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5 protocols using acrylamide bis acrylamide 30 solution

1

Protein Gel Electrophoresis and Mass Spectrometry

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All reagents used were HPLC grade or electrophoresis grade. Acrylamide/bis-acrylamide 30% solution (37.5:1), ammonium bicarbonate (ambic), β-mercaptoethanol, Coomassie Brilliant Blue R250 (CBB), dithiothreitol (DTT), iodoacetamide (IAA), formic acid, glycerol 86–88%, sodium borohydride (NaBH4), sodium carbonate, sodium citrate tribasic dihydrate (HOC(COONa)(CH2COONa)2·2H2O), (N,N,N, N′-tetramethylethylenediamine (TMED), trifluoroacetic acid, tris-base, trypsin, and the Sigma Marker wide range 6.5–200 KDa were all from Merck (Barcelona, Spain). Acetonitrile, formaldehyde, methanol and sodium dodecyl sulfate (SDS) were supplied by Panreac Química SLU (Barcelona, Spain). Bromophenol-blue was purchased from Riedel-de Haen (Seelze, Germany). Pierce™ trypsin Protease, MS Grade was purchased from Thermo Fisher Scientific (Bremen, Spain). Hydrogen tetrachloroaurate (III) hydrate (HAuCl4·xH2O) (99.9% Au) (49% Au) at 10% w/v was acquired from Strem Chemicals (Kehl, Germany).
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2

Proteomics Sample Preparation Protocol

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All reagents and solvents used were HPLC-grade or higher. Acrylamide/bis-acrylamide 30% solution (37.5:1), β-mercaptoethanol (molecular biology grade), chloroplatinic acid hexahydrate (≥37.50% Pt basis), Coomassie Brilliant Blue R250 (CBB), DL-dithiothreitol (DTT, 99%,), glycerol (86%–88%), iodoacetamide (IAA, 99%), sodium borohydride (99%), sodium citrate tribasic dihydrate (99%), sodium carbonate (99%), tris-base, trifluoroacetic acid (99%), trypsin from bovine pancreas, and the Sigma Marker wide range 6.5–200 KDa were purchased from Merck (Hohen-Brunn, Germany). Formaldehyde for molecular biology (36.5–38% in H2O) and sodium dodecyl sulfate (SDS) were purchased from Panreac (Barcelona, Spain). Bromophenol-blue was purchased from Riedel-de Haen (Seelze, Germany). Hydrogen tetrachloroaurate (III) hydrate (99.9%-Au) (49% Au) at 10% w/v was purchased from Strem Chemicals (Newburyport, MA, USA). Ammonium bicarbonate (AMBIC, 99.5%) and formic acid (95%) were purchased from Fluka (Steinheim, Germany).
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3

Polyacrylamide Gel Electrophoresis Protocol

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Acrylamide/bis-acrylamide 30% solution (37.5:1, A3699), sodium deoxycholate (D6750), sodium dodecyl sulfate (SDS; L3771), and Triton X-100 (X100) for cell lysis buffer, ammonium persulfate (A3678) and N,N,N′,N′-Tetramethylethylenediamine (T9281) for gel polymerization, dichlorodimethylsilane (440272) and 3-(trimethoxysilyl)propyl methacrylate (440159) for wafer and glass silanization, respectively, and bovine serum albumin (BSA, A7030) were all purchased from Sigma-Aldrich. N-(3-((3-benzoylphenyl)formamido)propyl) methacrylamide (BPMAC) was custom-synthesized by PharmAgra Labs. Gels were cast on wafers (WaferPro C04009) microfabricated with SU-8 3050 photoresist (Kayaku Advanced Materials Y311075), coated with dichlorodimethylsilane and gel slick solution (Lonza 50640). 1.5 M Tris-HCl, pH 8.8 (T1588) was purchased from Teknova, 10x tris-glycine buffer (1610734) was purchased from Biorad, and 10x Tris buffered saline with Tween 20 (TBST, 9997 S) was purchased from Cell Signaling Technologies. Purified Turbo GFP (tGFP) protein (FP552) was purchased from Evrogen. Rabbit anti-TurboGFP primary antibody (PA5-22688, lots UC2733591 and UD2749791) and donkey anti-rabbit Alexa Fluor 647 secondary antibody (A31573, lot 1964354) were purchased from ThermoFisher.
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4

Comprehensive Protein Extraction and Separation

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All reagents used were HPLC grade or electrophoresis grade. Albumin, from bovine serum (BSA), urea, thiourea, 3-[(3-Cholamidopropyl) dimethylammonio]-1- propanesulfonate (CHAPS), β-mercaptoethanol, glycerol 86-88%, bradford reagent, coomassie blue R-250 (CBB), DL-dithiotreitol (DTT), iodoacetamide (IAA), trypsin sequencing trifluoroacetic acid (TFA), sodium deoxycholate (DOC) and acrylamide/bis-acrylamide 30% solution (37.5:1) were purchased from Sigma-Aldrich (St. Louis, USA). (N, N, N’, N’–tetramethylethylene-diamine (TMED), ammonium persulphate (APS), glycine were purchased from NZYTech (Lisbon, Portugal). Ampholytes pH 3–10, formic acid, and ammonium bicarbonate were purchased from Fluka (Steinheim, Germany). Hydrochloride acid (HCl), glacial acetic acid, tris-base, trichloroacetic acid (TCA), sodium dodecyl sulfate (SDS), methanol, acetonitrile were purchased from Panreac (Barcelona, Spain). Bromophenol blue was from Riedel-de Haën. Agarose and Mineral oil were purchased from Biorad (Hercules, USA).
Molecular weight marker for gel electrophoresis NZYColour Protein Marker II was purchased from NZYTech (Lisbon, Portugal). α-Cyano-4-hydroxycinnamic acid puriss for MALDI-MS from Fluka was used as MALDI matrix.
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5

Silver Nanoparticle Synthesis and Characterization

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All reagents and solvents used were HPLC-grade or higher. Sodium citrate tribasic dihydrate, tannic acid, silver nitrate, ammonium hydroxide, iron(III) chloride hexahydrate and iron(II) sulfate heptahydrate, sodium borohydride (NaBH4), trypsin, trifluoroacetic acid, DL-Dithiothreitol (DTT), Iodoacetamide (IAA), acrylamide/bis-acrylamide 30% solution (37.5:1), Glycerol 86-88%, Tris-base, Coomassie Brilliant Blue R250 (CBB), sodium carbonate, and the Sigma Marker wide range 6.5-200 kDa were purchased from Sigma-Aldrich (St. Louis, MO, USA). Sodium dodecyl sulfate (SDS) and formaldehyde were purchased from Panreac (Barcelona, Spain). β-mercaptoethanol was purchased from Merck (Hohen-Brunn, Germany), and bromophenol-blue was purchased from Riedel-de Haen (Seelze, Germany). Hydrogen tetrachloroaurate (III) hydrate (99.9%-Au) (49%Au) at 10%w/v was purchased from Strem Chemicals (Newburyport, MA, USA). Ammonium bicarbonate (ambic) and formic acid were purchased from Fluka (Steinheim, Germany).
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