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23 protocols using synergy ultrapure water system

1

NMR Metabolomics Sample Preparation

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Methanol, chloroform, monosodium phosphate (NaH2PO4), disodium phosphate (Na2HPO4), sodium
salt of 3-(trimethylsilyl)propionic acid-2,2,3,3-d4 (TSP),
potassium hydroxide, and perchloric acid were obtained from Sigma-Aldrich
(St. Louis, MO). Standard compounds used for chemical shift data and/or
spiking experiments were all obtained from Sigma-Aldrich or Fisher
(Waltham, MA), except for the coenzymes, NAD+, NADH, NADP+, and NADPH, which were generously provided by Dr. Jianhai
Du, University of Washington (Table S1).
Deuterium oxide (D2O) was obtained from Cambridge Isotope
laboratories, Inc. (Andover, MA). Deionized (DI) water was purified
using an in-house Synergy Ultrapure Water System from Millipore (Billerica,
MA). All chemicals were used without further purification.
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2

NMR Analysis of Metabolites in Biofluids

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Methanol, chloroform, sodium phosphate (monobasic; NaH2PO4), sodium phosphate (dibasic; Na2HPO4), and 3-(trimethylsilyl)propionic acid-2,2,3,3-d4 sodium salt (TSP) were obtained from Sigma-Aldrich (St. Louis, MO). Standard compounds used to obtain spectra under conditions identical to blood and plasma and for spiking experiments to confirm assignments were obtained from Sigma-Aldrich (St. Louis, MO). Deuterium oxide (D2O) was obtained from Cambridge Isotope Laboratories, Inc. (Andover, MA). Deionized (DI) water was purified using an in-house Synergy Ultrapure Water System from Millipore (Billerica, MA). All chemicals were used with no further purification.
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3

NMR Metabolomics Analysis of Human Serum

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Methanol; sodium phosphate, monobasic (NaH2PO4); sodium phosphate, dibasic (Na2HPO4); and 3-(trimethylsilyl)propionic acid-2,2,3,3-d4 sodium salt (TSP) were obtained from Sigma-Aldrich (St. Louis, MO). Deuterium oxide (D2O) and a mixture of uniformly 13C,15N-labeled (97–99% enrichment) standard amino acids that included leucine, methionine, tryptophan, and tyrosine were obtained from Cambridge Isotope laboratories, Inc. (Andover, MA). Human-serum samples from eight healthy subjects (four male and four female, Table S1) were obtained from Innovative Research, Inc. (Novi, MI). A commercial, pooled human serum was also obtained from Innovative Research, Inc. Deionized (DI) water was purified using an in-house Synergy Ultrapure Water System from Millipore (Billerica, MA). All chemicals were used with no further purification.
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4

Comprehensive Metabolomics Sample Preparation

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Methanol, acetonitrile, perchloric
acid (PCA), trichloroacetic
acid (TCA), hydrochloric acid (HCl), sodium hydroxide (NaOH), (2-bromoethyl)
trimethylammonium bromide, dimethylformamide (DMF), 3-(trimethylsilyl)propionic
acid-2,2,3,3-d4 sodium salt (TSP) were
all obtained from Sigma-Aldrich (St. Louis, MO). 4-(4,6-Dimethoxy[1,3,5]triazin-2-yl)-4-methylmorpholinium
chloride (DMTMM) was obtained from Acros Organic (Pittsburgh, PA),
while 15N-phthalimide potassium and deuterium oxide were
obtained from Cambridge Isotope Laboratories (Andover, MA). All chemicals
were used without further purification. Pooled human serum sample
was obtained from Innovative Research, Inc. (Novi, MI). Deionized
(DI) water was purified using an in-house Synergy Ultrapure Water
System from Millipore (Billerica, MA). Centrifugal filters (3-kDa
cutoff; Amicon Microcon, YM-3) were purchased from Sigma-Aldrich.
Standard compounds used for spiking and confirming the peak assignments
were 1-methylhistidine, 2-hydroxybutyrate, 2-hydroxyisocaproate, 2-hydroxyisovalerate,
2-oxocaproate, 3-methylbutyrate, 3-methylhistidine, 3-methyl-2-oxobutanoate,
arginine, benzoate, betaine, carnitine, citrulline, dimethylglycine,
pyridoxine, pyroglutamate, ornithine, sarcosine, serine and succinate
(all from Sigma-Aldrich).
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5

Metabolic Profiling Reagents and Sources

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Methanol, chloroform, trichloroacetic acid, hydrochloric acid, sodium hydroxide, monosodium phosphate (NaH2PO4), disodium phosphate (Na2HPO4), sodium salt of 3-(trimethylsilyl)propionic acid-2,2,3,3-d4 (TSP), GSH, GSSG, ATP, ADP, and AMP were obtained from Sigma-Aldrich (St. Louis, MO). NAD+ (β-nicotinamide adenine dinucleotide hydrate), NADH (β-nicotinamide adenine dinucleotide (reduced) disodium salt hydrate), NADP+ (β-nicotinamide adenine dinucleotide phosphate hydrate), and NADPH (β-nicotinamide dinucleotide, 2′-phosphate (reduced) tetra sodium salt hydrate) were generously provided by Dr. Jianhai Du, University of Washington. Deuterium oxide (D2O) was obtained from Cambridge Isotope Laboratories, Inc. (Andover, MA). Deionized (DI) water was purified using an in-house Synergy Ultrapure Water System from Millipore (Billerica, MA). All chemicals were used without further purification.
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6

Nuclear Magnetic Resonance Metabolomics

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Monosodium phosphate (NaH2PO4), disodium phosphate (Na2HPO4), fumaric acid, sodium salt of trimethylsilylpropionic acid-d4 (TSP), acetanilide, N-ethylmaleimide (NEM), reduced glutathione (GSH), oxidized glutathione (GSSG), ethanol, methanol, and chloroform were obtained from Sigma-Aldrich (St. Louis, MO) or Fisher (Waltham, MA). Deuterium oxide (D2O) was procured from Cambridge Isotope Laboratory (CIL) (Tewksbury, MA). Deionized (DI) water was purified using an in-house Synergy Ultrapure Water System from Millipore (Billerica, MA). All chemicals and solvents were used without further purification.
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7

Preparation of NMR Reagents

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Monosodium phosphate (NaH2PO4), disodium phosphate (Na2HPO4), maleic acid, fumaric acid, trimethylsilylpropionic acid-d4, and trimethylsilylpropanesulfonic acid, acetanilide, methanol and chloroform were obtained from Sigma-Aldrich (St. Louis, MO) or Fisher (Waltham, MA). Deionized (DI) water was purified using an in-house Synergy Ultrapure Water System from Millipore (Billerica, MA). All chemicals and solvents were used without further purification.
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8

Electrochemical DNA Sensing Probes

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Hydrochloric acid, nitric acid, 6-mercapto-1-hexanol, sulfuric acid, sodium perchlorate, tris-(2-carboxyethyl) phosphine hydrochloride, monosodium phosphate, sodium chloride, sodium phosphate dibasic, ethylenediaminetetraacetic acid, 10% sodium dodecyl sulfate, zinc chloride, nickel chloride, aluminum chloride, cobalt acetate, manganese acetate, iron chloride, chromium chloride, and silver sulfadiazine were used as received (Sigma-Aldrich, St. Louis, MO). FLUKA TraceCERT standards for silver, lead, and cadmium purchased from Sigma-Aldrich (St. Louis, MO). These reagents and chemicals were used without further purification. The solutions were made with DI water purified through a Synergy Ultrapure Water System (18.2 Mω•cm, Millipore, Billerica, MA). The sensors were interrogated in 10 mM PBS supplemented with 2 M NaClO4 at pH 6.7 (PBS-6.7).
Four DNA probes were purchased from Biosearch Technologies, Inc. (Novato, CA) and used as received. Two DNA probes (5′CA and 5′CT) were modified with a six carbon (C6) alkanethiol linker at the 5′ end and a MB redox label at the 3′ end (Figure S1A). Two other probes (3′CA and 3′CT) were modified at the 3′ end with a C6 alkanethiol linker and at the 5′ end with a MB redox label (Figure S1B).
CA Probes:
CT Probes:
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9

Metabolite Sample Preparation Protocol

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Methanol, chloroform, monosodium phosphate (NaH2PO4), disodium phosphate (Na2HPO4), 3-(trimethylsilyl)propionic acid-2,2,3,3-d4, sodium salt (TSP), sodium azide, potassium hydroxide and perchloric acid were obtained from Sigma-Aldrich (St. Louis, MO). Standard compounds including coenzyme A (CoA), oxidized coenzyme A (CoA-S-S-CoA), acetyl coenzyme A (acetyl-CoA), succinyl coenzyme A, malonyl coenzyme A, reduced glutathione (GSH) and oxidized glutathione (GSSG) used for chemical shift/spectral databases and/or spiking experiments were all obtained from Sigma-Aldrich or Fisher (Waltham, MA). Deuterium oxide (D2O) was obtained from Cambridge Isotope laboratories, Inc. (Andover, MA). Deionized (DI) water was purified using an in-house Synergy Ultrapure Water System from Millipore (Billerica, MA). All chemicals were used without further purification.
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10

HPLC-MS Lipid Standards Characterization

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HPLC-grade ammonium formate and LC-MS-grade formic acid were purchased from Fluka Chemie (Buchs, Switzerland). LC-MS-grade acetonitrile (ACN), methanol (MeOH), and ACS-grade chloroform were purchased from J.T. Baker or Mallinckrodt (Mallinckrodt Baker Inc. Phillipsburg, NJ, USA). 2,6-di-tert-butyl-4-methylphenol (butylated hydroxytoluene; BHT) was purchased from Sigma Chemical Co. (St. Louis, MO, USA). 2,3,5-triphenyl-tetrazolium chloride (TTC) was purchased from Alfa Aesar (Lancashire, U.K.). Water (18.2 MΩ/cm) was purified in house using a Synergy Ultrapure Water System (Millipore Co., Burlington, MA, USA). The following lipid standards were purchased from Avanti Polar Lipids Inc. (Alabaster, AL, USA): 1-myristoyl-2-hydroxy-sn-glycero-3-phosphocholine (LPC 14:0), 1-myristoyl-2-hydroxy-sn-glycero-3-phosphoethanolamine (LPE 14:0), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (PC 14:0/14:0), 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine (PE 14:0/14:0), N-lauroyl-D-erythro-sphingosylphosphorylcholine (SM d18:1/12:0), and N-heptadecanoyl-D-erythro-sphingosine (ceramide d18:1/17:0).
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