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11 protocols using lc ms water

1

HILIC Separation of 54 Metabolites

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Acetic acid (≥95.0%), formic acid (≥95.0%), ammonia (25%), LC-MS water and Acetonitrile (ACN, LC-MS grade) were obtained from Merck (Darmstadt, Germany). Ammonium acetate (≥99.0%) was supplied by Sigma-Aldrich (St. Louis, MO, USA).
A mixture of 54 metabolites was used to evaluate the HILIC stationary phases behavior. Table 1 shows the metabolites contained in the analyzed mixture. All standards were purchased from Sigma-Aldrich (St. Louis, MO, USA). Nucleosides and amino acids were from two mix solutions provided by Sigma-Aldrich (St. Louis, MO, USA). A summary of the polarity of the analyzed metabolites is shown in Table S1 in the supplementary information.
Standard stock solutions (1000 μg mL−1) of metabolite mixture were prepared by dissolving an appropriate amount of each metabolite in water and stored at −20 °C until their use. Working standard solutions (20 μg mL−1) were prepared by diluting the stock solution in ACN:H2O (1:1).
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2

Optimized Purification of L-Arginine

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All reagents were HPLC grade. LC/MS Water and LC grade ethanol were purchased from EMD Millipore (Burlington, MA). L-Arginine was purchased from J.T. Baker Avantor (Center Valley, PA). 10X PBS (10 mM KH2PO4, 1.54 M NaCl, 56 mM Na2HPO4, pH 7.3–7.5) was purchased from Lonza (Basil, Switzerland). Gel Filtration Standard was ordered from BioRad (Hercules, CA).
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3

Characterization of Nusinersen by HPLC-MS

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Nusinersen is the sodium salt of an 18-mer 2’-O-methyl-phosphorothioate oligoribonucleotide dissolved in sodium dihydrogen phosphate dihydrate, disodium phosphate, sodium chloride, potassium chloride, calcium chloride dihydrate, magnesium chloride hexahydrate, sodium hydroxide, hydrochloric acid, and water (Spinraza™). The full sequence of the ASO is 3’-mU-mC-A-mC-mU-mU-mU-mC-A-mU-A-A-mU-G-mC-mU-G-G-5′, while the molecular mass equals 7110 g/mol.
Mobile phases were prepared using high purity solvents such as methanol, 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP), as well as N,N-dimethylbutylamine (DMBA), N,N-diisopropylethylamine (DIPEA), dipropylamine (DPA) and LC-MS water (Merck KGaA, Darmstadt, Germany). The mixture of phenol/chloroform/isoamyl alcohol (25:24:1) (VWR International, Gdańsk, Poland), acetonitrile, chloroform, 10 mM ammonium acetate (pH 4.5 and 9.0), acetic acid, ammonia solution 25% (Sigma-Aldrich, Gillingham, Dorset, UK) was also used during sample preparation step.
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4

Quantification of β-Lactam Antibiotics in Plasma

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LC-MS acetonitrile, LC-MS dimethyl sulfoxide (DMSO), LC-MS formic acid, LC-MS methanol and LC-MS water, were supplied by Merck KGaA (Darmstadt, Germany).
Certified reference materials of cefepime (FEP) (93.1%), ceftazidime (CAZ) (85.3%), and piperacillin (PIP) (94.4%), were purchased from European Pharmacopeia ( European Directorate for the Quality of Medicines-Council of Europe, Strasburg, France). Reference material of aztreonam (ATM) (99.8%) was obtained from United States Pharmacopeia (Rockville, MD, USA).
Drug-free human plasma was obtained from the blood of patients who presented at Emergency Laboratory in our hospital. Blood was collected in a lithium-heparin tube (Vacuette, Kremsmünster, Austria) and centrifuged at 2000 g for 10 min at room temperature. The plasma obtained was pooled and stored at -80 °C until its use. An aliquot was separated to confirm the absence of any of the β-LA.
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5

Purification and Preparation of Recombinant Proteins

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PCR reagents, PCR and Gel purification kit, polymerases and restriction enzymes were purchased from Fermentas (Fermentas Inc., Glen Burnie, MD) and Kapa biosystems (Kapabiosystems, Inc., Woburn, MA). pCDF2 vector system with the Ek/LIC cloning kit was purchased from Novagen (Novagen (EMD), Philadelphia, PA) Ni-Sepharose resin was purchased from GE Healthcare (GE Healthcare Life Sciences, Piscataway, NJ). Ampicillin, streptomycin and isopropyl b-D-thiogalactopyranoside (IPTG) were purchased from Sigma- Aldrich (Sigma-Aldrich Inc., MO, USA). LC-MS water and extra pure ammonium acetate were purchased from Merck Millipore (Billerica, MA, USA).
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6

Skeletal Muscle Fiber Type Analysis

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LC-MS grade methanol (MeOH) and LC-MS water were purchased from Sigma-Aldrich (St Louis, MO). Lipid standards lyso-phosphatidylcholine (LPC) 19:0, lyso-phosphatidylethalonamine (LPE) 17:1, lyso-phosphatidylglycerol (LPG) 17:1, lyso-phosphatidylserine (LPS) 17:1 and lyso-phosphatidylinositol (LPI) 17:1 were purchased from Avanti Polar Lipids (Alabaster, AL). Arachidonic acid (AA)-d8 standard was purchased from Cayman (Ann Arbor, MI).
Primary antibodies used for fiber types staining were purchased from Developmental Studies Hybridoma Bank (DSHB) (Iowa City, IA): Myh7 MyHC-1 (BA-F8) for type I fiber, Myh2 MyHC-2A (2F7) for type IIA fiber, and Myh4 MyHC-2B (10F5) for type IIB fiber. Secondary antibodies used in the staining were purchased from Thermo Fisher Scientific (Waltham, MA): goat anti-mouse IgG1, Alexa Fluor 568 (A-21124); goat anti-mouse IgG2b, Alexa Fluor 647 (A-21242); goat anti-mouse IgM, Alexa Fluor 488 (A-210420).
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7

Protein Extraction and Digestion Protocol

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A 40 μl of 4% SDS in 100 mM HEPES‐KOH pH 8.5 was preheated to 70°C and added to the cell pellet for further 10‐min incubation at 70°C on a ThermoMixer (shaking: 550 rpm). The protein concentration was determined using the 660 nm Protein Assay (ThermoFisher Scientific, catalog number 22660). 50 μg of protein was subjected to tryptic digestion. Proteins were reduced (10 mM TCEP) and alkylated (20 mM CAA) in the dark for 45 min at 45°C. Samples were subjected to SP3‐based digestion as described above (Hughes et al, 2019 (link)). Generated peptides were eluted from magnetic beads in 10 μl 5% DMSO in LC–MS water (Sigma Aldrich) in an ultrasonic bath for 10 min. Samples were then dried and stored at −20°C until subjected to LC–MS/MS analysis. Peptides were then reconstituted in 10 μl of 2.5% formic acid and 2% acetonitrile and 3 μl were used for an LC–MS/MS run.
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8

Isotopic Standards for Mass Spectrometry

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HPLC grade acetonitrile and methanol, LC-MS water and 98% formic acid were obtained from Sigma-Aldrich (St. Louis, MO). A mixture of 14 stable isotopic chemicals were used as internal standards [18 (link)], including [13C6]-D-glucose, [15N]-indole, [2-15N]-L-lysine dihydrochloride, [13C5]-L-glutamic acid, [13C7]-benzoic acid, [3,4-13C2]-cholesterol, [15N]-L-tyrosine, [trimethyl-13C3]-caffeine, [15N2]-uracil, [3,3-13C2]-cystine, [1,2-13C2]-palmitic acid, [15N,13C5]-L-methionine, [15N]-choline chloride and 2’-deoxyguanosine-15N2,13C10-5’-monophosphate from Cambridge Isotope Laboratories, Inc (Andover, PA).
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9

Comprehensive Metabolite Quantification Protocol

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HPLC grade acetonitrile and methanol, LC-MS water and 98% formic acid were obtained from Sigma-Aldrich (St. Louis, MO). A mixture of 14 stable isotopic chemicals were used as an internal standard (Go et al. 2015 (link)) included [13C6]-D-glucose, [15N]-indole, [2-15N]-L-lysine dihydrochloride, [13C5]-L-glutamic acid, [13C7]-benzoic acid, [3,4-13C2]-cholesterol, [15N]-L-tyrosine, [trimethyl-13C3]-caffeine, [15N2]-uracil, [3,3-13C2]-cystine, [1,2-13C2]-palmitic acid, [15N,13C5]-L-methionine, [15N]-choline chloride and 2′-deoxyguanosine-15N132, C10-5′-monophosphate from Cambridge Isotope Laboratories, Inc (Andover, PA).
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10

Targeted Metabolomics Stable Isotope Profiling

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HPLC grade acetonitrile and methanol, LC-MS water and 98% formic acid were obtained from Sigma-Aldrich (St. Louis, MO). A mixture of 14 stable isotopic chemicals used as an internal standard [57 (link)] included [13C6]-D-glucose, [15N]-indole, [2-15N]-L-lysine dihydrochloride, [13C5]-L-glutamic acid, [13C7]-benzoic acid, [3,4-13C2]-cholesterol, [15N]-L-tyrosine, [trimethyl-13C3]-caffeine, [15N2]-uracil, [3,3-13C2]-cystine, [1,2-13C2]-palmitic acid, [15N,13C5]-L-methionine, [15N]-choline chloride and 2’-deoxyguanosine-15N2,13C10-5’-monophosphate from Cambridge Isotope Laboratories, Inc (Andover, PA).
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