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Ultimate 3000 uhplc

Manufactured by Thermo Fisher Scientific
Sourced in United States, Germany, Spain, Italy, United Kingdom

The UltiMate 3000 UHPLC is a high-performance liquid chromatography system designed for a wide range of analytical applications. It features a modular design, high-pressure capabilities, and advanced control and data analysis software.

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232 protocols using ultimate 3000 uhplc

1

Quantitative Analysis of PI-103 Metabolites

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Plasma samples were processed following a similar protocol.32 (link) These samples were injected on the Hypersil GOLD C18 column (1.8 μm, 2.1mm × 50 mm) with UHPLC ultimate 3000 from Dionex coupled with a TSQ Vantage mass spectrometer coupled with a UHPLC ultimate 3000 from Dionex to quantitate the concentration of the main metabolites of PI-103BE (9) and PI-103 (7). The 10 μL samples were run with the gradient starting at 0.6 mL/min from 10% mobile phase B (Acetonitrile with 0.05% formic acid) and 90% mobile phase A (water with 0.05% formic acid) until 0.5 min, up to 100% B at 3 min, and until 6 min, then came back to 10% B until equilibration. The TSQ Vantage was set at spray vantage at 3200 V, vaporizer temperature at 365 °C, Sheath gas pressure at 42 PSI, Aug Gas pressure at 12 psi, Capillary temperature at 350 °C.
All procedures involving the animals were conducted in compliance with State and Federal laws, standards of the U.S. Department of Health and Human Services, and guidelines established by Xavier University Animal Care and Use Committee. The facilities and laboratory animals program of Xavier University are accredited by the Association for the Assessment and Accreditation of Laboratory Animal Care.
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2

Quantitative Proteomics of Macrophage Subtypes

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WT iMPs and WASP-KO-iMPs were harvested after 1-month differentiation with M-CSF and GM-CSF cytokines. About 2 × 106 macrophages were lysed in 500 µl RIPA buffer with protease inhibitor cocktail and were sheared by sonication on ice (Qsonica XL-2000 ultrasonic liquid processor, US; 10 s per pulse, 3 pulses, 2-min interval time). The protein concentration of the supernatant was determined by PierceTM BCA protein assay kit (Thermo Fisher), after 14,000×g centrifugation for 20 min at 4 °C. A filter-aided sample preparation protocol89 (link),90 (link) with modifications was used for the sample processing. Briefly, the sample supernatant containing 10 µg total protein was mixed with 200 µl of 8 M urea in 0.1 M Tris/HCl (PH 8.5) in a Microcon-10kDa centrifugal filter unit (Millipore) and centrifuged at 14,000×g for 40 min. The samples were digested by trypsin (enzyme to protein ratio 1:50) at 37°C overnight. The filtrates were desalted using Sep-Pak column C18 cartridges (Waters). Approximately 1.5 µg of peptide mixture per sample was injected in single technical replicates and an Orbitrap Fusion Lumos mass spectrometer (Thermo Scientific) coupled with an UltiMateTM 3000 UHPLC was used for DIA-MS analysis. A Spectronaut software against the Pan-Human library91 (link) was applied for protein/peptide identification and quantification.
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3

HPLC Analysis of N-acetylcysteine Thioester

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HPLC set up consisted of Thermo ScientificTM UltiMateTM 3000 UHPLC controlled by the Chromeleon 7.2 software and equipped with an autosampler (WPS-3000TSL), a column oven (TCC-3100), and a diode array detector (UV-vis DAD-3000RS). Samples were separated on Hypersil GOLD C18 columns (150 × 2.1 mm, 1.9 μm, Thermo Scientific). A mixture of 20 mM phosphoric acid and acetonitrile (99:1 v/v) was filtered through a 0.45-μm filter and used as a mobile phase for isocratic elution. Separation was performed at a flow rate of 0.3 mL/min at 35 °C. The volume of injection was 5 μL, and the absorbance of the effluent was recorded at 240 nm for a total run time of 6 min. The use of a diode array detector allowed absorption spectra of separate peaks to be retrieved in the 190–800 nm range after the run. N-acetylcysteine thioester of 3-phosphoglyceric acid eluted at 2.6–2.7 min.
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4

Metabolomic Analysis of Serum-Starved Cells

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A total of 5 × 106 cells were cultured without serum for 24 h and then cultured in DMEM with 10% FBS for 12 h. Then, the cells were frozen in liquid nitrogen and subjected to analysis. The metabolites were separated and analyzed using an Ultimate 3000 UHPLC (Dionex, Sunnyvale, CA, USA) coupled with a Q ExactiveTM Hybrid Quadrupole‐Orbitrap Mass Spectrometer (QE‐MS, Thermo Fisher Scientific, Wilmington, DE, USA) system. An Acquity HSS T3 column (100 × 2.1 mm i.d., 1.8‐µm particle size, Waters) was used in the study. The Orbitrap Q Exactive‐MS was equipped with an HESI probe.
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5

Comparative Proteomic Analysis of BRCA1-KO Fibroblasts

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Plasma membranes proteins were enriched from fibroblast lysates (Fibroblasts control vs. BRCA1-KO fibroblasts) using the Plasma Membrane Protein Extraction Kit (Abcam, MA, USA). Proteins were also prepared from pelleted EVs. Protein samples were run on a stacking gel, and gel bands were reduced with DTT, alkylated with iodoacetic acid and then digested with trypsin with re-solubilization in 0.1% aqueous formic acid/2% acetonitrile. Peptides were loaded onto a Thermo Acclaim Pepmap precolumn (Thermo, 75uM ID X 2 cm C18 3uM beads), and onto an Acclaim Pepmap Easyspray analytical column separation (Thermo, 75uM X 15 cm with C18 2uM beads) using a Dionex Ultimate 3000 uHPLC at 220 nl/min with a gradient of 2–35% organic (0.1% formic acid in acetonitrile) over 4 h. Peptides were analyzed using a Thermo Orbitrap Fusion mass spectrometer operating at 120,000 resolution (FWHM in MS1, 15,000 for MS/MS) with HCD sequencing all peptides with a charge of 2+ or greater. The raw data were converted into MGF format (Mascot Generic Format) searched using Mascot 2.3 against human sequences (Swissprot). The database search results were loaded onto Scaffold Q+ Scaffold_4.7.2 (Proteome Sciences) for spectral counting, statistical treatment and data visualization.
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6

Quantitative Proteomics of Biological Samples

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Samples were analyzed by both liquid chromatography – selected reaction monitoring (LC-SRM) and liquid chromatography – data dependent acquisition (DDA) tandem mass spectrometry (LC-MS/MS) as previously described46 (link),48 (link). Global analysis was performed on an Orbitrap – Velos coupled with an Eksigent 2D nano-LC, while targeted (LC-SRM) analysis was performed on a Qtrap 5500 coupled with a Dionex Ultimate 3000 UHPLC utilizing optimized conditions described previously. LC-SRM data was directly loaded into Skyline and transition quality, peak shape, and peak boundaries were manually validated. Resulting integrated peak areas were directly exported and protein quantity (pmol/g) was calculated against the known spike of stable isotope labeled peptides. LC-MS/MS data was queried against the SwissProt human database using Mascot (v2.3.1) and directly loaded into Scaffold™ (Proteome Software). Peptide Spectral Matches (PSMs) were directly exported with a 99% confidence in protein identifications and at least 2 unique peptides per protein, resulting in a false discovery rate of 0.54%. Statistical analysis for proteomics data, including principal component analysis, was performed using the MetaboAnalyst (v3.0) software suite49 (link).
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7

Non-targeted Metabolomics Profiling

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Samples were detected by performing non-targeted UPLC-MS/MS using an Ultimate 3000 UHPLC (Dionex) system combined with a Thermo Q-Exactive (Orbitrap) mass spectrometer (Thermo Fisher Scientific, San Jose, CA, USA). Data identifications were performed using a Trace Finder. First, based on the endogenous MS database, metabolites were identified by accurate masses. Subsequently, the metabolites were identified at the MS/MS level using in-house MS/MS library, which was built using chemical standards. The matching confidence of experimental MS/MS spectra with MS/MS in the library was evaluated using library score. Normally, the metabolites with library score >30 were considered as MS/MS confirmed (Tang et al., 2016 (link)). The MS/MS spectra of representative metabolites were shown in the Supplementary Figure. A 0.25-min retention time deviation was applied, and the mass shifts of the primary and secondary identifications were 10 and 15 ppm, respectively (Ning et al., 2018 (link)).
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8

BALF Metabolomic and Lipidomic Analysis

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The detailed method of BALF sample pretreatment is described in the Supplement 3. All compounds in BALF were analyzed using a Cortecs C18 column (2.1 × 100 mm, Waters) on an Ultimate 3000 UHPLC (Dionex) system coupled with a Q Exactive (Orbitrap) mass spectrometer (Thermo Fisher, CA). Detailed parameters for the untargeted metabolic and lipidomic analyses were set following the protocols of our previously reported study.23 (link) Data-dependent MS/MS acquisition (DDA) of all samples was analyzed using TraceFinderTM (Thermo, CA). Metabolites and lipids were identified based on matching precursor and characteristic fragment masses and then assigned using in-house databases in “screening” mode. Any metabolite feature with more than 20% missing values was removed from the result.24 (link),25 (link) Missing values were estimated by the Bayesian PCA (BPCA) method. Data were normalized by the QC group and then auto-scaled using MetaboAnalystR 3.0.26 (link) The normalized data were used for downstream analysis. Principal component analysis (PCA) and orthogonal projections to latent structures discriminant analysis (OPLS-DA) were conducted using SIMCA v14.1 (Umetrics, Sweden).
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9

UHPLC Analysis of Compound Mixture

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A Dionex Ultimate 3000 UHPLC equipped with an auto-sampler, quaternary solvent delivery pump and diode array detector (Germany). The software used was Chromeleon software. The stationary phase used was a ZORBAX Eclipse Plus® C18 column with dimensions of 250 × 4.6 mm, 5 μm (California, USA). On the other hand, the used mobile phase was a mixture of 0.5 mM KH2PO4 solution : methanol (65 : 35, v/v) which was filtered through a 0.45 μm millipore membrane filter.
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10

Metabolic profiling of regulatory T cells

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CD4+CD25hi Treg cells, isolated from lymphoid organs of C57BL/6 mice, were purified and resuspended in complete Click’s medium. Then, 1.3 × 106 Treg cells were treated with medium alone or immobilized anti-CD3 antibody (10 μg ml−1) and anti-CD28 antibody (10 μg ml−1) for 16 h in the presence Torin 1 (50 nM) or vehicle control. Intracellular metabolites, isolated using methanol extraction of two technical replicates, were analyzed using the Ultimate 3000 UHPLC (Dionex) coupled to Q Exactive Plus-Mass spectrometer (QE-MS, Thermo Fisher Scientific) for metabolite profiling. Detailed methods were previously described68 (link), except that mobile phase A was replaced with water containing 5 mM ammonium acetate (pH 6.8). Differentially expressed metabolites were identified by Limma (Bioconductor) and the Benjamini-Hochberg method was used to estimate the false discover rate (FDR). MetaboAnalyst was used to analyze range-scale data and provide KEGG pathway analysis of significantly altered metabolic pathways (log2 = 0.5) (www.metaboanalyst.ca/)49 (link).
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