in H2O), Glutaraldehyde, Formic acid, Quercetin (>98%), Quercetin-3,4′-diglucoside, Quercetin 3-β-D-glucoside, Citric acid monohydrate, Disodium hydrogen phosphate, Trans-trans muconic acid, Tetradecanedioic acid, Dodecanedioic acid, DIC, Oxyma, EDC-HCl, NHS, Tetraethyl orthosilicate (TEOS 98%), Ammonium hydroxide solution 31.5% (NH4OH), Tetraethyl orthosilicate (TEOS 98%), Ammonium hydroxide (NH4OH), Chitosan (C6H11NO4) with MW 60 kDa, tween-80, CTAB, and Cellulase microcrystalline powder from Aspergillus niger were obtained from Sigma Aldrich (Bangalore, India). FeCl2 was obtained from LOBA Chemie, KOH from SRL, Ethanol Methanol, Ultra-pure water, Acetic acid, Butanol (C4H9OH), and Propanol (C3H7OH) were obtained from Merck. Onion (Allium cepa) was obtained from local groceries. All glassware were soaked in piranha solution (concentrated H2SO4 and 35% H2O2, 3:1 v/v) for 1 h and rinsed with deionized water before use.
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4

Purification and Characterization of HMGB1 Protein

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LC-MS grade ACN was purchased from VWR Chemicals BDH (Radnor, Pennsylvania, USA). HPLC grade >98% FA and >99% TFA, 37% hydrochloric acid (HCl), 70–72% PCA, Trizma base, DL-dithiothreitol (DTT), NEM, NMM, 25% ammonium hydroxide, Tween, and ammonium bicarbonate (AMBIC) were purchased from Merck (Darmstadt, Germany). Ethanol (99.9%, EtOH) was purchased from Antibac (Asker, Norway). Glycine >99%, iodoacetamide (IAA), and CaCl2 were purchased from Sigma-Aldrich (St. Louis, MO, USA). Phosphate-buffered saline (PBS) was obtained from Thermo Fisher Scientific (Waltham, MA, USA). Crystalline porcine trypsin (4500 K) was obtained from Novozymes A/S (Bagsværd, Denmark). Recombinant HMGB1 for biochemistry and dsHMGB1 were obtained from HMGBiotech S.r.l. (Milano, Italy). Anti-HMGB1 antibodies (Ab18256, polyclonal, rabbit) were purchased from Abcam (Cambridge, UK). Antihuman haptoglobin antibodies from immunoturbidimetry clinical chemistry reagents (Roche Diagnostics, Rotkreuz, Switzerland) were purified to remove the tris-buffer by three rounds of dialysis with 0.1% sodium chloride, using cellulose membrane dialysis tubing of approximately 14k MWCO (Merck, Darmstadt, Germany).
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5

Synthesis and Characterization of Polymer Composites

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The monomers maleic anhydride (MA) and styrene (S); the amino acids L-glutamine (Gln), Lmethionine (Met) and L-tyrosine (Tyr); and 3-aminopropyltriethoxysilane (APTES,> 98%) were obtained commercially from Sigma-Aldrich. The NaCl and NaHCO3 salts and all the solvents used, including benzene, dimethylsulfoxide (DMSO), ethanol, 25% ammonium hydroxide, hydrogen peroxide and deuterated dimethylsulfoxide (DMSO-D6) were obtained commercially from Merck. Silicon wafers were obtained commercially from Silicon Quest, USA. Deionized water (0.055 μS/cm) used to prepare the aqueous solutions was obtained from a LabStar 4-DI deionizer.
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6

Metabolite Profiling via LC/MS

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Liquid chromatography/mass
spectrometry (LC/MS) grade acetonitrile, methanol, and water were
purchased from Millipore Sigma or Fisher Scientific. Ammonium bicarbonate,
ammonium hydroxide, and methylenediphosphonic (medronic) acid were
purchased from Millipore Sigma and used as eluent additives for LC/MS.
Metabolite standards were purchased from Sigma-Aldrich. Authentic
standards were weighed and dissolved in an appropriate solvent. A
10 μM standard mix was prepared in 50:50 acetonitrile/water
(v/v).
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7

Silicone-Derived Bioactive Coatings

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The silicon preceramic polymer used in this study is Loctite 5248
(AG & Co., Germany, Henkel), a UV-curable alkoxy silicone with
thixotropic behavior and a viscosity range of 50–80 cP at 25
°C. The Si/O/C ratio calculated by XPS spectra was 19:27:54 (see
Figure S1 in the Supporting Information), while the number-average molecular weight was = 55 kDa, as measured from static light scattering analysis (SLS,
Zetasizer Nano ZEN3600, Malvern Instruments). Loctite 5248, which
is a straw-colored one-component liquid solution, was directly dissolved
in ethyl acetate (vapor pressure = 73 mmHg at 20 °C; Sigma-Aldrich)
to prepare BFTSA precursor solutions at 2 and 5% w/v (mg/mL). The
solution was stirred overnight at room temperature and wrapped into
an aluminum foil to prevent curing from ambient light. Double-side
mechanically polished Ti6Al4V discs of a diameter of 10 mm and a thickness
of 2 mm (provided by Eurocoating SpA, Italy) were used as substrates.
Calcium nitrate, Ca(NO3)2 (Sigma-Aldrich, USA);
diammonium phosphate, (NH4)2HPO4 (Sigma-Aldrich,
USA); gelatin from cold water fish skin (Sigma-Aldrich, USA); deionized
(DI) water; and ammonium hydroxide (28%, Millipore, USA) were used
to synthesize HAp NPs.
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8

Synthesis of Conductive Polymer Composite

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Ammonium persulfate (APS), aniline hydrochloride (ANI-HCl), acetone, hydrochloric acid, glycerol, and 30% ammonium hydroxide were purchased from Sigma Aldrich (St. Louis, MO, USA), while ethanol, methanol, toluene, and cassava starch were purchased from R&M Chemicals (Petaling Jaya, Malaysia), Systerm (Shah Alam, Malaysia), ChemSoln (Shah Alam, Malaysia), and Cap Kapal ABC (Georgetown, Malaysia), respectively.
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9

Silane-PEG-COOH Functionalization Protocol

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Silane-PEG-COOH (average Mw 5000) were purchased from Biochempeg Scientific Inc. Ethanol and 30% ammonium hydroxide were obtained from Sigma-Aldrich. MilliQ-grade water was used in the preparation of buffers and aqueous solutions.
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10

Quantifying Osteogenic Mineralization

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After 28 days, osteogenic cultures were washed three times with PBS and fixed with 4% (wt/vol) PFA and washed thrice with deionized water. Mineralized matrices were stained with 2% (wt/vol) alizarin red solution and quantified using an earlier protocol 16. Briefly, the stained wells were washed three times with PBS, and 200 μl of 10% (vol/vol) acetic acid (Sigma, Irvine, U.K.) was added to each well (24 well plate) and incubated for 30 minutes in a shaker to elute the stain. The eluted stain was heated to 85°C for 10 minutes, cooled, and neutralized with 10% ammonium hydroxide (Sigma, Irvine, U.K.) read at 405 nm using a spectrophotometer. Fold increase in the absorbance value was calculated by comparing with un‐induced cells in osteo‐permissive medium.
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