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26 protocols using lc ms grade ammonium formate

1

Analytical Procedures for Phytochemical Extraction

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Organic
solvents used for extractions were
HPLC grade obtained from Rathburn (Mikrolab, Aarhus, Denmark), except
for ethanol (96%), which was obtained from Kemetyl AB (Haninge, Sweden).
Acetonitrile and methanol for LC–MS analysis was LC–MS
grade purchased from Fisher Scientific (Roskilde, Denmark). Analytical
grade formic acid and LC–MS grade ammonium formate were obtained
from Sigma-Aldrich (Copenhagen, Denmark), LC–MS grade acetic
acid was obtained from VWR (Søborg, Denmark), and analytical
grade ammonium hydroxide was obtained from Merck (Darmstadt, Germany).
All water used was Milli-Q water collected from a Dionex (Hvidovre,
Denmark) Milli-Q purifier. Gelsemine, senecionine, senkirkine, atropine,
aucubin, and amygdalin were obtained from Extrasynthese (Genay, France).
Triptolide was purchased from BioNordika (Herlev, Denmark), whereas
methyllycaconitine was supplied by Sigma-Aldrich. Sucrose (>99%)
for
the feeding solutions was purchased from Sigma-Aldrich.
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2

Phospholipid Internal Standards Procurement

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The internal standards (ISs) 1-pentadecanoyl-2-oleoyl(d7)-sn-glycero-3-phosphocholine (PC (d7–33:1)) and 1-pentadecanoyl-2-oleoyl(d7)-sn-glycero-3-phosphoethanolamine (PE (d7–33:1)) were purchased from Avanti Polar Lipids (Alabaster, AL, USA). LC-MS grade ammonium formate and ammonium acetate were purchased from Sigma-Aldrich (St. Louis, MO, USA). LC-MS grade methanol (MeOH) and methyl tert-butyl ether (MTBE) were obtained from Wako Pure Chemical Industries (Osaka, Japan).
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3

Fatty Acid Profiling by LC-MS

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Methanol was purchased from VWR (Radnor, PA, USA), and pentane was obtained from Fluka Analytical (Honeywell International Inc., Charlotte, NC, USA). Hexane and sodium methoxide solution 25 wt.% were purchased from Sigma Aldrich (St. Louise, MO, USA). Sodium sulfate was purchased from Titolchimica (Rovigo, Italy, IT) and the CPFA cis-9,10-methylene-octadecanoic acid (dihydrosterculic acid DHSA, as methyl ester, purity ≥98%) was obtained from Chem Cruz (TE Huissen, The Netherlands, NL). LC-MS grade formic acid and LC-MS grade ammonium formate were purchased from Sigma Aldrich (Steinheim, Germany). LC-MS grade Methanol and LC-MS grade acetonitrile were purchased from Honeywell (Selze, Germany), and LC-MS grade 2-propanol and methyl tert-butyl ether (MTBE) were purchased from Merck KGaA (Darmstadt, Germany) and not purified further. If not otherwise stated, Milli-Q water was employed.
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4

Quantitative Metabolite Analysis in Liver Cytosol

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EXE was purchased from Sigma-Aldrich (St Louis, MO) and gamma-L-glutamyl-L-cysteinyl-glycine (glutathione; GSH) was obtained from Alfa Aesar (Haverhill, MA). Liquid chromatography-mass spectrometry (LC-MS) grade formic acid and acetonitrile were obtained from Thermo-Fisher Scientific (Waltham, MA), and LC-MS grade ammonium formate was purchased from Sigma-Aldrich (St Louis, MO). An Acquity UHPLC BEH C18 column (2.1 × 100 mm) was purchased from Waters (Milford, MA). Pooled human liver cytosol (HLC) was obtained from Xenotech (Kansas City, KS). Pierce BCA protein assay kits, PureLink Genomic DNA Isolation kits, TaqMan Copy Number Reference Assays (RNase P, Human; catalog #A30064), GSTM1 TaqMan Copy Number Variant Assays (catalog # 4400291), and GSTA1 TaqMan SNP Genotyping Assays (catalog # 4351374) were purchased from Thermo-Fisher Scientific. All other chemicals were purchased from Thermo-Fisher Scientific unless otherwise specified.
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5

Comprehensive Glycoprotein Analysis Reagents

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Bevacizumab (Avastin) and
trastuzumab (Herceptin)
were purchased from Chugai Pharmaceutical (Tokyo, Japan). Nivolumab
(Opdivo) was purchased from Ono Pharmaceutical (Osaka, Japan), and
ramucirumab (Cyramza) was purchased from Eli Lilly Japan (Hyogo, Japan).
Rituximab (Rituxan) was obtained from Zenyaku Kogyo (Tokyo, Japan).
Rapid PNGase F was purchased from New England Biolabs (Tokyo, Japan).
The BlotGlyco kit was from Sumitomo Bakelite Co. Ltd. (Tokyo, Japan),
and PA-glucose oligomer was obtained from TaKaRa (Kyoto, Japan). Sepharose
CL-4B, ribonuclease B (RNase B), bovine fetuin, and LC/MS-grade ammonium
formate were obtained from Sigma-Aldrich (St. Louis, MO). All other
unspecified reagents were products of FUJIFILM Wako Pure Chemical
Corporation (Osaka, Japan).
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6

Synthesis of Lipid Standards for Gaucher's Disease

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GCase specific inhibitor (ME656) (34 (link)), 13C5-sphinganine, 13C5-sphingosine, 13C5-GlcSph, 13C5-lyso-globotriaosylceramide (LysoGb3), C17-lysosphingomyelin (LysoSM), 13C6-GlcChol, and C17-dihydroceramide (38 (link), 39 (link)) were synthesized as reported. All chemicals and reagents were obtained from Sigma-Aldrich (St Louis, USA) unless mentioned otherwise. The standards Cer (d18:1/16:0), dhCer (d18:0/16:0), GlcCer (d18:1/16:0), galactosylceramide (GalCer) (d18:1/16:0), and LacCer (d18:1/16:0) were obtained from Avanti Polar lipids (Alabaster, USA) and glucosylated cholesterol (GlcChol) from Sigma-Aldrich. LC-MS grade methanol, 2-propanol, water, formic acid, acetonitrile, and HPLC grade chloroform were purchased from Biosolve (Valkenswaard, the Netherlands). LC-MS grade ammonium formate, ammonium acetate, and sodium hydroxide from Sigma-Aldrich, and butanol and hydrochloric acid from Merck Millipore (Billerica, USA).
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7

Lipid Quantification via LC-MS

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The LC–MS grade ammonium formate, formic acid, methyl tertbutyl ether (MTBE), and toluene were purchased Sigma Aldrich (St. Louis, Missouri, USA). LiChroSolv® LC–MS grade solvents including water, methanol, acetonitrile, and isopropanol were purchased from Merck KGaA (Darmstadt, Germany). The SPLASH Lipidomix® Mass Spec Standard was purchased from Avanti Polar Lipids (Alabama, USA).
Acquity charged surface hybrid technology (CSH) C18 2.1 × 100 mm, 1.7 μm column and Acquity VanGuard CSH C18 2.1 × 5 mm, 1.7 μm pre-column were purchased from Waters (Milford, MA, USA).
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8

Steroid Metabolism Assay Protocol

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Sigma-Aldrich (St Louis, MO) supplied 4-andostene-3,17-dione, estrone, and estrone-2,3,4-13C3. Corning (Bedford, MA) provided the NADPH regeneration system (1.3 mM NADP, 3.3 mM 6-phosphate, and 0.4 U/ml glucose 6-phosphate dehydrogenase) and DMSO. The 17β-DHE-Gluc and 17β-DHE were purchased from Toronto Research Chemicals (Toronto, ON), and EXE was purchased from Cayman Chemical Company (Ann Arbor, MI). Liquid chromatography–mass spectrometry (LC-MS)-grade formic acid and methanol as well as Dulbecco’s modified Eagle’s medium cell culture media and geneticin were obtained from Thermo-Fisher Scientific (Waltham, MA), and LC-MS–grade ammonium formate was purchased from Sigma-Aldrich. Acquity UPLC BEH C18 columns (1.7µm 2.1 × 50 mm) were purchased from Waters (Milford, MA). Pooled human liver cytosol was obtained from Xenotech (Kansas City, KS). FBS was provided by Avantor (Radnor Township, PA) and Pierce BCA protein assay kits were purchased from Thermo-Fisher Scientific. All other chemicals and reagents were purchased from Thermo Fisher Scientific and Sigma-Aldrich.
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9

Lipid Profiling Protocol with HPLC-MS

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HPLC-grade isopropanol and acetonitrile were bought from Merck (Darmstadt, Germany). LC–MS-grade ammonium formate and ammonium acetate were bought from Sigma-Aldrich (St Louis, USA). HPLC-grade ethyl acetate n-butanol and n-heptane were bought from Macklin (Shanghai, China). Water (Ω > 18.0) was purified by Milli-pore Milli-Q Ultra-pure water purification system (Alsace, France). All lipid standards in current study were bought from Avanti Polar Lipids lnc (Alabaster, AL, USA).
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10

Quantitative LC-MS Analysis of Standards

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LC–MS grade acetonitrile (CH3CN), methanol (MeOH), isopropanol (IPA), and water (H2O) were purchased from the U.S. division of VWR International
(Radnor, PA). The LC–MS grade ammonium formate and reagent
grade sodium hydroxide (NaOH) were purchased from Sigma-Aldrich (St.
Louis, MO). Each reference standard, 16 and their deuterated analogue, were purchased from Toronto Research
Chemicals (TCW, Toronto, ON, Canada). All analytical runs were carried
out at SC Laboratories, Santa Cruz, CA and used the same columns and
analysis data collection methods as previously reported.9 (link) Method validation protocols were followed from
those previously described.9 (link) The research
described herein implemented analytic measurements that began with
workups on SPE-treated samples subjected to UHPLC separations. These
steps used Phenomenex Strata-X 33 μm polymeric reversed-phase
SPE cartridges and Raptor ARC-18 100 × 4.6 mm, 2.7 μm particle
HPLC columns purchased from Phenomenex (Torrance, CA) and Restek Pure
Chromatography (Edmond, OK), respectively.
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