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29 protocols using exion lc

1

Dual LC-MS Methods for Quantitative and Qualitative Analysis

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Two separate liquid-chromatography-mass spectrometry (LC-MS) methods were utilised to analyse the samples, one quantitative (LC-MS/MS) and one qualitative (LC-HRMS). The quantitative method incorporated a Sciex ExionLC coupled to a Sciex 6500 + QTrap (Toronto, Canada), fitted with a TurboSpray Ion-Drive source. The qualitative screening method used a Sciex Ex-ionLC coupled to a Sciex Triple TOF 5600 spectrometer. MS data were collected over a m/z range of 50-600. Data were acquired in Sequential Window Acquisition of all THeoretical fragment-ion spectra (SWATH) mode, utilising one full scan MS (collision energy of 10 V) and 33 subsequent experiments, each of which had a collision energy of 25 V with a collision energy spread of 15 V. The first experiment gave information relating to the parent mass, while the other 33 gave information relating to the fragment ions. For specific information regarding instrumental parameters, please refer to the previous publications. ( Bade et al., 2020c ( Bade et al., , 2020a ) ) 2.5. Criteria for Quantitative and Qualitative Analysis
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2

Vitamin D Metabolite Profiling by LC-MS

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The vitamin D metabolite profile (25(OH)D3, 24,25(OH)2D3, and epi-25(OH)D3) was analyzed by high-performance liquid chromatography coupled with mass spectrometry following an isotope dilution methodology. Whole blood was collected on Whatman 903 cards, and dried blood spots were prepared. Two 3-mm discs were cut out, pooled together, and subjected to methanol extraction. Before analysis, vitamin D metabolites were derivatized with 4-(4′-dimethylaminophenyl)-1,2,4-triazoline-3,5-dione (DAPTAD) [32 (link)]. Chromatographic separation (Exion LC, Sciex) was performed on a Kinetex 1.7 µm F5 100 Å, 50 × 2.1 mm column in 8-min gradients of water and acetonitrile with 0.1% formic acid (0.45 mL/min; 40 °C). Detection was conducted using an MRM technique on 4500QTRAP (Exion LC, Sciex) in the electrospray positive ionization mode. The results were multiplied by hematocrit values to determine the serum concentrations of vitamin D metabolites [33 (link)].
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3

UHPLC-MS/MS Quantification of Compounds

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Sample analysis was achieved in a UHPLC (Exion LC, SCIEX, Wilmington, DE, USA) coupled to a triple quadrupole linear ion trap mass spectrometer (Qtrap 6500+, SCIEX, Wilmington, DE, USA) system. The analytical column setup was a ZORBAX RRHD Eclipse Plus C18 (3.0 mm × 150 mm, 1.8 μm, Agilent Technologies, Santa Clara, CA, USA) with a flow rate of 0.4 mL/min at 40 °C. The mobile phase A was H2O, B was MeOH, and both phases included 5 mmol/L NH4FA and 0.1% FA. The elution gradient started with 2% B for 0.5 min, which was followed by 25% B, 3 min; 30% B, 6 min; 35% B, 9.5 min; 80% B, 15 min; 100% B, 18 min; 100% B, 22 min; 2% B, 22.1 min; and 2% B, which was maintained for 4 min. The sample injection volume was 2 μL. The parameters of the ion source were as follows: source temperature was set at 500 °C, curtain gas was 30 psi, and GAS 1 and GAS 2 were 55 psi and 50 psi, respectively. In this experiment, MRM analyses were carried out with both positive and negative mode for regular detection. For confirming the positive samples, the MRM-IDA-EPI mode was used. The MRM parameters, declustering potential (DP), and collision energy (CE) are listed in Table S1.
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4

Liquid Chromatography-Mass Spectrometry Metabolomics

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Metabolites analyses were performed by liquid chromatography on an ExionLC (Sciex) coupled with electrospray mass spectrometry TripleQuad 7500 (Sciex). For each analysis, 1 μL of the sample was injected on a Premier BEH amide 1.7 μm, 2.1×150 mm column (Waters) using a flow rate of 0.40 mL/min at 40°C. Mobile phase A consisted of water with 10 mM ammonium formate + 0.1% formic acid. Mobile phase B consisted of acetonitrile with 0.1% formic acid. The gradient was programmed as follows: 0.0–1.0 min at 95% B; 1.0–7.0 min to 50% B; 7.0–7.1 min to 95% B; and 7.1–10.0 min at 95% B. Electrospray ionization was performed in positive ion mode. We applied the following settings: curtain gas at 40 psi; collision gas was set at 9; ion spray voltage at 1600 V; the temperature at 350°C; ion source Gas 1 at 30 psi; ion source Gas 2 at 50 psi; entrance potential at 10 V; and collision cell exit potential at 10 V. Data acquisition was performed in MRM mode with the CE values reported in Supp. Table 3. Area ratios of endogenous metabolites and surrogate internal standards (Supp. Table 3) were quantified using SCIEX OS 3.1 (Sciex).
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5

UPLC-MS/MS Analysis of Vinblastine Metabolites

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An ultrahigh performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) system was used to analyze VCR and its M1 metabolite. The UPLC system (SCIEX ExionLC™, Framingham, MA, USA) was coupled with an API 5500-Qtrap triple quadrupole mass spectrometer (Applied Biosystem/AB SCIEX, Framingham, MA, USA) equipped with an electron spray ionization (ESI) source in the positive mode. Chromatographic separation was achieved using Inertsil ODS-3 C18 column (5 μm, 3.0 x 150 mm). The mobile phases consisted of methanol: 0.2% formic acid in water (20:80 v/v, mobile phase A) and methanol: 0.2% formic acid in water (80:20 v/v, mobile phase B). Gradient elution was used for separation as follows: 25% B—55% B (0–0.4 min), 55% B—25% B (0.4–3.5 min), 25% B (3.5–5 min). The elution was performed at a flow rate of 0.4 mL/min with an injection volume of 10 μL, while column and autosampler temperatures were set at 25 °C and 5 °C, respectively. The quantifications of VCR, M1 metabolite, and VRL internal standard were performed with their respective mass transition pairs presented in Table 1.
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6

Quantifying Enzyme-Inhibited Substrate Turnover

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After the enzyme reaction (0.25 μM enzyme) with the quinone (0–1 μM), the substrate AVLQSGFR (10 μM) was added and further incubated for 20 min at 37 °C. Then, an equal volume of a solution containing 0.1% formic acid in CH3CN and the internal standard stable AVLQ (100 nM) was mixed to terminate the reaction. The formed AVLQ and stable AVLQ were separated using a Kinetex C18 column (2.1 × 50 mm, 2.6 μm) with a gradient elution system (ExionLC™, Sciex) at a flow rate of 0.5 mL/min. Solvent A was 0.1% formic acid in H2O, while solvent B was CH3CN. The linear gradient program was as follows: initial B0%, 1 min B45%, 1.1 min B0%, 2.5 min B0%. The eluate was introduced into a quadrupole-time-of-flight tandem mass spectrometer (Q-TOF-MS, X500R, Sciex) in positive mode and monitored using MRMHR at the following transitions: m/z 201.1/185.1077 ± 0.01 (to quantify), m/z 202.1/143.0607 ± 0.01 (to confirm), and m/z 202.1/102.0341 ± 0.01 (to confirm) for AVLQ, and m/z 248.0/129.0218 ± 0.01 (to quantify) for the internal standard stable AVLQ. TOF-MS for AVLQ (C19H36N5O6, [M+H]+ 430.2660) and stable AVLQ ([13C3]C16H35[15N1]N4O6, [M+H]+ 434.2731) were also monitored. The standard curve for AVLQ was prepared with concentrations ranging from 0 to 1 μM, and the IC50 value was calculated using Prism v.9.5 (GraphPad Software, LLC., CA, USA). The experiment was performed twice.
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7

Oxidolipidomic Analysis by LC-MS/MS

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Oxidolipidomics samples were analyzed on the SCIEX 7500 system coupled with ExionLC (SCIEX, Concord, Canada) using multiple reaction monitoring analysis. Mobile phase A is composed of 93:7 acetonitrile:dichloromethane containing 2 mM ammonium acetate and mobile phase B is composed of 50:50 acetonitrile:water containing 2 mM ammonium acetate. A Phenomenex Luna NH2 column with 3 µm particle size (4.6×150 mm2) was used for separation and column temperature was kept at 40°C. The total flow rate is 0.7 mL/min with a total run time of 17 min. Samples were extracted using the Bligh and Dyer method. Lower layer was collected, dried down, and resuspended in mobile phase A.
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8

Metabolome Analysis via LC-MS/MS

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The metabolome was analyzed using Exion LC (SCIEX) equipped with mass spectrometer of QTRAP6500+ (SCIEX, Framingham, USA). Samples were detected using BEH C8 column (1.7 μm × 2.1 mm × 100 mm, Waters) with flow rate of 0.35 ml/min in positive electrospray ionization mode. The mobile phases used were 0.1% (v/v) formic acid-water and 0.1% (v/v) formic acid-acetonitrile. Samples were detected using the HSS T3 column (3.5 μm × 4.6 mm × 250 mm, Waters) with flow rate of 0.35 ml/min in negative electrospray ionization mode. The mobile phase was 6.5 mmol/L ammonium bicarbonate and 6.5 mmol/L ammonium bicarbonate-95% (v/v) methanol. Metabolites were further analyzed according to the previous method.
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9

GSH Adduct Standard and LC-MS Analysis

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GSH adduct standard and LC-MS Analysis A glutathionylated 15-oxo-LXA4 standard was made by incubation of 10 µM 15-oxo-LXA4-Me with 100 µM GSH in 50 mM potassium phosphate buffer (pH = 8) for 1 hr at 37°C (91 (link),97 (link)). GSH conjugates were extracted from 1 mL of cell supernatant using Oasis HLB 1 cc solid phase extraction columns (Waters) and applied to a Luna C18 column (2 x 100 mm, Phenomenex) at a flow rate of 0.25 mL/min and eluted with a linear consisting of solvent A (H2O + 0.1% acetic acid) and Solvent B (ACN + 0.1% acetic acid). The gradient started at 20% B at 5 min and increasing to 98% B at 25 min. The gradient was held at 100% B for 2 min and equilibrated at 20% B for 35 min. GSH adducts were analyzed on a 6500+ QTRAP coupled to an Exion LC (Sciex) using multiple reaction monitoring (658→308) and positive ionization with the following MS conditions: CUR 40, CAD med, IS 4500, GS1 70, GS2 65, Temp 550°C, DP 80, EP 7, CE 17, CXP 7.
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10

UPLC-QTOF-MS/MS Metabolomic Analysis

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UPLC separation was carried out on Sciex Exion LC equipped with a binary pump, an auto-sampler, a thermostatically controlled column apartment, and a Phenomenex C18 (2.1 × 100 mm, 2.6 μm). The mobile phases were 0.05% formic acid in water (phase A) and a mixture of methanol and acetonitrile (50:50 v/v, phase B). The flow rate was 0.3 mL/min and the injection volume was 2.0 μL. The gradient program was used as follows: 0–1.0 min, 5% B; 3.5–18.0 min, 28–98% B; 18.0–22.0 min, 98% B; 22.1–25.0 min, 5% B.
The eluates from the UPLC system were directly entered into an X500R Q-TOF-MS/MS system. The electrospray ionization (ESI) source was operated with a mass range of 80–1250 m/z in positive and negative ionization mode, respectively. Ion source temperature was set at 550 °C. Appropriate MS/MS productions were obtained by different collision energies under 20, 40, and 60 eV.
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