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4 protocols using d4 alanine

1

Hair Sample Preparation for Analysis

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Hair sample preparation was conducted according to the published protocol by Sulek et al with minor modifications (Sulek et al. 2014 (link)). All hair samples were randomised prior to sample preparation and weighed to 3.5 mg ± 0.5 mg. All weighed hair samples were washed with distilled water and methanol twice. Three internal standards, 20 μL of D4-alanine (Sigma, USA, 10 mM), D5-phenylalanine (Sigma, USA, 10 mM), and D2-tyrosine (Sigma, USA, 10 mM) were added to the hair samples and incubated with 1 ml potassium hydroxide (1 M) at 54 °C for 18 h. The hair extracts were then neutralized by adding 67 μL sulphuric acid (3 M). To precipitate the salt and protein, 1 ml of methanol was added to the hair extracts, followed by vortexing for 30 min, and centrifugation at 4000 g for 5 min. The 350 μL of supernatant was concentrated to dryness in a SpeedVac (Labconco, Kansas, USA) at 37 °C for 6 h and stored at − 20 °C prior to derivatization. Quality control (QC) samples were also prepared by combining a small portion of all hair extracts together and following the identical preparation steps to the samples.
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2

GC-MS Metabolomic Analysis of Plasma

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For each sample, a 300 µL aliquot of plasma was spiked with 20 µL of internal standard (10 mM d4-alanine; 2,3,3,3-d4-dl-alanine, 98 atom % D; Sigma-Aldrich), then lyophilised overnight before being extracted first with 500 µL of 50% methanol, then with 500 µL of 80% methanol. Extracted supernatants were pooled and freeze-dried. Dried samples were chemically derivatised by methyl chloroformate and analyzed by Gas Chromatography-Mass spectrometry (Agilent 7890A coupled with a 5975 inert Mass Spectrometry Detector). Chromatograms were processed using an in-house metabolite library and a custom-made R-software package, with manual checking and correction of information (GC-MS peak intensities). Metabolomic data for each sample were normalized using the internal standard prior to calculation of relative abundances of the separate metabolites in the four different groups.
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3

Metabolomic Analysis of Linear Alkanes

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Methyl chloroformate and a linear alkane series from heptane to triacontane were obtained from Sigma Aldrich (Sigma-Aldrich Pty Ltd., Sydney, Australia). Optima LC-MS grade methanol and analytical grade pyridine, chloroform, sodium acetate and sodium hydroxide were from Thermo Fisher (Thermo Fisher Scientific Inc., Auckland, New Zealand). Ultrapure water was obtained from a Purite Select Fusion system (Total Lab Systems, Auckland, New Zealand). Analytical grade standards of 2-hydroxybutyric, 3-hydroxybenzoic, adipic, benzoic, cis-aconitic, citric, fumaric, itaconic, lactic, malic, malonic, 4-toluic, succinic, syringic, cinnamic and vanillic acids, as well as d4-alanine, were obtained from Sigma Aldrich (Sigma-Aldrich Pty Ltd., Sydney, Australia).
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4

Metabolite Extraction from Biological Samples

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All samples were processed with a standard operating procedure.150 µL aliquots of thawed plasma or urine were mixed with three internal standards (IS) [20 μL of d4-alanine (Sigma, USA, 10 mM), d5-phenylalanine (Sigma, USA, 10 mM), and d5-tryptophan (Sigma, USA, 10 mM)]. To precipitate protein from the plasma or urine samples, 400 µL of cold methanol was added, followed by freezing at - 20°C for 30 min. Then the supernatant was isolated by centrifugation at 12,000 rpm for 15 min at 4°C. The tissue sample was prepared by dissecting 30.00 ± 0.50 mg into new tubes. After adding three internal standards and 400 μL cold methanol, tissues were homogenized via TissueLyser II (QIAGEN, USA) and centrifuged (10,000g, 15 min, 4°C) to isolate the supernatant. The hair sample was washed with methanol and distilled water twice, then air-dried in a fume hood. 5.00mg ± 0.50 mg hair was prepared and added to three internal standards, and then incubated with 1 ml sodium hydroxide (1 M) at 54°C for 18 h. To precipitate the salt and protein, 1 ml of methanol was added to the hair extracts, followed by vortexing for 30 seconds, and centrifuged at 4000 g for 5 min. The supernatant was mixed with 50 µl of 4M NaOH. Then these mixtures underwent derivatization consecutively.
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