Synthesis and Characterization of Alkylated Aromatic Compounds

All chemicals and reagents were used as received without further purification unless otherwise noted. Sodium nitrate (NaNO₃), sodium sulfite (Na₂SO₃), 4-nitrophenyl chloroformate, sodium carbonate, 4-n-hexylaniline, 4-n-octylaniline, 4-n-decylaniline, 4-n-dodecylaniline, N-(3-Dimethylaminopropyl)-N′-ethylcarbodiimide hydrochloride (EDC), 4-(bromomethyl)-3-nitrobenzoic acid, octylamine, decylamine, dodecylamine, N-ethyldiisopropylamine (EDIPA), piperidine, 1,4-butanesultone, anhydrous N,N-dimethylforamide (DMF), N,N,N′,N′-Tetramethyl-O-(1H-benzotriazol-1-yl) uronium hexafluorophosphate (HBTU), and dinitrophenylhydrazine (DNP) were obtained from TCI America (Portland, OR, USA). Fmoc-photolabile linker was purchased from Advanced Chemtech (Louisville, KY, USA). Tetrahydrofuran (THF), ammonium hydroxide (NH₄OH), hexafluoroisopropanol (HFIP), dichloromethane, heptane, acetone, trimethylamine (Et₃N), magnesium sulfate (MgSO₄), sodium carbonate and silica were purchased from Sigma-Aldrich Inc. (St. Louis, MO, USA). Extraction solutions were made in nanopure deionized (DI) water (H₂O) from Milli-Q water (Millipore, Corp., Billerica, MA, USA). HEPES, ammonium bicarbonate (NH₄HCO₃), sucrose, sodium fluoride (NaF), phenylmethanesulfonyl fluoride (PMSF), ethylenediaminetetraacetic acid (EDTA), n-dodecyl β-D-maltoside (DDM), octyl β-D-glucopyranoside (OG), sodium dodecyl sulfate (SDS), digitonin (DGT), protease inhibitor cocktail, tri(2-carboxyethyl) phosphine hydrochloride (TCEP), dithiothreitol (DTT), 2-mercaptoethanol (2-ME), β-casein from bovine milk, ubiquitin from bovine erythrocytes (Ubi), bovine serum albumin (BSA), myoglobin from equine heart (Myo) and cytochrome c (Cytc) from equine heart, ribonuclease A (RNase A) and ribonuclease B (RNaseB) from bovine pancreas were purchased from Sigma-Aldrich Inc. (St. Louis, MO, USA). ProteaseMax™ (PM)^{21 (link)} was obtained from Promega (Fitchburg, WI, USA). RapiGest™ (RG also known as ALS)^{11 (link), 13 (link)} was purchased from Waters (Milford, MA, USA). Sodium orthovanadate, HPLC grade H₂O, acetonitrile (ACN), methanol (MeOH), ethanol (EtOH), optima LC-MS grade formic acid, optima LC-MS grade isopropanol (IPA), Pierce protein-free tris-buffered saline (TBS) blocking buffer, tween 20, and molecular weight cutoff (10 and 30 kDa MWCO) (0.5 mL) centrifugal filters, Coomassie blue R-250, and Dulbecco’s modified eagle medium (DMEM) were purchased from Fisher Scientific (Waltham, MA). Goat Anti-Antigen: Rabbit IgG (H+L), Goat Anti-Antigen: mouse IgG (H+L), BCA protein assay, and Pierce 660 nm Protein Assay Reagent, Ionic Detergent Compatibility Reagent were purchased from Thermo Fisher (Waltham, MA). Protein Assay Dye Reagent Concentrate was purchased from BioRad (Hercules, CA). Voltage-dependent anion-selective channel (VDAC) antibody was purchased from Biovision (Milpitas, CA). Mitochondrial import receptor subunit (TOM20) was purchased from Santa Cruz Biotechnology (Dallas, Tx). Sodium potassium adenosine triphosphate (Na-K ATPase) and cadherin antibodies were purchased from Abcam (Cambridge, United Kingdoms). Phospholamban antibody was purchased from Bioss (Woburn, MA). Fetal bovine serum (FBS) was purchased from Life Technologies (Carlsbad, CA). Mini-gels (12.5%) for SDS polyacrylamide gel electrophoresis (SDS-PAGE) were prepared in house using acrylamide/Bis-Acryamide (37.5:1) 40% solution purchased from Hoefer (Holliston, MA). MS-compatible degradable surfactant (MaSDeS) was synthesized by Promega and provided to us as a gift as described previously^{10 (link)}.