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Dionex ultimate 3000 lc system

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

The Dionex Ultimate 3000 LC system is a high-performance liquid chromatography (HPLC) instrument designed for efficient separation, identification, and quantification of a wide range of analytes. It features a modular architecture, allowing for customization to meet specific analytical requirements. The system includes a solvent and sample delivery system, a column compartment, and a variety of detection options, providing a comprehensive solution for liquid chromatography applications.

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46 protocols using dionex ultimate 3000 lc system

1

Comprehensive LC-MS Analysis of Underivatized Acids

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LC-MS(MSn) was performed in the positive-ion mode as described in Abdel-Khalik et al. utilizing the Orbitrap-Elite hybrid MS preceded by a Dionex Ultimate 3000 LC system (Dionex, now Thermo Fisher Scientific) [52 (link)]. For analysis of underivatized acids in the negative-ion mode, other than for polarity reversal and a change of column from a Hypersil Gold C18 to a Kinetex core-shell technology XB-C18 column (2.6 µm, 2.1 mm × 50 mm, Phenomenex, Macclesfield, UK), the method was as for positive-ion mode LC-ESI-MS(MSn) as described in Abdel-Khalik et al. [52 (link)].
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2

Quantitative Mass Spectrometry Analysis

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Analysis was performed on a LTQ-Orbitrap Elite (Thermo Fisher Scientific, Hemel Hempstead, UK) equipped with an electrospray probe, and a Dionex Ultimate 3000 LC system (Dionex; now Thermo Fisher Scientific), essentially as described previously (22 (link), 23 (link)). For each injection, three to five scan events were performed: one high-resolution (120,000, full-width at half maximum height at m/z 400) MS scan event in the Orbitrap analyzer in parallel with two to four multistage fragmentation (MSn) scan events in the LTQ linear ion trap. Quantification was performed by stable isotope dilution or by using isotope-labeled structural analogs.
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3

Reductive Amination of Enoxaparin Sodium

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The enoxaparin sodium size-fractionated samples were re-dissolved with water and acetic acid. 0.4 M AEAB in DMSO and 1 M sodium cyanoborohydride in DMSO were added. The ratio of DMSO and acetic acid was varied with acetic acid contents of 10%, 20%, 30% and 40% v/v tested, with 40% acetic acid used as an optimized condition. The mixture was then incubated at 37 °C overnight and dried with nitrogen gas. The dried sample was resuspended in water/methanol (80:20, v/v). It was analyzed and purified by HPLC SEC column (4.6 mm × 300 mm, 1.7 µm, Waters) using a Dionex UltiMate 3000 LC system (Thermo Fisher Scientific) following the method of Dr. Zaia and coworkers51 (link). Based on high-resolution SEC separation of derivatized II-S disaccharide standard, the reductive amination reaction had a yield of ~99% at 40% acetic acid (data not shown). Fractions were collected with an online auto-sampler and further dried down with nitrogen gas. Each synthetic hexasaccharide followed the same protocol.
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4

Quantification of EE2 in Water

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Water samples were collected from different tanks at nine separate occasions during the exposure and stored in darkness at −20°C until analysis. EE2 concentrations were analyzed in single or duplicate samples as previously described in Volkova et al. (2015b (link)). Briefly, water samples (100 mL) were extracted on 100 mg Strata X-33μ Polymeric Reversed Phase cartridges, reconditioned with MeOH. Dionex ultimate 3000 LC system (Thermo Scientific, San Jose, CA, USA), coupled to a triple quadruple mass spectrometer (TSQ Vantage, Thermo Scientific, San Jose, CA, USA) was used for quantitation of EE2 content. The quantification range was 0.5–100 ng/L, using EE2-d4 as internal standard.
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5

UPLC-MS-based Metabolomics Protocol

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10 µL of each sample was loaded into a Dionex UltiMate 3000 LC System (Thermo Scientific Bremen, Germany) equipped with a C-18 column (Acquity UPLC -HSS T3 1. 8 µm; 2.1 x 150 mm, Waters) coupled to a Q Exactive Orbitrap mass spectrometer (Thermo Scientific) operating in negative ion mode. A step gradient was carried out using solvent A (10 mM TBA and 15 mM acetic acid) and solvent B (100% methanol). The gradient started with 5% of solvent B and 95% solvent A and remained at 5% B until 2 min post injection. A linear gradient to 37% B was carried out until 7 min and increased to 41% until 14 min. Between 14 and 26 min the gradient increased to 95% of B and remained at 95% B for 4 min. At 30 min the gradient returned to 5% B. The chromatography was stopped at 40 min. The flow was kept constant at 0.25 mL/min and the column was placed at 40°C throughout the analysis. The MS operated in full scan mode (m/z range: [70.0000-1050.0000]) using a spray voltage of 4.80 kV, capillary temperature of 300°C, sheath gas at 40.0, auxiliary gas at 10.0. The AGC target was set at 3.0E+006 using a resolution of 140000, with a maximum IT fill time of 512 ms. Data collection was performed using the Xcalibur software (Thermo Scientific). The data analyses were performed by integrating the peak areas (El-Maven - Polly - Elucidata) (37 ).
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6

Quantitative Analysis of Tocopherols in Oils

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Tocopherols were analyzed according to Pignitter et al. [31 (link)]. Briefly, 0.05 g of oil sample was dissolved in 1 mL 2-propanol, vortexed and filtered through a nylon filter (0.22 µm). Analysis was carried out by means of a UHPLC (Dionex Ultimate 3000 LC system, Thermo Fisher Scientific, Vienna, Austria) with a flow rate of 1 mL/min using a C18 column (Kinetex EVO, 150 × 4.6 mm, 5 µm, Phenomenex). For separation of the tocopherols, a methanol gradient was used, starting with 75% methanol and 25% double-distilled water, reaching 100% methanol after 10 min and holding the plateau for 3 min. The initial conditions were reached again at 15 min. The tocopherol homologs were detected at a wavelength of 295 nm and quantitated using the standard addition method. Total tocopherol content was calculated by summing up the concentrations of α-, γ- and δ-tocopherol homolog. Limit of detection of α-, γ- and δ-tocopherol was determined by a signal-to-noise ratio of 3 with 0.30 µg/mL, 0.53 µg/mL and 0.23 µg/mL, respectively.
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7

Veratrum Alkaloid Identification in Biological Samples

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Veratrum steroidal alkaloids were identified in blood, breastmilk, and root/rhizome extracts using HPLC-QTOF and commercially available standards. Analysis was performed on a Bruker maXis ESI Q-TOF mass spectrometer (Bruker Corporation, Billerica, MA) coupled with a Dionex Ultimate 3000 LC system (Thermo Scientific, Waltham, MA). The samples were injected onto a Waters Xterra MS C18 column (5 μm, 2.1 × 150 mm) maintained at 40 °C at an injection volume of 5 μL. A gradient elution consisting of 0.1% formic acid in water (solvent A) and 0.1% formic acid in acetonitrile (solvent B) was used with a 300 μL/min flowrate. The elution method began at 10% solvent B before increasing to 20% solvent B after 1 min. Between minute 1 and 16, solvent B was increased to 40%. After 16.1 min, solvent B was increased to 100% and maintained until minute 20. Solvent B was decreased to 5% at 20.1 min and held constant until minute 25. The electrospray ionization (ESI) source was operated under the following conditions: positive ion mode, 4000 to −500 V voltage between capillary and end plate offset, 10.0 L/min flow rate of N2 drying gas at 200 °C.
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8

Targeted Metabolomics Analysis Using LC-MS

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A total of 10 µL of each sample was loaded into a Dionex UltiMate 3000 LC System (Thermo Scientific, Bremen, Germany) equipped with a C-18 column (Acquity UPLC -HSS T3 1. 8 µm; 2.1 × 150 mm, Waters, Milford, MA, USA) coupled to a Q Exactive Orbitrap mass spectrometer (Thermo Scientific), operating in negative ion mode. A step gradient was carried out using solvent A (10 mM TBA and 15 mM acetic acid) and solvent B (100% methanol). The gradient started with 5% of solvent B and 95% solvent A and remained at 5% B until 2 min post injection. A linear gradient to 37% B was carried out until 7 min and increased to 41% until 14 min. Between 14 and 26 min the gradient increased to 95% of B and remained at 95% B for 4 min. At 30 min the gradient returned to 5% B. The chromatography was stopped at 40 min. The flow was kept constant at 0.25 mL/min and the column was placed at 40 °C throughout the analysis. The MS operated in full scan mode (m/z range: (70.0000–1050.0000)) using a spray voltage of 4.80 kV, capillary temperature of 300 °C, sheath gas at 40.0, auxiliary gas at 10.0. The AGC target was set at 3.0 × 106 using a resolution of 140,000, with a maximum IT fill time of 512 ms.
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9

Qualitative Analysis of Saikosaponins

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The qualitative identification of saikosaponins in XG was carried out using a Q Exactive™ hybrid quadrupole-orbitrap mass spectrometer equipped with a Dionex Ultimate 3000 LC system (Thermo Fisher Scientific, USA). Analytes were detected at 30°C on a Waters CORTECTS C18 column (4.6 mm × 150 mm, 2.7 μm). The mobile phase was comprised of 0.01% acetic acid (A) and acetonitrile (B) with gradient elution program: 0∼9 min, 5–25% B, 9∼16 min, 25–35% B, 16∼23 min, 35–60% B, and 23∼30 min, 60–80% B. The flow rate was 0.3 mL·min−1. The heated ESI (H-ESI) source was operated, and MS parameters were optimized as follows: spray voltage, 3.5 kV; sheath gas flow, 40 L/min; aux gas flow, 10 L/min; capillary temperature, 320°C; aux gas heater temperature, 350°C. A full MS/dd-MS2 (data dependent MS2) method was used for acquisition. The full scan range was from 100 to 1500 in negative ion mode at a resolution of 70000 and 17,500 for MS2 scan. MS/MS spectra were fragmented by high-energy collision-induced dissociation (HCD) of normalized collision energy (NCE) values at the levels of 10%, 20%, and 30%. Date acquisition and processing were accomplished with Xcalibur software (version 4.2, Thermo Fisher Scientific, USA).
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10

Tracking Glucose Metabolism in Pro-T Cells

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Pro-T cells were cultured for 24 h in 10% glucose-free RPMI medium supplemented with 13C-labeled glucose (2 g/l). Metabolite measurements were performed using a Dionex UltiMate 3000 LC System (Thermo Scientific, Carlsbad, CA, USA) in-line connected to a Q-Exactive Orbitrap mass spectrometer (Thermo Scientific).
A detailed description of all methods used in this study is given in the Supplementary Materials and Methods.
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