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29 protocols using qtrap 5500 ms

1

Plasma Metabolite Analysis by LC-MS

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Plasma samples were deproteinized using dry sulfosalicylic acid, and frozen at −80°C until analysis. Enrichment analysis was performed by Liquid Chromatography-Electrospray Ionization-Mass Spectrometry (LC-ESI-MS) (QTrap 5500 MS; AB Sciex) with ExpressHT Ultra LC (Eksigent Div.; AB Sciex) after derivatization with 9-fluoren-9-ylmethoxycarbonyl (Fmoc) [23 ]. Ions of mass to charge ratios of 234, 235, and 239 for phenylalanine and 466, 467, 468, and 470 were utilized. Plasma insulin concentrations were measured by using commercially available human insulin ELISA kit (Alpco Diagnostics, Salem, MA). Plasma human growth hormone concentrations were measured using a commercially available ELISA kit (Invitrogen; Thermo Fisher Scientific, Carlsbad, CA). Plasma amino acid concentrations were measured using liquid chromatography-mass spectrometry (QTrap 5500 MS; AB Sciex) using the internal standard method [24 (link)].
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2

Metabolite Extraction from Leaf Samples

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Fine powder from leaf samples (~50 mg) was mixed with 600 μL of acetonitrile: chloroform (7: 3, v/v) solution and vortexed for 30 s. The quantitation control was prepared by adding 20 ng L-lactate (Sigma−Aldrich, L1750) into the acetonitrile: chloroform solution. The mixture was sonicated for 1 h on ice and then centrifuged for 5 min at 7,000 g at 4°C. Three hundred microlitres of H2O was added to each supernatant prior to the two-step liquid−liquid partitioning. The upper aqueous fractions from the same sample were pooled and dried under a nitrogen stream. The dried extracts were then dissolved in 750 μL of H2O and filtered through a 0.22 μm membrane prior to measurement. LC–MS/MS analysis was performed on a UPLC system (Waters, Milford, Ohio, USA) combined with a 5500 Qtrap MS equipped with an ESI source (AB SCIEX). Each sample (5 μL) was injected onto an HSS T3 C18 column for further analysis.
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3

Quantification of Malate in Plants

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Leaves from 4-week-old plants were ground into fine powder under liquid nitrogen, and ~30 mg of powder was extracted with 600 μL of acetonitrile:chloroform (7:3, v-v) using 20 ng of D3-Malice acid as internal standards for quantitation. After ultrasonic-assisted extraction in an ice-water bath for 1 h and centrifugation at 7000×g for 5 min, the supernatant was collected. 300 μL H2O was then added to the supernatant for two steps of liquid-liquid partitioning. The upper aqueous fractions were pooled and dried under a nitrogen stream. The samples were redissolved in 300 μL H2O and filtered through a 0.22 μm membrane for detection. LC-MS/MS detection was performed on a UPLC (Waters) combined with a 5500 Qtrap MS equipped with an ESI source (AB SCIEX), and 5 μL of each sample was injected onto a HSS T3 C18 column.
Measurements of malate concentration in freshly isolated mitochondria and chloroplasts were carried out in the same way. However, when preparing samples all the solvent volumes used were reduced to 1/6.
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4

Comprehensive Plasma Metabolite Profiling

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Two liquid chromatography-mass spectrometry (LC-MS) methods were used to measure polar plasma metabolites. Amino acids, amino acid metabolites, acylcarnitines, dipeptides, nucleotides, and other cationic polar metabolites were measured in 10 μL of plasma using hydrophilic interaction liquid chromatography coupled with positive ion mode analysis on a Q Exactive Plus Orbitrap MS (Thermo Scientific, Waltham, MA, USA). Sugars, sugar phosphates, organic acids, bile acids, nucleotides and other anionic polar metabolites were measured in 30 μL of plasma using hydrophilic interaction liquid chromatography and multiple reaction monitoring in the negative ion mode on a 5500 QTRAP MS (AB Sciex, Framingham, MA, USA). Details on plasma extraction, isotope internal standards, and chromatographic conditions for both methods have been published [4 (link),15 (link)]. Metabolite identifications were confirmed using synthetic mixtures of reference compounds as well as characterized pooled plasma reference samples. All samples for a given study design (i.e. CRIC or renal arterio-venous sampling) were assayed in a single LC-MS run.
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5

HPLC-MS Lipidomic Analysis Workflow

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HPLC is necessary for analyzing low-abundance and isomeric metabolites. [ 27 ] This method was performed by Beijing Mingde Zhengkang Technologies Co., Ltd (Beijing, China). Lipidomic data were mean-centered and pareto-scaled using Simca 14.1 (Umetrics, Umeå, Sweden) to reduce the noise and artifacts. Shinazu LC-20AXR Rapid Separation LC system from Agilent series 1290 UHPLC instrument (Agilent, Waldbronn, Germany) was used for reverse-phase liquid chromatography column based on the gradient conditions. Multiple reaction monitoring analysis was performed using a 5500 Qtrap MS (AB Sciex, Framingham, MA, USA). All experiments were performed in positive electrospray ionization mode.
The quality of each OPLS-DA model was evaluated using the R2Y (cum) value, identifying changes in all the components in the model. An additional 7-fold cross-validation was performed in the OPLS-DA model. In this process, Q2 (cum) is calculated to represent the predictability of the model. An R package termed Mfuzz, which implemented SoftClustering tools, was utilized for microarray data analysis.
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6

Quantifying Dopamine and Metabolites in Striatum

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Liquid chromatography tandem mass spectrometry (LC–MS/MS) was used to evaluate the content of dopamine (DA) as well as the dopamine metabolites dihydroxy‐phenyl acetic acid (DOPAC) and homovanillic acid (HVA) in the striatum. Tissue samples were ground in 500 μL of 80% methanol for 5 min and subsequently sonicated for 30 min at 4°C and let stand for an additional hour. After centrifugation at 12,000 rpm for 15 min, the supernatant was collected and filtered through a 0.22 μm mesh prior to preparation for LC–MS/MS analysis. The various apparatuses used for LC–MS/MS analysis were as follows: liquid chromatography (Water Acuity UPLC); mass spectrography (AB SCIEX 5500 Qtrap‐MS); and chromatographic column (Acquity UPLC HSS T3; 1.8 μm, 2.1 mm × 100 mm).
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7

Comprehensive Analysis of c-PAHs and Metabolites in Breast Milk

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Both parent compounds (c-PAHs) and their hydroxy-metabolites were analyzed in the human breast milk samples. Since the amount of sample was limited, a new sample preparation procedure was developed in the first part of the project. For isolation of analytes SPE or a modified QuEChERS method employing ethylacetate or acetonitrile extraction was used. In the latter case dispersive SPE was applied for clean-up of primary extract. The final measurements was done on both GC-MS/MS (GC Agilent 7890 with triple quadrupole 7000B or GCT Premier) and LC-MS/ MS (Xevo TQ-S/UPLC Acquity or AB SCIEX 5500 QTRAP MS /UPLC Acquity) based on the type of analyte.
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8

Chromatographic Separation of Organic Acids

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For the chromatographic separation of organic acids, an Acquity BEH C18 column was used (1.7 µm, 2.1 × 100 mm; Waters, Eschborn, Germany). The flow rate was set to 0.4 mL/min, and 0.1% formic acid in water (solvent A) and acetonitrile (solvent B) served as solvents. The gradient started with an isocratic step at 7% solvent B (2 min) and increased to 45% (7.5 min) and then to 100% solvent B (0.5 min). After isocratic elution (1 min), the starting conditions we re-established (0.1 min) followed by the equilibration of the system at 7% solvent B (2.9 min). The UPLC System (Shimadzu Nexera X2, Shimadzu, Duisburg, Germany) was coupled to a 5500 Q-Trap MS (Sciex, Darmstadt, Germany) with Analyst 1.6.2. Ionisation was performed in negative electrospray mode. The setting was 35 psi for curtain gas, −4500 V for ion spray voltage, 55 psi for heater gas, and 65 psi for turbo gas. The source temperature was set to 500 °C. MS/MS analysis was done in MRM mode, in which each transition was recorded with a dwell time of 5 ms. See Supporting Table 2 for MS/MS parameters.
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9

Targeted Metabolite Analysis of Cell Lysates

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Negatively charged polar analytes including
alpha-hydroxybutyrate and citric acid cycle intermediates were measured
in 10 μL of extracted cell lysates separated using a 150 ×
2.0 mm Luna NH2 column (Phenomenex); mobile phase A: 20mM ammonium
acetate, 20mM ammonium hydroxide in water; mobile phase B: l0mM ammonium
hydroxide in 25% methanol/75% acetonitrile. The column was eluted
isocratically with a linear gradient from 90% to 0% mobile phase B over
10 minutes, then 2 minutes at 0% mobile phase B. MS data were acquired
with multiple reaction monitoring in the negative ion mode on a 5500
QTRAP MS (SCIEX). Raw data were integrated and visually inspected using
MultiQuant software (version 2.1, SCIEX).
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10

Comprehensive LC-MS/MS Characterization of Compounds

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All biological samples participated in LC–MS/MS measurements. All chromatographic separations were conducted on Shimadzu LC modular system (Kyoto, Japan) equipped with a Waters ACQUITY UPLC HSS T3 column (2.1 × 100 mm, 1.8 μm, Milford, CT). Mobile phase consisting of 0.1% aqueous formic acid (A) and ACN (B) was delivered in gradient at a total flow rate of 0.2 mL/min by operating the program as follows: 0–4 min, 2–10% B; 4–20 min, 10–30% B; 20–25 min, 30–65% B; 25–28 min, 65–100% B; and 28–32 min, 100% B. After each analytical run, 2% B was delivered for another five minutes for the re-equilibration. Column oven and injection volume were set as 40 °C and 2 μL, respectively.
The column outlet was directly connected to ESI interface of either Qtof-MS (TripleTOF 6600+, SCIEX, Foster City, CA) or Qtrap-MS (5500 Qtrap-MS, SCIEX) device. Actually, the whole measurement consisted of three progressive steps: UPLC–Qtof-MS/MS for acquiring HR-m/z values of precursor and fragment ions, online ER-MS for obtaining OCEs of the targeted 1st-generation fragment ions, and post-CID ER-MS for gaining the trajectories from selected 1st-generation fragment ions to 2nd-generation fragment ions.
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