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Analytical Chemistry Protocol for Metabolomics

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HPLC- or MS-grade solvents acetonitrile (ACN), methanol (MeOH), and chloroform (CHCl3) were purchased from Merck (Darmstadt, Germany) or Sigma-Aldrich (Steinheim, Germany or St. Louis, MO). MS grade water or ultrapure water was purchased from Merck (Darmstadt, Germany) or using a Milli-Q purity system (Millipore, Billerica, MA).
MeOH-dissolved internal standard solution (ISS-1) containing L-methionine sulfone, D-camphor-10-sulfonic acid sodium salt, leucine-d3, phenylalanine-d5, tryptophane-d5, succinic acid-13C4, and cholic acid-d4 (all from Sigma-Aldrich, Steinheim, Germany) was used to normalize signal intensity of the CE-TOF/MS data. ACN-dissolved ISS-2 consisting of N,N-diethyl-2-phenylacetamide, trimesic acid, disodium 3-hydroxynaphthalene-2,7-disulfonate (all from Wako, Japan), and 3-aminopyrrolidine dihydrochloride (Aldrich, St. Louis, MO) was used to adjust the migration time of the CE-TOF/MS analysis. Internal standards of free fatty acid (FFA) 16:0-d4 (Cambridge Isotope Laboratories, Tewksbury, MA, USA), and FFA 22:0-d4 (ten Brink laboratories, Amsterdam, Netherlands) dissolved in CHCl3/MeOH (2:1, v/v) were used to normalize signal intensity of the UHPLC-Q-TOF/MS-based FFA analysis.
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Dialyzer Flux Comparison for Metabolomics

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The dialyzer with low flux used in this study was the Fresenius F6, and the dialyzer with high flux was the Fresenius F60. Liquid chromatography grade methanol and chloroform were purchased from Merck (Darmstadt, Germany). Liquid chromatography grade ammonium acetate was purchased from Sigma-Aldrich (St. Louis, Mo, USA), and 98% formic acid was purchased from Fluka (Darmstadt, Germany). Ultrapure Water (18.2 MΩ-cm, TOC = 6 ppb) was prepared with a Milli-Q system (Millipore, Billerica, MA, USA). 10 mM D-camphor-10-sulfonic acid sodium salt (Wako, Japan) and 10 mM L-methionine sulfone (Wako, Japan) in methanol were used as internal standard solution 1 (ISS1). A mixture of 1 mM disodium 3-hydroxynaphthalene-2,7-disulfonate (Wako, Japan), trimesic acid (Wako, Japan), N,N-diethyl-2-phenylacetamide (Wako, Japan), and 3-aminopyrrolidine dihydrochloride (Aldrich, USA) in water was used as internal standard solution 3 (ISS3). ISS1 was used to standardize the metabolite intensity and ISS3 was used to adjust the migration time of the metabolites.
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Quantitative Metabolite Analysis of Quadriceps

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A quantitative analysis of charged metabolites in the quadriceps femoris was performed using CE-TOFMS as described previously (66 (link), 67 (link)). Quadriceps femoris muscle samples (50 mg) were submerged in methanol (500 μl) containing internal standards [methionine sulfone (Wako, Tokyo, Japan), 2-(N-morpholino)ethane sulfonic acid (Dojindo Laboratories, Tokyo, Japan), and d-camphor-10-sulfonic acid (Wako) each at 20 μM]. The mixture was combined with four 3-mm zirconia beads (BioSpec Products, Bartlesville, OK, USA) and vigorously shaken for 5 min using a Shake Master NEO (Biomedical Science, Tokyo, Japan). Subsequently, deionized water (200 μl) and chloroform (500 μl) were added, and the suspension was vigorously shaken for 5 min and centrifuged at 4600g and 4°C for 30 min. The supernatant was filtered through a 5-kDa-cutoff filter column (Millipore, Burlington, MA, USA). The filtrate was concentrated via centrifugation (3 hours at 40°C) and dissolved in water containing reference compounds [200 μM each of 3-aminopyrrolidine (Sigma-Aldrich, St. Louis, MO, USA) and trimesic acid (Wako)] before CE-TOFMS analysis. As described previously (68 (link)), the CE-TOFMS experiments were performed using an Agilent CE-TOFMS system (Agilent Technologies).
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