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3 protocols using sodium cyanoborodeuteride

1

Glycopeptide Analysis by Mass Spectrometry

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Acetic acid (AA), acetonitrile (ACN), atovaquone, dimethyl sulfoxide (DMSO), formic acid (FA), methanol (MeOH), and water were purchased from Fisher Scientific (Pittsburgh, PA). Glycine, 2,2-d2-Glycine, leucine, 1-13C, 15N-leucine, 1,2-13C2-leucine, 2-13C, 15N-leucine, formaldehyde, formaldehyde-d2 solution, sodium cyanoborohydride, sodium cyanoborodeuteride, triethylammonium bicarbonate buffer (TEAB, 1.0 M), tris(2-carboxy-ethyl) phosphine hydrochloride (TCEP), RPMI-1640 medium were purchased from Sigma-Aldrich (St. Louis, MO). Maltooctaose was purchased from Toronto Research Chemicals (Toronto, Canada). PNGase F was purchased from Promega (Madison, WI). Bovine thyroglobulin (BTG) and human IgG subtypes were purchased from Thermo Fisher Scientific (Rockford, IL). ECC1 cells were obtained from ATCC (Manassas, VA). Oasis HLB 1cc cartridges were purchased from Waters Corporation (Milford, MA). Microcon-30kDa centrifugal filters (30K MWCO) were purchased from Merck Millipore Ltd. (Darmstadt, Germany). PolyGLYCOPLEX A beads (3 μm) were purchased from PolyLC Inc. (Columbia, MD). Fused silica capillary tubing (i.d., 75 μm, o.d., 375 μm) was purchased from Polymicro Technologies (Phoenix, AZ). All reagents were used without additional purification.
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2

Silica-based Nanoparticle Synthesis and Functionalization

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Hexadecyltrimethylammonium chloride (≥98%, CTAC), tetraethyl orthosilicate (98%, TEOS), 1,6-diisocyanatohexane (≥99.0%), tridecane (≥99%), ammonium hydroxide solution (28 wt%, NH3·H2O), ammonium fluoride (≥98%, NH4F), 3- aminopropyltriethoxysilane (99%, APS), formaldehyde (37 wt% in water), sodium cyanoborohydride (NaBH3CN), sodium cyanoborodeuteride (NaBD3CN), trypsin (from bovine pancreas), protease inhibitor cocktail, formic acid (FA), urea, trifluoroacetic acid (TFA), dithiothreitol (DTT), iodoacetamide (IAA), and ammonium acetate were purchased from Sigma-Aldrich (St. Louis, MO, USA). Phosphatase inhibitor cocktail was ordered from Thermo Fisher Scientific (Rockford, USA). 13C-D2-formaldehyde was purchased from Cambridge Isotope Laboratories, Inc. (Andover, USA). Dry pyridine was provided by Aladdin (99.8%, Shanghai, China). Toluene and chloroform (≥99.0%) were bought from Kaixin (Tianjin, China), and toluene was purified by refluxing (110 °C) over sodium and distilling (136 °C). Acetone (≥99.5%) and ethanol (≥99.8%) were obtained from Kermel (Tianjin, China). Acetonitrile (≥99.9%, ACN) was purchased from Merck (Darmstadt, Germany). Deionized water was used throughout the experiments (Millipore, Milford, MA, USA). Other reagents were all analytical grade. All the standard non-phosphorylated peptides were purchased from ChinaPeptides (Shanghai, China).
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3

Mass Spectrometry Sample Preparation

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Formic acid, 30% hydrogen peroxide, sodium chloride, and HPLC-grade solvents were purchased from Thermo Fisher (Waltham, MA). Catalase, L-glutamine, L-methionine, ammonium bicarbonate, sodium phosphate monobasic/dibasic, iodoacetamide, dithiothreitol (DTT), triethylammonium acetate, formaldehyde solution, formaldehyde-13C, d2 solution, sodium cyanoborohydride, and sodium cyanoborodeuteride were obtained from Sigma Aldrich (St. Louis, MO). Trypsin and chymoTrypsin were purchased from Promega Corp. (Madison, WI). C18 zip tips were obtained from Millipore (Billerica, MA).
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