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Thermo dionex ultimate 3000 hplc system

Manufactured by Thermo Fisher Scientific
Sourced in United States

The Thermo DIONEX UltiMate 3000 HPLC system is a liquid chromatography instrument designed for high-performance separations. It features a modular design, allowing users to configure the system to meet their specific analytical requirements. The system includes a pump, autosampler, column compartment, and detector, all controlled by a dedicated software interface.

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8 protocols using thermo dionex ultimate 3000 hplc system

1

Metabolite Identification by LC-MS/MS

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All samples were analyzed in random order on a Thermo Q Exactive HF Hybrid Quadrupole-Orbitrap Mass Spectrometer coupled with a Thermo DIONEX UltiMate 3000 HPLC system (Thermo Fisher Scientific, Waltham, MA, USA). The UltiMate 3000 HPLC system was equipped with a reversed-phase chromatography column [20 (link)]. To obtain full MS data, every sample was analyzed by liquid chromatography (LC)–MS in positive mode (+). For metabolite identification, one pooled sample for each group was analyzed by LC–MS/MS in positive mode to acquire MS/MS spectra at three collision energies (20, 40 and 60 eV).
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2

Methylglyoxal Trapping Assay Protocol

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The methylglyoxal trapping assay followed a published method with some modifications [5 (link),8 (link)]. Methylglyoxal (10 mM), o-phenylenediamine (50 mM) were freshly prepared in phosphate buffer (50 mM, pH 7.4). The final concentration of test samples (the five fractions, compounds 13 and kaempferol) and aminoguanidine was 5 mg/mL. Three mL methylglyoxal were incubated with 0.75 mL test samples or phosphate buffer in pH 7.4 at 37 °C water bath for 0, 0.25, 0.5, 0.75, 1, 1.5, 2, 3, 4, 6, 8, 12 and 24 h. After incubation, 200 μL of o-phenylenediamine were added with 200 μL of each test solution. Before HPLC analysis, the mixtures were kept in dark at room temperature for 1 h. The remaining methylglyoxal was detected on an Thermo Dionex Ultimate 3000 HPLC system (Thermo Fisher Scientific Inc., Massachusetts, USA) equipped with a diode array detector, and a Thermo Syncronis-C18 column (250 mm × 4.6 mm i.d., 5 μm; Thermo Fisher Scientific Inc., Massachusetts, USA). Mobile phases were composed of 0.1% formic acid in water (A) and methanol (B). The elution started at 50% B and then increased to 55% in 10 min, and then increased to 100% in 11 min and lasted for 5 min, then returned to 50% in 16.5 min and lasted for 5 min. The flow rate was 1 mL/min and the injection volume was 20 μL. Detection wavelength was monitored at 315 nm.
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3

Herbs Decoction for Traditional Chinese Medicine Treatment

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SND herbs (150 g) were consisted of 30 g Lonicerae japonicae Flos (Jin Yin Hua), 30 g Angelicae sinensis Radix (Dang Gui), 30 g Lonicerae japonicae Caulis (Ren Dong Teng), 30 g Spatholobi Caulis (Ji Xue Teng), and 30 g Glycyrrhizae Radix et Rhizoma (Gan Cao). All of them were purchased from the Zhejiang Chinese Medical University (Zhejiang, China), and were further authenticated by pharmacologist, Professor Jingxia Wang. A total of 150 g SND herbs were decocted twice with eightfold of water for 1 h. The extracts were combined, filtered, and then concentrated to a volume of 200 mL at 100 °C. The extracts were named as SND. SND used in this study were analyzed by a validated reversed-phase HPLC system (Thermo Dionex Ultimate 3000 HPLC system, Thermo Fisher Scientific, Waltham, MA, USA) using an Agilent Zorbax SB C18 column (4.6×150 mm, 5µm). A representative HPLC chromatogram of the SND was shown in Figure 1.

HPLC analysis of the Shouzu Ning Decoction (SND)

Administration method: The patients were treated with the SND twice a day. For each treatments, 200 mL SND was diluted with water to a final volume of 1000 mL. Temperature was kept at 35 °C to 40 °C in a thermostatic bath. Then the hands and feet of the patients were soaked in the bath for 20 minutes.
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4

Metabolomic Analysis of Cardiac Ischemia-Reperfusion

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Frozen left ventricular tissues from the young-WT-sham, aged-WT-sham, Sesn2-KO-sham, young-WT-I/R, aged-WT-I/R, Sesn2-KO-I/R mice were homogenized to extract polar metabolites for 2DLC-MS/MS analysis with Thermo Q Exactive HF Hybrid Quadrupole-Orbitrap Mass Spectrometer coupled with a Thermo DIONEX UltiMate 3000 HPLC system (Thermo Fisher Scientific, Waltham, MA, USA) [22 (link)]. Each sample was respectively analyzed by 2DLC-MS in positive mode (+) and negative mode (−) to obtain the full MS data. For 2DLC-MS data analysis, XCMS software was used for spectrum deconvolution, and MetSign software was used for metabolite identification, cross-sample peak list alignment, normalization, and statistical analysis [[23] (link), [24] (link), [25] (link)]. Enrichment analysis of significantly altered metabolites were performed with MBROLE 2.0 by searching against KEGG, UniPathway, and BioCyc SMPDB database to obtain significantly regulated pathways [26 (link)].
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5

Proteomic Analysis of Protein Samples

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Protein samples were separated by SDS–PAGE electrophoresis and target protein bands were excised, and then alkylated by incubating with 25 mM chloroacetamide for 45 min in the dark at 55 °C followed by digesting using trypsin (Promega, Fitchburg, WI) for 14 h at 37 °C. The peptides were extracted three times with 50% acetonitrile supplemented with 0.1% formic acid and then vacuum-dried peptides were dissolved in 20 µl 0.1% (v/v) formic acid and analyzed by LC–MS/MS analysis.
For LC–MS/MS analysis, peptides were loaded in a trap column and then separated by the Thermo-Dionex Ultimate 3000 HPLC system (Thermo Fisher Scientific, Waltham, MA, USA), and detected by the Obitrap Fusion LUMOS Tribrid mass spectrometer (Thermo Fisher Scientific, Waltham, MA, USA). Identification of protein modification was performed by Proteome Discoverer 2.3 software using the label-free quantification method.
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6

Comprehensive 2DLC-MS/MS Metabolomics

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2DLC‐MS/MS analysis was completed by first collecting left ventricular tissue samples at 4°C to retain metabolites. Polar metabolites were mixed with methanol and centrifuged to acquire a metabolite supernatant. The supernatant was analyzed by the Thermo Q Exactive HF Hybrid Quadrupole‐Orbitrap Mass Spectrometer coupled to the Thermo DIONEX UltiMate 3000 HPLC system (Thermo‐Fisher Scientific). Utilizing reverse‐phase chromatography (RPC) and hydrophilic interaction chromatography (HILIC) in the HPLC, each sample was analyzed by 2DLC‐MS. Each sample group were split into six pooled samples and analyzed in both positive and negative modes to obtain the full MS/MS spectra at 20, 40, and 60 eV collision energies.
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7

Untargeted and Targeted Metabolomic Profiling

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All samples were analyzed in random order on a Thermo Q Exactive HF Hybrid Quadrupole-Orbitrap Mass Spectrometer coupled with a Thermo DIONEX UltiMate 3000 HPLC system (Thermo Fisher Scientific, Waltham, MA, USA). For untargeted metabolic profiling, the UltiMate 3000 HPLC system was equipped with a parallel 2DLC (a reversed-phase chromatography (RPC) column and a hydrophilic interaction liquid chromatography (HILIC) column) [22 (link)]. For the targeted metabolomic study, the UltiMate 3000 HPLC system was equipped with an RPC column [21 (link)]. To obtain full MS data, every sample was analyzed by LC-MS in positive and/or negative modes depending on the chemical properties of the metabolites of interest. One pooled sample of each group was analyzed by LC-MS/MS to acquire MS/MS spectra at three collision energies (20, 40, and 60 eV) for metabolite identification.
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8

Parallel 2DLC-MS/MS for Metabolite Profiling

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All samples were analyzed in random order on a Thermo Q Exactive HF Hybrid Quadrupole-Orbitrap Mass Spectrometer coupled with a Thermo DIONEX UltiMate 3000 HPLC system (Thermo Fisher Scientific, Waltham, MA, USA) equipped with a reversed-phase chromatography (RPC) column and a hydrophilic interaction chromatography (HILIC) column configured to form a parallel 2DLC-MS system(Klavins et al., 2014 (link)). To obtain full MS data, every sample was analyzed by parallel 2DLC-MS in positive (+) and negative (−) modes. One unlabeled sample in each group was analyzed by 2DLC-MS/MS in positive and negative modes to acquire MS/MS spectra at 20, 40, and 60 eV collision energies as a quality control for metabolite identification. Data of unlabeled samples were first matched to an in-house database that contains parent ion m/z, MS/MS spectra, and retention time of authentic standards (MSI Level 1 identification). Data without a match (MSI Level 2 identification) were analyzed using Compound Discoverer software v2.0 (Thermo Fisher Scientific, Germany).
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