Super dhb

Manufactured by Merck Group

Sourced in Germany, United States

Super-DHB is a laboratory equipment product developed by Merck Group. It is designed to perform specific functions in a research or testing environment. The core function of Super-DHB is to provide accurate and reliable measurements or data processing capabilities. No further details can be provided without the risk of extrapolation or interpretation.

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Super-DHB (9:1 mixture of 2,5-dihydroxybenzoic acid 2-hydroxy-5-methoxybenzoic acid (super-DHB, Super-DHB matrix Super DHB solution

25 protocols using super dhb

MALDI-TOF Glycoconjugate Analysis Protocol

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For glycan analysis, 1 or 2 μL
of the glycoconjugate samples in their original buffer were spotted
onto a ground-steel MALDI target plate with 1 μL of either a
10 mg/mL “super-DHB” (a 9:1 (w/w) mixture of 2,5-dihydroxybenzoic
acid and 2-hydroxy-5-methoxybenzoic acid; purchased from Sigma-Aldrich,
Germany) solution in 50:50 (v/v) ACN/water and NaOH 1 mM or a 100
mg/mL super-DHB solution in 50:50 (v/v) ACN/water. The spots were
left to dry at room temperature. For the analysis of the protein backbone,
the glycoconjugate samples were desalted by C18-ZipTip SPE as described
above, by direct elution onto a polished-steel MALDI target plate
and the addition of 1 μL of a saturated solution of 1,5-diaminonaphtalene
(1,5-DAN) in water/ACN/formic acid (v/v, 50:49.95:0.05). The spots
were left to dry at room temperature.

Nicolardi S., Danuser R., Dotz V., Domínguez-Vega E., Al Kaabi A., Beurret M., Anish C, & Wuhrer M. (2022). Glycan and Protein Analysis of Glycoengineered Bacterial E. coli Vaccines by MALDI-in-Source Decay FT-ICR Mass Spectrometry. Analytical Chemistry, 94(12), 4979-4987.

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Oxime Formation of Heterologous Enzymes

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A refactored plasmid containing genes mpaA1, mpaB, and mpaC was heterologously expressed as described above. After desalting by SPE column, 1 mL (sample in aq. 70% acetonitrile/0.1% TFA) was added each to two scintillation vials (reaction vs. control). The pH of the eluent was adjusted to pH 4 using 0.1 M NaOH and checked by pH paper. To one vial, O-benzylhydroxylamine was added to 10 mM and scintillation vials were left overnight (~16 h) at room temperature to ensure maximal oxime formation. Reaction products were mixed 1:1 with 50 mg/mL Super-DHB (Sigma-Aldrich) in aq. 60% acetonitrile/0.1% formic acid and dried under ambient conditions on a polished steel MALDI target. Samples were analyzed using a Bruker UltrafleXtreme MALDI-TOF MS using manufacturer’s methods for reflector positive mode.

Ren H., Dommaraju S.R., Huang C., Cui H., Pan Y., Nesic M., Zhu L., Sarlah D., Mitchell D.A, & Zhao H. (2023). Genome mining unveils a class of ribosomal peptides with two amino termini. bioRxiv.

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Arabidopsis Root Xyloglucan Analysis

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Arabidopsis roots were preserved in 100% ethanol. At 37°C overnight, 1 unit of xyloglucanase (Megazyme, Brae, Ireland) was treated with 50 mM sodium acetate buffer (pH 5.0) to remove ethanol and rehydrated to produce xylooligosaccharide. MALDI-TOF mass spectrometry of XyG oligosaccharides was recorded with an Applied Biosystems using super-DHB (Sigma-Aldrich, USA) as a matrix [62 (link), 63 (link)].

Xu P, & Cai W. (2019). Nitrate-responsive OBP4-XTH9 regulatory module controls lateral root development in Arabidopsis thaliana. PLoS Genetics, 15(10), e1008465.

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Protein-Polymer Hybrid Nanostructure Fabrication

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β-Casein, trypsin (from bovine pancreas), anisole, poly(methyl methacrylate) (PMMA, MW ~ 996 kDa), poly(allylamine hydrochloride) (PAH, MW ~ 56 kDa), titanium(IV)bis(ammo-niumlactato)dihydroxide solution (TALH, 50 wt% in H₂O), trifluoroacetic acid (TFA, 99%), Super-DHB, and n-octadecyltri-chlorosilane (C18, 90%) were from Sigma-Aldrich (St. Louis, MO). Ethanol (200 proof) and acetonitrile (ACN) were from Fisher Scientific (Pittsburgh, OH). Phosphoric acid (85% w/w) was from EMD Millipore (Billerica, MA). Poly(-diallyldimethylammonium chloride) solution (PDDA, 20%) and carboxylated polystyrene nanospheres (0.2 μm, 2.6% solids) were from Polysciences, Inc. (Warrington, PA). BK7 glass substrates were from Corning (Painted Post, NY). Chromium and gold used for electron-beam evaporation were acquired as pellets of 99.99% purity from Kurt J. Lesker (Jefferson Hills, PA). Nanopure water (≥18 MΩ cm), purified through a Barnstead E Pure filtration system (Thermo Scientific, Rockford, IL), was used for all reagent preparations.

Hinman S.S., Nguyen R.C, & Cheng Q. (2017). Plasmonic nanodisc arrays on calcinated titania for multimodal analysis of phosphorylated peptides. RSC advances, 7(76), 48068-48076.

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Protein-Polymer Hybrid Nanostructure Fabrication

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Hinman S.S., Nguyen R.C, & Cheng Q. (2017). Plasmonic nanodisc arrays on calcinated titania for multimodal analysis of phosphorylated peptides. RSC advances, 7(76), 48068-48076.

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Rapid Heat-Killed Mycobacteria Sample Prep

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Once optimal growth of the bacteria was obtained, 100 μL of bacterial suspension were placed into 1.5 mL Eppendorf tubes and heat-killed at 95°C for 30 min before leaving the BSL3 containment area. The heat-killed Mtb and NTM pellets were washed four times with 200 μL of double-distilled water. Then, a 0.4 μL aliquot of the resuspended pellet was pipetted onto the MALDI matrix plate and mixed with 0.8 μL of the MALDI matrix. The matrix used consisted of a 9:1 mixture of 2,5-dihydroxybenzoic acid and 2-hydroxy-5-methoxybenzoic acid (super-DHB, Sigma-Aldrich) at a concentration of 10 mg/mL in chloroform:methanol 9:1. (Supplementary Material Fig. S1). All solvent manipulations and handling were carried out under a fume hood.

Gonzalo X., Broda A., Drobniewski F, & Larrouy-Maumus G. (2021). Performance of lipid fingerprint-based MALDI-ToF for the diagnosis of mycobacterial infections. Clinical Microbiology and Infection, 27(6), 912.e1-912.e5.

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Oxime Formation of Heterologous Proteins

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Ren H., Dommaraju S.R., Huang C., Cui H., Pan Y., Nesic M., Zhu L., Sarlah D., Mitchell D.A, & Zhao H. (2023). Genome mining unveils a class of ribosomal peptides with two amino termini. Nature Communications, 14, 1624.

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Rapid Xyloglucan Oligosaccharide Analysis

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Xyloglucan analysis was based on the rapid phenotyping method using enzymatic oligosaccharide fingerprinting previously described (Lerouxel et al., 2002 (link); Sechet et al., 2016 (link)). Mature rosette leaves were harvested and cleared in ethanol overnight at room temperature. After removal of ethanol and rehydration in water, xyloglucan oligosaccharides were generated by digesting the samples with endoglucanase in 10 mM sodium acetate buffer, pH 5, in a final volume of 20 µl, overnight at 37 °C. An aliquot of 0.5 µl of the supernatant was dried on a matrix-assisted laser desorption/ionization time-of-flight mass (MALDI-TOF) target, followed by the addition of 0.5 µl of super-DHB (9:1 mixture of 2,5-dihydroxy-benzoic acid and 2-hydroxy-5-methoxy-benzoic acid, Sigma-Aldrich) matrix, and dried under a fume hood prior to spectra acquisition. The MALDI-TOF mass spectra of the xyloglucan oligosaccharides were acquired with a MALDI/TOF Bruker Reflex III.

Gonçalves B., Maugarny-Calès A., Adroher B., Cortizo M., Borrega N., Blein T., Hasson A., Gineau E., Mouille G., Laufs P, & Arnaud N. (2017). GDP-L-fucose is required for boundary definition in plants. Journal of Experimental Botany, 68(21-22), 5801-5811.

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Rapid MALDI-TOF Bacterial Identification

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A 10 μL inoculation loop of bacteria, grown on Mueller-Hinton agar for 18–24 h, was resuspended in 200 μL of water. Mild-acid hydrolysis was performed on 100 μL of this suspension, by adding 100 μl of acetic acid 2 % v/v and incubating the mixture at 98°C for 10 min. Hydrolyzed cells were centrifuged at 17,000 ×g for 2 min, the supernatant was discarded and the pellet was resuspended in ultrapure water to a density of McFarland 10. A volume of 0.4 μL of this suspension was loaded onto the MALDI target plate and immediately overlaid with 1.2 μL of a matrix consisting of a 9:1 mixture of 2,5-dihydroxybenzoic acid and 2-hydroxy-5-methoxybenzoic acid (super-DHB, Sigma-Aldrich) solubilized in chloroform/methanol 90:10 v/v to a final concentration of 10 mg/mL.
The bacterial suspension and matrix were mixed directly on the target by pipetting and the mix dried gently under a stream of air. MALDI-TOF mass spectrometry analyses were performed with a MALDI Biotyper Sirius (Bruker Daltonics) using the linear negative-ion mode.

Dortet L., Bonnin R.A., Le Hello S., Fabre L., Bonnet R., Kostrzewa M., Filloux A, & Larrouy-Maumus G. (2020). Detection of Colistin Resistance in Salmonella enterica Using MALDIxin Test on the Routine MALDI Biotyper Sirius Mass Spectrometer. Frontiers in Microbiology, 11, 1141.

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Purification and Analysis of Recombinant Peptides

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Polymerase chain reaction (PCR) amplifications were carried out using an automated thermocycler (C1000, Bio-Rad). DNA sequencing was performed using appropriate primers by ACGT, Inc. MALDI-TOF MS analyses were conducted at the Mass Spectrometry Facility at UIUC using an UltrafleXtreme spectrometer (Bruker Daltonics). For MALDI–TOF MS analysis, samples were desalted using ZipTipC18 (Millipore), and spotted onto a MALDI target plate with a matrix solution usually consisting of a saturated aqueous solution of super DHB (2,5-dihydroxy benzoic acid; Sigma Aldrich). Peptides obtained from expression in E. coli were purified by preparative reversed-phase high performance liquid chromatography (RP–HPLC) on an Agilent 1260 Infinity II instrument equipped with a Phenomenex C5 column at a flow rate of 8 mL/min or with a Macherey Nagel C18 (MN_C18) column at a flow rate of 4 mL/min. For RP–HPLC, solvent A was 0.1% TFA in H₂O, and solvent B was pure MeCN containing 0.1% TFA. An elution gradient from 0% solvent B to 100% solvent B over 30 min was used unless specified otherwise.

Biswas S., Wu C, & van der Donk W.A. (2021). The antimicrobial activity of the glycocin sublancin is dependent on an active phosphoenolpyruvate-sugar phosphotransferase system. ACS infectious diseases, 7(8), 2402-2412.

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