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5 protocols using phenylalanine d 5

1

Solvent and Standard Procurement

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All solvents were of LC-MS grade and were purchased from Scharlau (Barcelona, Spain). Additives and standards were purchased from Sigma-Aldrich Quimica SA (Madrid, Spain). Phenylalanine-D 5 (Phe-D 5 ) and methionine-D 3 (Meth-D 3 ) supplied by Cambridge Isotope Laboratories (Tewksbury, MA) with purities >98% were employed as internal standards .
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2

Urine Metabolite Extraction Protocol

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Urine samples, once collected were kept at −80 °C until analysis. Samples were thaw at room temperature on ice, vortexed for 10 s and centrifuged at 10000 × g (4 °C, 10 min). Then, 100 µL of supernatant was withdrawn and 200 µL of HCOOH 0.1% v/v in H2O was added and the solution was vortexed 10 s and centrifuged at 10000 × g (4 °C, 10 min). No molecular weight cutoff (MWCO) filters were used during sample preparation. Thereafter, 100 µL of the supernatant was transferred to a 96 well plates where each sample was spiked with 5 µL of an internal standard solution containing Phenylalanine-D5 (Cambridge Isotopes Laboratory Inc., Andover, MA, USA), caffeine-D9 (Toronto Research Chemicals, Toronto, Ontario, Canada), leukine enkephalin (Sigma-Aldrich Química SA, Madrid, Spain) and reserpine (Sigma-Aldrich Química) in H2O:CH3OH (1:1, 0.1% v/v HCOOH), at a final concentration of 1 µM each. Control blanks were prepared by replacing urine by H2O. A quality control (QC) sample was prepared by mixing 5 µL of each prepared sample. All solvents were of LC-MS grade and were purchased from Scharlau (Barcelona, Spain). Ultra-pure water was generated with a Milli-Q water purification system (Merck Millipore, Darmstadt, Germany). Formic acid (≥95%) was obtained from Sigma-Aldrich Química.
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3

Comprehensive Metabolite and Lipid Analysis

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Reverse-osmosed ultrapure water was obtained from a Milli-Q Plus185 system (Millipore, Billerica, MA, USA). A MS grade methanol (MeOH), used for standards preparation, and acetonitrile (ACN) were obtained from Fisher Scientific (Hampton, NH, USA). Analytical grade ammonia solution (28%, GPR RECTAPUR®) and acetic acid glacial (AnalaR® NORMAPUR®) were obtained from VWR Chemicals (Radnor, PA, USA).
Arachidonic acid, LPC 14:0, LPC 16:0, LPC 17:0, LPC 17:1, LPC 18:0, LPC 18:1, LPC 19:0, LPE 18:0, LPI 16:0, LPI 20:4, palmitoleic acid, oleamide, SPA-1P, sphinganine-C17, sphingosine, S1P, sphingosine d7, LPC 18:1 d7 were purchased from Avanti lipids (Birmingham, AL, USA). Bilirubin, lactic acid, lauric acid, oleic acid, adenosine, arginine, betaine, carnitine, cortisol, creatine, creatinine, hexanoylcarnitine, hippuric acid, hypoxanthine, leucine/isoleucine, phenylalanine, proline, propionylcarnitine, urea, carnitine d3, isoleucine d7, and palmitic acid d31 were purchased from Sigma-Aldrich (Darmstadt, Germany). phenylalanine d5 and valine d8 were purchased from Cambridge Isotope Laboratories Inc. (Andover, MA, USA).
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4

Plasma/Serum Metabolite Extraction for LC-MS

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All solvents used below were of HPLC grade (Fisher Chemicals) and the water was Milli-Q (Millipore).
Plasma and serum samples were thawed on ice and 50 µl aliquots were mixed with 150 µl MeOH for protein precipitation. Samples were then centrifuged for 15 min at 15800×g. The supernatant was transferred to a new tube and then evaporated to complete dryness in a vacuum concentrator. Prior to LC-MS analysis, samples were reconstituted in 50 µl MeOH:H2O 1:1 and the two isotopically labelled internal standards phenylalanine (D5) and palmitic acid (D4) (Cambridge Isotope Laboratories) were added at a final concentration of 5 µM.
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5

Comprehensive Lipidomic and Metabolomic Protocol

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Ammonium acetate, LC-MS-grade formic acid (FA), isopropanol and acetonitrile, and HPLC-grade methanol and methyl tert-butyl ether (MTBE) were purchased from Fisher Scientific (Geel, Belgium). Lipidomics Isotope-labelled internal standards (13 (link)) and Lyso-phosphatidylcholine (LPC) 19:0 (for metabolomics analysis) were purchased from Avanti Polar Lipids (Alabaster, AL, USA). Isotope-labeled internal standards for metabolomics analysis, including tryptophan-d5, valine-d8, phenylalanine-d5, palmitic acid-d3, cholic acid-d4, stearic acid-d3, carnitine C8:0-d3, and carnitine C16:0-d3, were obtained from Cambridge Isotope Laboratories (Tewksbury, MA, USA). Ultrapure water was prepared using the Milli-Q system (Millipore, Billerica, USA).
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