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6 protocols using 2 4 6 trihydroxyacetophenone

1

Comprehensive Polysaccharide Analysis Protocol

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Ammonium acetate (NH4Ac), Triton X-100, l-arabinose, xylose, potassium chloride (KCl), 50% sodium hydroxide (NaOH, for HPLC), sodium acetate (NaAc), Sodium chloride (NaCl), 2,4,6-trihydroxyacetophenone (THAP), glucose, maltose, maltodextrins mixture (DP 3–30), potassium sodium tartrate (KNa-tartrate), para-hydroxy benzoic acid hydrazide (PAHBAH), acetonitrile (ACN), D2O (99.9 atom% D), and methanol were purchased from Sigma Aldrich (St. Louis, Missouri, USA). MilliQ was prepared with a MILLI-Q ACADEMIC 230V/50HZ purchased from Merck (Darmstadt, Germany). HCl and NaOH were purchased from Merck (Darmstadt, Germany). Low-viscosity wheat arabinoxylan (AX), arabinan (AB) from sugar beet, rhamnogalacturonan (RG) from soybean, azurine-cross-linked (AZCL) xylan (beechwood), 3-α-l-plus 2-α-l-arabinofuranosyl-xylotetraose (XA3XX/XA2XX) mixture, 2,3-di-α-l-arabinofuranosyl-xylotriose (A2,3XX), 3-α-l-arabinofuranosyl-xylotetraose (XA3XX), 2-α-l-arabinofuranosyl-xylotriose (A2XX), xylobiose (X2), xylotriose (X3), xylotetraose (X4), xylopentaose (X5), and xylohexaose (X6) were purchased from Megazyme (Bray, Wicklow County, Ireland). Insoluble corn fiber, defatted by hexane extraction and destarched by amylase treatment, was supplied by Novozymes A/S (Lyngby, Denmark). Finally, 10 mM NH4Ac buffer was prepared and adjusted to pH 5.0 using 2 M HCl.
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2

Lipid and Peptide Synthesis Protocol

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DOPE and DOPC were purchased from Avanti Polar Lipids. Phosphoramidites for DNA synthesis were purchased from Glen Research. Peptide antigens were custom ordered from GenScript. 2,2’-dipyridyldisulfide, hexadecylphosphonic acid, tris(2-carboxyethyl)phosphine hydrochloride, maleimide and 2,4,6-trihydroxyacetophenone were purchased from Sigma– Aldrich. Monolayer disulfides were purchased from Chemtos. Peptide synthesis reagents were purchased from AnaSpec and MilliporeSigma.
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3

Analytical Techniques for Explosive Compound Detection

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Solvents for LC–MS/MS, such as acetonitrile (ACN), methanol, and water were HPLC or MS grade and were obtained from Carl Roth (Karlsruhe, Germany). All other chemicals used were HPLC or analytical grade (p.a.). The solvent additives ammonium hydroxide and ammonium acetate were purchased from Carl Roth and Honeywell Riedel-de Haën (Seelze, Germany), respectively. Matrices for MALDI-TOF MS, such as DAN, 9-aminoacridine (AA), α-cyano-4-hydroxycinnamic acid (CHCA), 2,4,6-trihydroxyacetophenone (THAP), and multiwalled carbon nanotubes, as well as standard explosive solutions of 2-amino-4,6-dinitrotoluene (2-ADNT), 4-amino-2,6-dinitrotoluene (4-ADNT), 1,3,5-trinitrobenzene (TNB), 1,3-dinitrobenzene (DNB), 2-nitrotoluene (NT), and 5-chloro-2,4-dinitrotoluene (CDNT) were obtained from Sigma-Aldrich (St Louis, MO, USA). TNT, 2,4-dinitrotoluene (2,4-DNT), and 2,6-dinitrotoluene (2,6-DNT) were provided by terracon (Jüterbog, Germany). Mefenamic acid and chlorogenic acid were from Sigma-Aldrich. Citric acid was purchased from Merck (Darmstadt, Germany). Standard stock solutions were prepared as a mixture of each explosive at 50 ng/μL (TNT, 2-ADNT, 4-ADNT, 2,4-DNT, 2,6-DNT, TNB, DNB, NT) in ACN for LC–MS/MS measurements. For MALDI-TOF MS, a stock solution consisting of TNT, TNB, DNB, NT, 1:10 2-ADNT/4-ADNT, and 1:1 2,4-DNT/2,6-DNT each at 100 ng/μL in ACN was used.
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4

Mass Spectrometry Oligonucleotide Analysis

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The stainless steel AnchorChip var /387 and the low molecular weight (LMW) mass spectrometry calibration standard (comprising 4-mer, 5-mer, 7-mer, 9-mer, and 11-mer oligonucleotides) were obtained from Bruker Daltonics (Billerica, MA, USA). The 2,4,6-trihydroxyacetophenone (THAP), ammonium citrate dibasic (AHC), disodium adenosine-5'-monophosphate (AMP), disodium guanosine-5'-monophosphate (GMP), disodium uridine-5'-monophosphate (UMP), disodium cytidine-5'-monophosphate (CMP), disodium inosine-5'-monophosphate (IMP), Dowex 50WX8 hydrogen form cation exchange resin, RNase free sodium chloride, acetonitrile, and imidazole were obtained from Sigma-Aldrich (St. Louis, MO, USA). C18 ZipTips (Ref ZTC18S960) were purchased form Millipore (Billerica, MA, USA). Montmorillonite clay (MMC) in the form of volclay SPV-200 was a gift from The American Colloid Company (Arlington Heights, IL, USA). Ultrapure, 18 MΩ cm-1 deionized water was used for all solution preparations and experiments.
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5

Phosphopeptide Synthesis and Detection

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Armadillo PCR Plates, 384-well, were purchased from Thermo Fisher Scientific. Low-volume, 384-well plates were purchased from Corning. Horseradish Peroxidase, and the luminescent HRP substrate, SuperSignal™ West Femto Maximum Sensitivity Substrate, were also purchased from Thermo Fisher Scientific. PhosSTOP Inhibitor Tablets, Roche cOmplete™ mini EDTA-free Protease Inhibitor Tablets, tris(2-carboxyethyl)phosphine (TCEP), hexadecyl phosphonic acid (HDPA), ethylenediaminetetraacetic acid (EDTA), and 2,4,6-tri-hydroxyacetophenone (THAP) were purchased from Sigma-Aldrich. The phosphopeptide (Ac-IpYERC-NH2) was synthesized using Fmoc solid phase as previously described.26
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6

Mass Spectrometry Sample Preparation

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Chemicals and solvents (analytical grade)
were purchased from the following sources: α-cyano-4-hydroxycinnamic
acid 98% (CHCA) (Sigma-Aldrich), 2,5-dihydroxybenzoic acid 98% (DHB)
(Sigma-Aldrich), norharmane 98% (Nor) (Acros Organics), 1,5-diaminonaphthalene
97% (DAN) (Sigma-Aldrich), 2′,4′,6′-trihydroxyacetophenone
99.5% (THAP) (Sigma-Aldrich), 2,6-dihydroxyacetophenone 99.5% (DHAP)
(Sigma-Aldrich), acetonitrile (ACN) (Honeywell), chloroform (Acros
Organics), methanol (Carl Roth), ammonium acetate (AmAc) (VWR). ammonium
sulfate (AmS) (Sigma-Aldrich), heptafluorobutyric acid (HFBA) (Sigma-Aldrich),
and trifluoroacetic acid (TFA) (Sigma-Aldrich). All chemicals used
in this study were stored, handled, and disposed of according to good
laboratory practices (GLP).
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