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30 protocols using api5000 triple quadrupole mass spectrometer

1

Quantifying Cisapride and Metabolites

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The cisapride drug and norcisapride metabolite were extracted from efflux media and analyzed using a Shimadzu UFLC system (Carlsbad) coupled with a Sciex API5000 triple quadrupole mass-spectrometer (Foster City) using positive ionization mode. Cisapride and norcisapride were further separated by a gradient mode of 10 mM ammonium acetate–acetonitrile as a mobile phase using an Acclaim Trinity P1 reverse phase column (2.1 × 50 mm, 3 μm; Thermo Fisher Scientific). Mass ion transitions (Q1/Q3) of cisapride and norcisapride were m/z 468.3/186.0 and m/z 314.2/184.0, respectively. 1-naphthol, 1-naphthol-s-glucuronide, p-nitrophenol, and p-nitrophenol sulfate were separated by a gradient elution with 0.1% formic acid in H2O and 0.1% formic acid in acetonitrile as mobile phases using a XTerra MS C18 reverse phase column (4.6 × 50 mm, 3 μm; Waters). Mass ion transitions of 1-naphthol, 1-naphthol-s-glucuronide, p-nitrophenol, and p-nitrophenol sulfate were m/z 143.3/115.3, m/z 318.9/143.3, m/z 138.2/168.1, and m/z 217.9/138.2, respectively. The standard curve range of each drug and metabolite was 0.5–2,000 nM. Precision (defined by the coefficient of variation) and accuracy (defined by relative error) of LC-MS/MS analyses were both <15% for all drugs and metabolites.
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2

Sterol Profiling by LC-MS/MS

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Lipids were extracted from the samples by a modified Bligh–Dyer extraction, and sterols were analyzed by LC-MS/MS as described previously (Zhang et al., 2021). Briefly, lipid extracts from samples were dried under nitrogen and reconstituted in 90% methanol. Sterols were analyzed using a Shimadzu LC20ADxr high-performance liquid chromatograph equipped with an Agilent Poroshell 120 EC-C18 column (2.1 × 150 mm, 2.7-μm particles; Agilent Technologies). The elution was done using a solvent gradient that transitioned linearly from 93% methanol/7% H2O to 100% methanol in 7 min. The column was washed for 5 min in 100% methanol and then returned to the initial solvent. Sterols were detected using a SCIEX API 5000 triple quadrupole mass spectrometer equipped with a Turbo V APCI source in positive mode with atmospheric pressure chemical ionization at a temperature of 350 °C. Data were acquired under multiple reaction monitoring for mass pairs optimized for each sterol. The internal standards were commercially available for all but four of the sterols (dihydro-ff-MAS, dihydro-t-MAS, dehydrolathosterol, and dehydrodesmosterol) in the cholesterol biosynthetic pathway that were identified by their unique m/z values and retention times as described (Mitsche et al., 2015 (link); McDonald et al., 2012 (link)).
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3

LC-MS/MS Analysis of Small Molecules

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The LC system was an Agilent 1260 infinity system consisting of a binary LC pump, a vacuum degasser, a temperature-controlled microwell plate autosampler set at 4°C and a temperature-controlled column compartment set at 40°C (Agilent technologies, CA, USA). Data acquisition and processing were performed using Analyst 1.6.2 (Sciex, MA, USA). The analytes were separated on a Zorbax SB-CN 50 mm × 4.6 mm, I.D. 3.5 μm (Agilent Technologies), with a precolumn CN AJO-4305 4 mm × 3 mm, I.D. 3.5 μm (Phenomenex), at a flow rate of 700 μl/min. The mobile phase consisted of (A) acetonitrile-ammonium formate 20 mM with 1% formic acid pH approximately 2.6 (15–85, v/v) and (B) methanol–acetonitrile (75–25, v/v). The mobile phase gradient was A: 0–2 min, B: 2.2–3.7 min and A: 3.9–6.5 min (with 0.2 min linear gradient switch), resulting in a total runtime of 6.5 min per sample. The injection volume was 2 μl.
An API 5000 triple quadrupole mass spectrometer (Sciex) with a TurboV ionization source interface, operating in positive ion mode, was used for the MS/MS analysis. Ion spray voltage was set to 5500 V, with a drying temperature at 650°C. The curtain gas was 25 psi and the nebulizer (GS1) and auxiliary (GS2) gases were 60 psi.
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4

LC-MS/MS Analysis of Analytes

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LC-MS/MS was performed using an API 5000 triple quadrupole mass spectrometer (Sciex), coupled to an Agilent 1200 HPLC system (Agilent Technologies). Samples (20 μL) were injected using a CTC PAL Autosampler set at 4°C (CTC Analytics AG, Switzerland). Analytes were resolved through chromatographic separation using a 4-μm Synergi Hydro-RP C18 column (150×2 mm; Phenomenex, Torrance, CA), with column chamber set at 40°C, over a binary gradient with a flow rate of 0.5 mL/min. HPLC gradient conditions were as follows: 0 min, 25:75 A/B; 2.5 min, 20:80 A/B; 7.5 min, 10:90 A/B; 8 min, 0:100 A/B; 10 min, 25:75 A/B; 18 min, 25:75 A/B. Solvent A: 0.1% formic acid in water; Solvent B: methanol. Total run time was 18 min.
LC-MS/MS was performed in positive ion mode, [M + H]+, with quantifier and qualifier ion transitions selected for each analyte, at a dwell time of 50 ms. Source parameters were set as follows: positive ion spray voltage, 5000 V; ion source temperature, 500°C; collision gas, 7 psi; curtain gas, 35 psi; nebulizer gas, 25 psi; turbo gas, 45 psi. Transitions were optimized using direct infusion (10 μL/min) with each standard (100 ng/mL). MS/MS parameters are summarized in Table 1. Data were acquired and processed using Analyst® (Sciex), version 1.6.2.
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5

Quantitative Metabolomics in Biological Samples

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The samples were prepared, and targeted quantitative metabolomics was measured by LC/MS/MS as reported previously15 (link) or with minor modifications. Briefly, methanol was added to plasma or urine and kidney homogenate for deproteinization and extraction. Each mixture was vortexed and centrifuged. The supernatant was diluted with water. Analyte separation and quantification were performed using a Shimadzu Nexera UHPLC system (Shimadzu, Kyoto, Japan) coupled with an API5000 triple quadrupole mass spectrometer (SCIEX, Framingham, MA, USA) with electrospray ionization operated in positive ion mode. The separation was performed on a Triart C18 column (3.0 × 150 mm, 5 μm, YMC, Kyoto, Japan). Quantification was performed by multiple reaction monitoring. NAD + , NADH, NADP, and NADPH in kidney tissue were measured using the NAD + /NADH Assay Kit (E2ND-100, EnzyChrom) and the NADP + /NADPH Assay Kit (ECNP-100, EnzyChrom), respectively.
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6

Identification and Quantification of Labetalol Glucuronides

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Three glucuronide metabolites of labetalol have been detected (Martin et al., 1976 (link); Niemeijer et al., 1991 (link)). Glucuronidation at the phenolic-OH (Gluc-1) by UGT1A1 and at the benzylic-OH (Gluc-2) by UGT2B7 have been previously reported (Jeong et al., 2008 (link)); however, it has not been reported which UGT isoform catalyzes the N-glucuronidation of labetalol (Gluc-3).
Media samples, cell lysate or recombinant reaction mixture (30 µL) were extracted by protein precipitation with methanol (150 µL) containing the stable, isotopically labeled internal standard labetalol-d3. Samples were vortexed and centrifuged, and 20 µL of the supernatant was mixed with 80 µL of water prior to LC-MS/MS analysis. Chromatographic separation of the three glucuronide metabolites was achieved on a Waters Atlantis T3 (50 × 2.1 mm, 3 µm particle size) analytical column with 0.1% formic acid in water and acetonitrile under gradient conditions. Analytes and internal standards were detected on SCIEX API 5000 triple quadrupole mass spectrometer using TurboIonSpray in the positive ionization mode. Due to the unavailability of analytical standards for labetalol glucuronides, the levels of the three glucuronides were assessed by the peak areas of each labetalol glucuronide (Gluc-1, Gluc-2, and Gluc-3) normalized to the peak area of internal analytical standard.
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7

Quantifying bUPA and FUPA Metabolites

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After precipitating proteins by centrifugation at 14,000 × g for 5 min, the supernatant was vacuum-dried at 40 °C for 1.5 h and redissolved in 0.1% (v/v) formic acid in water. Samples were injected into a liquid chromatography-mass spectrometry (LC-MS) system (API5000 triple quadrupole mass spectrometer; SCIEX, Framingham, MA, USA). Using bUPA and FUPA metabolite standards, standard curves were constructed for concentrations ranging from 0.1 to 30 μM. The enzymatic activity was normalized to the corresponding DHPase expression levels determined by immunoblotting after SDS-PAGE.
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8

LC-MS/MS Quantification of Tetracycline

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All samples of tissue homogenate, plasma, cell lysate, and cell culture medium were precipitated with acetonitrile (containing IS, buspirone, 5 ng/mL) followed by quantitation against the corresponding standard curve prepared in the blank biomatrix. The concentration of TET was determined by an LC-MS/MS method with an API 5000 Triple quadrupole mass spectrometer (AB Sciex, Foster City, CA, USA) connected to a Shimadzu LC-20AD HPLC system (Shimadzu, Japan). The chromatographic column was the C18 column (3.0 mm × 50 mm, 2.6 µm, Phenomenex). The mobile phase consisted of water containing 0.1% of formic acid (A) and acetonitrile containing 0.1% of formic acid (B). Separation was achieved following a binary gradient elution procedure: 0–0.3 min B 10%, 0.3–1.4 min B 10%→90%, 1.4–1.8 min B 90%, 1.8–1.9 min B 90%→10%, 1.9–3.0 min B 10%. The volume of each injection was 5.0 µL, and the flow rate was 0.6 mL/min.
TET and IS were detected by multiple reaction monitoring (MRM) in the positive ion mode. The precursor and product ions used for quantification were as follows: m/z 609.0→381.1 for TET and m/z 386.4→122.1 for IS, respectively.
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9

Quantitative LC-MS/MS Bioanalysis of ST-246

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ST-246 concentrations in rat, dog, and monkey plasma were determined using the liquid chromatography–tandem mass spectrometry (LC-MS/MS) method. A total of 125 µL acetonitrile containing IS (20 ng/mL) was added into 25 µL plasma to precipitate plasma protein. After high-speed centrifugation, 20 µL of supernatant was added to 180 µL of 50% acetonitrile solution and injected onto LC-MS/MS. The chromatographic separation was performed using a C18 column (3.0 mm × 50 mm, 2.6 µm, Phenomenex) with a security guard column. The mobile phase consisted of water containing 0.1% formic acid (A) and acetonitrile containing 0.1% formic acid (B). Separation was achieved with a 3-min run time with the following gradient program: initial conditions start with an increase from 30 to 90% B over 1.2 min, hold at 90% B for 0.5 min, return to 30% B over 0.1 min, and hold at 30% B for 1.2 min. The constant flow rate is 0.6 mL/min. An AB Sciex API 5000 Triple quadrupole mass spectrometer was tuned to the multiple reaction monitoring (MRM) mode to monitor the m/z transitions, 377/173 for ST-246 and 381/177 for the IS, in the positive ion mode.
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10

Quantification of dCTP and FTCtp in CD4+ T cells

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CD4+ T cells were isolated from healthy donor PBMCs using immunomagnetic beads (Invitrogen). Quantification of concentrations of endogenous dCTP and FTC active metabolite FTCtp was done by a validated LC-MS/MS method [28 (link)], which has a calibration range of 0.02–20 ng/ml. Cells were lysed by incubation in cold 70:30 methanol: water for 15 min in ice, and stored at −80°C until time of analysis. Following protein precipitation, the metabolites FTC and dCTP were extracted using internal standards 13C5-TFVdp and 13C915N3-dCTP, respectively. Extracts were analyzed by anion exchange chromatography on a Thermo BioBasic AX (50*2.1 mm, 5 μm) column before detection on an AB Sciex API-5000 triple quadrupole mass spectrometer. Precision and accuracy of this assay is within 20%.
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