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Acetonitrile

Manufactured by Merck Group
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Acetonitrile is a colorless, volatile, flammable liquid. It is a commonly used solvent in various analytical and chemical applications, including liquid chromatography, gas chromatography, and other laboratory procedures. Acetonitrile is known for its high polarity and ability to dissolve a wide range of organic compounds.

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5 292 protocols using acetonitrile

1

Preparation of MBSH and Acetic Acid Solutions

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Acetonitrile (HPLC grade), p-toluene sulfonyl hydrazide (4-methylbenzenesulfonohydrazide/MBSH, 97%), acetic acid (100%), and formaldehyde (37% w/v in water, containing 10–15% methanol) were all purchased from Merck KGaA (Darmstadt, Germany). Formic acid (99–100%) was purchased from VWR (Radnor, Pennsylvania, USA). The UHQ water (≤18 MΩ) was supplied in house by a Milli-Q direct 8 water purification system (Millipore, Burlington, Massachusetts, USA).
A MBSH solution in Acetonitrile (2 mg/mL) was prepared by dissolving 100 mg of MBSH in Acetonitrile to a volume of 50 mL. An acetic acid solution (200 μg/mL) was prepared by dissolving 10 μL of acetic acid in 50 mL of water. Methylthioninium chloride (MTC) samples 1–6 were provided by TauRx Therapeutics Ltd (Aberdeen, United Kingdom).
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2

Solvent Extraction and SPME Analysis

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The solvents used were acetonitrile ≥99.9% v/v (Fisher Scientific, Glee, Belgium), methanol ≥99.9% v/v, hexane ≥95% v/v, ethanol ≥99.9% v/v, and chloroform ≥99.9% v/v (Sigma-Aldrich, Bellefonte, PA, USA). Deionized water (DI) was purified through a Milli-Q Biocel system (Millipore, Burlington, MA, USA).
Various combinations of mixed solvents were prepared and used, such as acetonitrile and ethanol (1:1 v/v), acetonitrile and water (1:1 v/v), ethanol and water (1:1 v/v), and acetonitrile and ethanol and water (2:2:1 v/v/v).
Individual external standards were purchased from Merck-Sigma Aldrich Co. and included palmitic acid ≥99% w/w, linolenic acid ≥99% w/w, linoleic acid ≥99% w/w, oleic acid ≥99% w/w, arachidic acid ≥99% w/w, cholesterol ≥99% w/w, p-benzoquinone ≥98% w/w, 2-methyl-p-benzoquinone ≥98% w/w and 1-pentadecene ≥98% v/v. In addition, n-alkane standard C7–C40 (1000 mg/mL in hexane) was purchased from (Supelco, Bellefonte, PA, USA).
The 50/30 µm divinylbenzene/carboxen/polydimethylsiloxane (DVB/CAR/PDMS) SPME fiber with a 2 cm coating was supplied by Sigma-Aldrich, Bellefonte, PA, USA. Prior to use, the fiber was activated according to the manufacturer’s recommendations by exposing the fiber’s coating to 270 °C for half an hour.
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3

Aniline Polymerization in Acidic Media

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The aniline (98%, Aldrich) used was distilled under vacuum before use and its solution in acetonitrile was prepared and stored in the dark at 5 °C. acetonitrile (99.99%, Sigma-Aldrich) was used as solvent. H2SO4 (98%, Aldrich), a strong acid in aqueous and acetonitrile media, was used to acidify the polymerization medium. Ammonium peroxidisulfate, (NH4)2S2O8 (99.5%, Aldrich) was used as an oxidant. Zinc nitrate, Zn(NO3)2 (99%, Aldrich), was used as the source of Zn2+. Sodium polystyrene sulfonate (PSS) was purchased from Aldrich. Methylene blue (≥ 95%) was purchased from Sigma-Aldrich. Except for aniline, all chemicals used in the experiment were analytical grade and used without any processing as taken.
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4

Protein Digestion and Mass Spectrometry

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Ultra-pure water and LC–MS grade solvents were used for protein digestion and MS experiments. De-staining buffer: 100 mM NH4HCO3 (Merck, Darmstadt, Germany), acetonitrile (Merck, Darmstadt, Germany), 1:1 v/v; reduction buffer: 10 mM dithiothreitol (Sigma-Aldrich, Saint Louis, USA) in 100 mM NH4HCO3 (Merck, Darmstadt, Germany), alkylation buffer: 55 mM iodoacetamide (Sigma-Aldrich, Saint Louis, USA) in 100 mM NH4HCO3 (Merck, Darmstadt, Germany), trypsin solution: 13 ng/μL trypsin (Promega, Madison, WI, USA) in 10 mM NH4HCO3 (Merck, Darmstadt, Germany) containing 10% (v/v) acetonitrile (Merck, Darmstadt, Germany); Pierce C18 pipette tips (Thermo-Scientific, Waltham, USA), elution buffer: 10 mg/mL of α-cyano-4-hydroxycinnamic acid (Bruker, Billerica, MA, USA) in acetonitrile: 0.1% TFA (Merck, Darmstadt, Germany) in H2O 7:3 v/v.
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5

Quantitative Analysis of Tranexamic Acid

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All solutions were prepared using water from an Arium water purification system (resistivity > 18 MΩ cm, Sartorius, Göttingen, Germany). LC-MS grade chemicals were employed for analysis, namely acetonitrile (Merck, Darmstadt, Germany), formic acid (Merck, Darmstadt, Germany), and ammonium bicarbonate (Fluka, Buchs, Switzerland). Mixtures of acetonitrile, water, and aqueous ammonium bicarbonate (pH 7.4; 100 mM) were used to prepare the mobile phase, being filtered through 0.45 μm Millipore (Billerica, MA) HVHP filters and degassed for 15 min in an ultrasonic bath prior to use.
High purity (≥99%) analytical standards of tranexamic acid (TXA, Scheme 1) and the corresponding isotopically labeled internal standard 13C2,15N,trans-tranexamic acid (TXA-IS) were supplied by Toronto Research Chemicals (Toronto, Canada). Individual stock solutions of TXA and IS were prepared on a weight basis in water at a concentration of 1 mg mL−1 and stored at −20 °C. A working standard solution of TXA was prepared in water at 10 µg mL−1 to perform ionization studies. For quantification assays, working standard solutions of TXA (30, 60, 90, 150, 300, 450, 600 ng mL−1) were prepared in mobile phase by dilution of appropriate amounts of intermediate solutions at 20 and 1.5 μg mL−1. The internal standard TXA-IS was added at a final concentration of 300 ng mL−1.
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6

Acetonitrile-Based Peptide Extraction

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The preparation of 50% acetonitrile was done by diluting 5 mL of 100% acetonitrile (Merck, Germany) stock solution with 5 mL of HPLC grade water then 0.1% TFA was prepared by diluting 10% TFA stock solution (Merck, Germany) with 49.5 mL of HPLC grade water (Merck, Germany). Finally, elution buffer, 75% ACN / 0.1% TFA was prepared by adding 7.5 mL of 100% acetonitrile stock solution, 0.1 mL of 10% TFA stock solution and 2.4 mL of HPLC grade water. Oasis columns were placed in 15 mL tube, 1 mL of 50% ACN was added and let it flow, 1 mL of 0.1% TFA was added to equilibrate column, let it flow. The equilibration step was repeated 3 times. The protein samples were added into column and slowly let it flow by gravity. Then 1 mL of 0.1% TFA was added and let it flow. Then, oasis columns were taken and placed in the new clean 15 mL tubes, peptide was eluted by adding 1 mL elution buffer, 75% ACN / 0.1% TFA, let it flow by gravity. The samples were taken to evaporate at speed vacumm centrifuge cincentrator machine (Meditop, Thailand), then kept samples in − 80 °C until further analysis.
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7

Fluorous Affinity Tag Attachment

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Example 28

2-Step Attachment of Fluorous Affinity Tag to Orthoester Linker

30 mg of 3′-RNA-CPG is treated with 100 μL 3% dichloroacetic acid in dichloromethane (Glen Research) twice for 1 min, followed by 8 mL acetonitrile, and dried with a stream of nitrogen. 45 μL of 1,2-bis((2-methoxy-1,3-dioxolan-4-yl)methyl)disulfane orthoester, 45 μL acetonitrile (Aldrich), and 10 μL 3% dichloroacetic acid in dichloromethane (Glen Research) are added to the 3′-RNA-CPG with a free 5′-hydroxyl group, and the mixture is heated at 60° C. for 1 hr. After removal of residual liquid, the CPG is washed with 8 mL acetonitrile, followed by drying with a stream of nitrogen. The RNA-CPG: orthoester conjugate is treated with 200 μL 50 mM TCEP (Aldrich) solution, prepared in 200 mM ammonium bicarbonate, pH 8.0, for 1 hour at 23° C. The reduced thiol containing RNA conjugate on CPG is then incubated with a solution of 1H,1H,2H,2H-Perfluorooctyl iodide (Aldrich) at a concentration of 10 mM in acetonitrile. The conjugate is then deprotected and released from the CPG by treatment with 100 uL neat ethylenediamine for 5 hours at 23° C., followed by washing with 8 mL of acetonitrile. The fluorinated-RNA conjugate is eluted from the CPG resin with 0.3 mL 0.1 M ammonium acetate buffer (pH=6.9), and analyzed by deconvoluted ESI/TOF mass spectrometry.

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8

Volatile Organic Compounds Analysis

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The solvent used for VOCs standard solutions was methanol (Fisher Chemical, Loughborough, UK, 99.99%), and the highest quality possible of pure compounds were used: benzene (Sigma-Aldrich, MO, USA, >99.9%), toluene (Sigma-Aldrich, WI, USA, 99.5%), styrene (Sigma-Aldrich, MO, USA >99%), naphthalene (Sigma-Aldrich, MO, USA, 99.9%), furfural (Fluka, Switzerland, >99%), furan (Aldrich, MO, USA, ≥99%), isoprene (Aldrich, MO, USA, 99%), 2-butenal (Aldrich, MO, USA, ≥99.5%), phenol (Sigma-Aldrich, Switzerland, 99%), 2-furyl methyl ketone (Aldrich, MO, USA, 99%). The solvent used for aldehydes with low molecular weight solutions was acetonitrile (Sigma-Aldrich, MO, USA, 99.9%), and the derivatives compounds of 2,4-DNPH were: formaldehyde-2,4-DNPH (Supelco, PA, USA, 99.9%), acetaldehyde-2,4-DNPH (Supelco, PA, USA, 99.9%), and acrolein-2,4-DNPH (solution in acetonitrile, Aldrich, PA, USA, 99.9%).
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9

Synthesis and Characterization of Novel Organic Compounds

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Isophthalic acid, benzoic acid, L-alanine, 1,3-phenylene diisothiocyanate, phenyl isothiocyanate, acetonitrile for reaction, and acetonitrile for spectroscopy were purchased from Sigma Aldrich Co. and used directly without purification. acetonitrile-D3 and dimethyl sulfoxide-D6 were purchased from Cambridge Isotope Laboratories Inc. All other starting materials were obtained from Sinopharm Chemical Reagent Ltd.
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10

Proteomic Glycan Analysis Workflow

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Acetonitrile (ACN, LC-MS grade), Acetonitrile with 0.1% formic acid (LC-MS grade), water (LC-MS grade), water with 0.1% formic acid (LC-MS grade), ammonium bicarbonate (purity ≥ 99%, LC-MS grade), iodoacetamide (purity ≥ 99%) and endoglycosidase F2 and F3 from Elizabethkingia miricola with Endo F Reaction Buffer (250 mM sodium acetate, pH 4.5) were supplied by Sigma-Aldrich (St. Louis,MO). α(2-3,6,8)-neuraminidase with GlycoBuffer 1 (5 mM calcium chloride, 50 mM sodium acetate, pH 5.5), PNGase F with G7 Reaction Buffer (500 mM sodium phosphate, pH 7.5) and β1-3,4 Galactosidase with GlycoBuffer 4 (50 mM sodium acetate, pH 4.5) were purchased from New England BioLabs, (Ipswich, MA). Glyko β N-Acetylhexosaminidase with Reaction Buffer (50 mM sodium phosphate, pH 5.5) was obtained from ProZyme (Hayward, CA,) and Trypsin Gold for MS from Promega (Madison, WI). Dithiothreitol (ultrapure grade) was purchased from Thermo-Fischer Scientific (Waltham, Massachusetts). HP and HPX from human plasma were supplied by Athens Research and Technology (Athens, Georgia,) and SHBG by Lee Biosolutions (Maryland Heights, MO). Stock solutions of the individual proteins at a concentration of 10 μg/μL were prepared by dissolving the compounds in water.
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