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Qtrap 5500 system

Manufactured by AB Sciex
Sourced in United States, Canada, Germany, Japan

The QTRAP 5500 system is a highly sensitive and versatile mass spectrometer designed for analytical applications. It combines the capabilities of a triple quadrupole mass spectrometer with the functionality of a linear ion trap, providing enhanced selectivity and sensitivity. The system offers high-performance quantitative and qualitative analysis across a wide range of analytes.

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48 protocols using qtrap 5500 system

1

Quantitative Serum 25(OH)D Measurement

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The following tests were performed at the screening visit: RBC, platelets, hematocrit, hemoglobin, WBC and differential count, sodium, potassium, urea, albumin, SGPT/ALAT, SGOT/ASAT, ALP, GGT, total bilirubin, creatinine, calcium, phosphate, TSH and blood β-HCG pregnancy test. A prick finger blood test for a glucose level was performed to confirm the fasting status at each period. All the analyses were performed at the ISO 151198 clinical chemistry laboratory of the University of Liège (Belgium). The LC MS/MS VDSP traceable method was used for serum 25(OH)D measurement as described previously [13 (link)]. The samples were measured with the MassChrom® 25-OH-Vitamin D3/D2 LC MS/MS kit (Chromsystems, Gräfelfing, Germany) including 3-epi-25-OH-Vitamin D3 upgrade on the AB SCIEX QTRAP® 5500 system (AB Sciex, Framingham, MA, USA). This method is able to measure the serum 25(OH)D2 and 25(OH)D3 separately from their epimeric forms 3-epi-25(OH)D. In the following analysis, only the serum 25(OH)D3 concentration was considered as the 25(OH)D2 concentration was <1 ng/mL in each sample.
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2

Cell Density and Metabolite Analysis

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The cell density was determined by measuring the turbidity of the culture medium at 600 nm using a spectrophotometer (Thermo Fisher Scientific).
The concentrations of glucose and organic acids were determined by the UltiMate 3000 HPLC (Thermo Fisher Scientific) using the following apparatus and operating conditions: Bio‐Rad Aminex HPX‐87H column (Bio‐Rad Laboratories) with RID and UV detectors; column temperature of 65°C; and 0.6 mL min−1 of 5 mM sulfuric acid as the mobile phase. The concentration of α‐aminoadipate was analyzed by LC‐MS using the AB SCIEX QTRAP 5500 system (AB SCIEX) equipped with a HILIC‐Z column (2.1 × 100 mm) (Agilent Technologies). The mobile phase was: A: water containing 0.1% (v/v) formic acid, B: acetonitrile containing 0.1% (v/v) formic acid, and 20 mM ammonium acetate with a flow velocity of 0.3 mL min−1 at 40°C. Also, α‐aminoadipate was further identified by gas chromatography‐mass spectrometry (GC‐MS) using the Agilent Technologies 7890B‐5977A system (Agilent Technologies) in which the appropriate amount of fermentation supernatant was dried by vacuum centrifugation or freeze‐drying and extracted using a silylation reagent at a ratio of N, O‐bis‐(trimethylsilyl) trifluoroacetamide to trimethylchlorosilane of 99:1.
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3

UHPLC-MS/MS Quantification of CPT-11, SN-38, and SN-38G

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A UHPLC-MS/MS system was used to determine the concentrations of CPT-11, SN-38, and SN-38G. A Shimadzu LC-20AD series UHPLC (Shimadzu, Kyoto, Japan) consisting of two LC-20AD XR pumps, an SIL-20A XR autosampler, a DGU-20A 3R degasser and a CTO-20AC column oven was employed. The UHPLC separation was performed on an ACQUITY UPLC® BEH C18 (2.1 × 100 mm, 1.7 μm) column using a gradient elution consisting of acetonitrile (A) and 0.1% aqueous formic acid (B) as the mobile phase at a flow rate of 0.3 mL/min. The injection volume was set to 10 μL. The gradient elution program was as follows: 10–10% A at 0–0.5 min, 10–20% A at 0.5–1.0 min, 20–20% A at 1.0–1.5 min, 20–40% A at 1.5–3.0 min, 40–100% A at 3.0–4.0 min, 100–100% A at 4.0–6.0 min, 100–10% A at 6.0–6.01 min, and 10–10% A at 6.01–8.0 min.
The UHPLC instrument was coupled to an AB SCIEX Qtrap 5500 system (AB Sciex, Framingham, MA, USA) via a Turbo IonSpray ionization interface. The data were analyzed using Analyst Data Acquisition and Processing software (Version 1.6, AB Sciex). The optimized conditions were as follows: curtain gas (CUR), 35.0 psi; collision gas (CAD), medium; IonSpray voltage (IS), 5,500 V; source temperature, 550°C; GS1, 40 psi; and GS2, 40 psi.
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4

Amino Acid Quantification in Ileal Contents

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Amino acids were measured by ultra‐high‐performance liquid chromatography (UHPLC) with mass spectrometry. First, 100 mg of ileal contents was mixed with 1 ml acetonitrile/methanol/water (2:2:1, v/v/v) and sonicated for 30 min (4°C), followed by centrifugation (15,000 rpm, 4°C, 20 min). Then 50 μl of plasma and 200 μl of methanol acetonitrile/methanol (1: 1, v/v) were mixed. This mixture was allowed to stand for 60 min before centrifugation (15,000 rpm, 4°C, 20 min). Then, the supernatant was collected and added to the UHPLC (Agilent, Santa Clara, CA, United States) that was coupled with a mass spectrometer (QTRAP 5500 system, Sciex, Redwood, VA, United States). If the relative standard deviations of the quality control (containing the same amount of contents from each sample) for all amino acids were less than 30%, the measurements were considered reproducible and stable (Han et al., 2019 (link)).
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5

Quantitative Amino Acid Profiling

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Amino acids were measured by liquid chromatography–mass spectrometry. We mixed 100 mg of ileal contents with 1 mL acetonitrile/methanol/water (2:2:1, v/v) and sonicated them for 30 min (4°C), followed by centrifugation for 20 min (15,000 × g, 4°C). Fifty microlitres of plasma and 200 μL of methanol acetonitrile/methanol (1:1, v/v) were mixed. We left the mixture to stand for 60 min before centrifugation for 20 min (15,000 × g, 4°C). Then, we applied the supernatant to UHPLC (Agilent, Santa Clara, CA, United States) and a QTRAP 5500 system (Sciex, Redwood, VA, United States). If the relative standard deviations of quality control (containing the same amount of contents from each sample) for all amino acids were less than 30%, the measurements were reproducible and stable. The information of amino acids standards used for liquid chromatography–mass spectrometry analysis was shown in Supplementary Table 1. The relative quantitative data for each amino acid was calculated based on the peak areas and retention times obtained from Multiquant software. The standards were used to calculate the retention time and identify amino acids.
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6

Quantitative Multianalyte Analysis via HPLC-MS

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Separation and analysis of all analytes and samples were achieved upon an HPLC-TQ MS platform. HPLC consisted of a Shimadzu Nexera X2 Ultra High Performance Liquid Chromatography (UHPLC) system (Shimadzu, Kyoto, Japan) coupled for identification and quantitation to a QTRAP 5500 system (Sciex, Darmstadt, Germany). The triple quadrupole was equipped with a Turbo V™ Source (ESI mode) which utilized nitrogen and air as sheath and reagent gas, respectively. To verify the exact mass values, we used an LTQ-Orbitrap high-resolution mass spectrometer (Thermo Scientific, Waltham, MA. USA) within mass accuracy of ±3 ppm and resolution of 30 k.
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7

LC-MS/MS Quantification of Analytes

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Blood serum samples were diluted 1000-fold with IS solution and centrifuged at 18,000×g for 5 min. The supernatant was transferred into a clean vial and 5 μL was injected into an LC-MS/MS system. LC analysis was performed using a Nexera LC system (Shimadzu, Kyoto, Japan). An L-column 2 ODS column (150 mm × 1.5 mm i.d.; 5 μm particle size; CERI, Tokyo, Japan), equipped with a guard column (OPTI-GUARD 1 mm C18; Optimize Technologies, Inc., Oregon City, OR, USA), was used for chromatographic separation. The mobile phase consisted of 10 mmol/L ammonium formate (95%) and methanol (5%) (solvent A), and 10 mmol/L ammonium formate (5%) and methanol (95%) (solvent B). The solvent gradient was increased linearly from 0 to 100% solvent B in 15 min and was maintained at this composition for 5 min. Subsequently, the gradient was changed to 0% solvent B and maintained for 10 min to re-equilibrate the column. The flow rate of the mobile phase was set at 0.1 mL/min and the column temperature was maintained at 40 °C. MS/MS detection was performed using a QTRAP 5500 system (SCIEX, Framingham, MA, USA). Quantitation was performed in SRM mode. The SRM transition 152 > 110 was used for quantitation, and the transition 152 > 65 was used as qualifier ions. The SRM transition 156 > 114 was used for IS (acetaminophen-D4). All experiments were conducted in positive ion mode.
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8

Quantification of Doxycycline in Plasma and Microdialysis

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Blood samples were centrifuged (2000 × g, 10 min, at 4°C) to extract plasma, which was snap frozen at −20°C within 60 min of the respective times of collection. Microdialysis samples were snap frozen at −20°C within 15 min of their respective times of collection. Blood and microdialysis samples were subsequently stored at −80°C until analysis. Doxycycline concentrations in microdialysate and plasma samples were analysed using a validated liquid chromatography–tandem mass spectrometry method, consisting of a Symbiosis™ ALIAS chromatographic system (Spark, The Netherlands) and a Qtrap 5500 system (Sciex, Framingham, MA, USA). Gradient elution was performed at a flow rate of 0.4 ml min−1. The mass spectrometer was operated in positive electrospray ionization mode. The analytical method was validated according to the European Medicines Agency guideline on bioanalytical method validation 12. Quantification was performed by multiple reaction monitoring, with chlortetracycline (Fluka 46 133, Sigma‐Aldrich, St. Louis, MO, USA) used as internal standard. Two calibration ranges were applied for microdialysate samples – a lower range at 1–100 ng ml−1, and a higher range at 50–600 ng ml−1. For plasma, the calibration range used was 100–750 ng ml−1.
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9

Lipidomic Profiling by QTRAP 5500

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The portion of the sample extract dedicated to lipidomic profiling was dried under nitrogen flow and reconstituted in ammonium acetate dichloromethane:methanol. The extracts’ infusion was performed on a Shimadzu LC with nano PEEK tubing as previously described [30 ]. The samples were analyzed in both positive and negative mode electrospray using QTRAP 5500 system with the SelexION device (Sciex). The molecules were detected in multiple reaction monitoring (MRM) mode with a total of more than 1100 MRMs. Individual lipid species were quantified by the ratio of the signal intensity of each target compound to that of its assigned internal standard, followed by the multiplication of the concentration of internal standard added to the sample. Lipid class concentrations were calculated from the sum of all molecular species within a class, and fatty acid compositions were determined by calculating the proportion of each class comprised of individual fatty acids, as previously described [30 ,48 (link)]. The process variability found on CLP was 8%.
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10

Clonidine Pharmacokinetics Monitoring Protocol

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Blood samples were taken from arterial catheters at 2, 4, 8 and 12 hours after the start of clonidine infusion. Subsequently, a sample was taken once daily until the termination of treatment. After stopping the infusion, blood samples were taken at 0, 8, 16, 24 and 48 h. Blood samples were stored at −20°C and transferred to Amsterdam University Medical Centre AUMC for analysis. Plasma concentrations were measured using a validated high‐perfomance liquid chromatography–mass spectrometry system (liquid chromatography: LC30 UPLC, Shimadzu, Kyoto, Japan; mass spectrometry: QTRAP 5500 system, Sciex, Framingham, MA, USA), as described previously by Kleiber et al.14 The lower limit of quantification (LLOQ) was 0.1 μg/L and the upper limit of quantification was 20 μg/L. The accuracy of the assay was between 99–114%.
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