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10 protocols using methyl chloroformate

1

Serum Sample Metabolite Derivatization

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Thawing was conducted in an ice bath to ensure the quality of serum samples. A 150 µl aliquot of serum was then mixed with 50 µl 4 M NaOH, 4 µl internal standard (10 mM 2,3,3,3-D4-alanine, Sigma, USA), and 200 µl methanol. After a 15-minute incubation at room temperature, the mixture underwent centrifugation at 12,000 rpm for 15 min. Following centrifugation, 300 µl of the supernatant was carefully transferred to a new glass test tube, where 34 µl pyridine (Sigma, USA) was added and thoroughly mixed. Next, 20 µl methyl chloroformate (Sigma, USA) was added twice, with a vortex mix for 30 s after each addition. Subsequently, 400 µl of chloroform and 400 µl of NaHCO3 solution were sequentially added, with a vortex mix for 10 s after each addition. To facilitate phase separation, the blended liquid was centrifuged at 2000 rpm for 10 min, and the upper water and intermediate protein layers were carefully discarded. Following this step, sodium sulfate, similar to mung beans, was added to the lowest chloroform layer for water absorption. Finally, 200 µl of the resulting liquid phase, containing derivatized metabolites, was transferred into the GS automatic sampler sample bottle for subsequent analysis.
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2

Synthesis of LTG Derivatives

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LTG
(>98%) and 2,3,4,6-tetra-O-acetyl-α-d-glucopyranosyl bromide (98.5%) were purchased
from TCI (Zwijndrecht, Belgium). LTG-N2-oxide (>95%),
LTG-13C3, and 5-desamino 5-oxo-2,5-dihydro LTG (OXO-LTG;
98%),
2-methyllamotrigine methanesulfonate (LTG-N2-methyl) were
purchased from TRC. All solvents (acetone, acetonitrile, methanol,
and water) were LC-MS grade (Biolab Co., Jerusalem, Israel). NaOH
was purchased from Honeywall Fluka (Tokyo, Japan). The following reagents
were purchased from Sigma-Aldrich (St. Louis, MO): methyl chloroformate
(99%), potassium carbonate, allyl bromide (99%), propionyl chloride
(98%), 2-(2-bromoethyl)-1,3-dioxolane (96%), iodomethane (99%), formamide
(99%), and sodium methoxide (99%).
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3

Yeast Genetic Manipulation Protocol

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All chemicals used in this study were of analytical grade. Methanol, chloroform, sodium bicarbonate, and sodium hydroxide were obtained from MERK (Damstadt, Germany). The internal standard 2,3,3,3-d4-alanine, the derivatisation reagent methyl chloroformate (MCF), and pyridine were purchased from Sigma-Aldrich (St. Louis, USA). Anhydrous sodium sulphate and farnesol were obtained from Fluka (Steinheim, Germany). U-13C5 l-proline and U-13C6 arginine were acquired from Cambridge Isotope Laboratory Inc. (Tewksbury, USA). Two types of DNA polymerases were utilised in this study: KOD hot start DNA polymerase from NovgenR (Darmstadt, Germany), used to construct the SAT1 flipper disruption cassette, and TaKaRa Ex TaqTM from Takara Bio Inc. (Shiga, Japan), used for colony PCR amplifications. The antibiotic nourseothricin was purchased from WERNER BioAgents (Jena, Germany). The QIAquick Gel Extraction kit was supplied by Qiagen (Valencia, CA, USA) and the Alkali-cation yeast transformation kit was obtained from Qbiogene (Heidelberg, Germany).
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4

Comprehensive Metabolite Extraction Protocol

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Alanine, aspartic acid, cysteine, glutamic acid, histidine, leucine, lysine, proline, threonine, tryptophan, valine, salicylic acid, pyridine, methanol, chloroform, methyl chloroformate (MCF), sodium bicarbonate, sodium sulfate, methoxyamine, ribitol, myo-inositol, xylose, pinitol, and iso-leucine were purchased from Sigma-Aldrich Chemie GmbH (Munich, Germany). Arginine and phenylAlanine were purchased from SERVA Electrophoresis GmbH (Heidelberg, Germany). Glycine, methionine, serine, malic acid, caffeic acid, succinic acid, arabinose, and saccharose from Carl Roth GmbH & Co. KG (Karlsruhe, Germany). Asparagine, mannitol, glucose, and galactose from Merck KGaA (Darmstadt, Germany). Sorbitol and glutamine from AppliChem GmbH (Darmstadt, Germany). MSTFA from Macherey-Nagel GmbH & Co. KG (Düren, Germany). Citric acid was purchased from Acros Organics (Thermo Fisher Scientific, Geel, Belgium).
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5

Quantitative Metabolite Profiling

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Methyl chloroformate (MCF), methyl tert-butyl ether (MTBE), sodium hydroxide, concentrated hydrochloric acid, pyridine, 1-propanol, propyl-acetate, N-acetyl-l-aspartic acid (NAA), N-acetyl-l-cysteine (NAC), essential free fatty acid and globulin free bovine serum albumin (BSA), sodium acetate, sodium U-13C-acetate, and sodium 2H3-acetate, all of analytical grade, were from Sigma-Aldrich.
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6

Targeted LC-MS Analysis of Phytohormones

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Reagents and standards including methyl chloroformate, pyridine, sodium bicarbonate, sodium hydroxide and sodium sulfate (anhydrous), n-alkanes (decane, dodecane, pentadecane, nonadecane, docosane, octacosane, dotriacontane, hexatriacontane), ABA, AZ, BA, CA, deuterated cinnamic acid (CA-d6), idole-3-acetic acid (IAA), JA, ACC, linolenic acid, linoleic acid and SA were purchased from Sigma-Aldrich (St Louis, MO, USA). 13-epi-12-oxophytodienoic acid (13-epi-OPDA) was purchased from Cayman Chemical (Ann Arbor, MI, USA). Chloroform (HPLC grade), and LC–MS grade methanol and water were purchased from Thermo Fischer Scientific (Scoresby, VIC, Australia).
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7

Synthesis and Characterization of Dyes

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Methyl chloroformate 98%, 3-amino phenol, ethyl acetoacetate, ethyl benzoate, diethylcarbonate 97% and 4-bromoacetophenone 98% were purchased from Sigma Aldrich (Germany) and used directly without any further purification. All solvents used (dioxan, dimethylsulfoxide, dimethylformamide, acetonitrile, acetic acid and acetone) were of spectroscopic grade. 100% polyester fabric (91 g/m2, yarn count: dtex 44) was supplied by El-Mahalla El-Kobra Company, Egypt. The fabrics were scoured before application in an aqueous bath containing 2 g.L−1 of nonionic detergent at 80 °C for 30 min to remove any processing oils and impurities. Thin-layer chromatography (TLC) was performed by a Kieselgel 60 F254 (Merck, Darmstadt, Germany), for observation of reaction progress and the purity of the prepared intermediates and synthesized dyes.
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8

Synthesis of Deuterated 2-Hydroxyglutaric Acid

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D- and L-2-hydroxyglutaric acid, R- and S-5-oxotetrahydro-2-furancarboxylic acid, pyridine, methyl chloroformate (MCF), and O-methylhydroxylamine hydrochloride were obtained from Sigma-Aldrich (Taufkirchen, Germany). N-methyl-N-(trimethylsilyl)-trifluoroacetamide (MSTFA) was purchased from Macherey-Nagel (Dueren, Germany). (2R)-2-hydroxyglutaric acid octyl ester sodium salt was bought from Toronto Research Chemicals (Toronto, ON, Canada), 13C5-L-glutamine was bought from CIL (Andover, MA, USA), and 2,3,3-D3-2HG was bought from C/D/N Isotopes Inc. (Pointe-Claire, QC, Canada). In all experiments, purified water from a PURELAB Plus system (ELGA LabWater, Celle, Germany) was used.
Deuterated 2-HG (510 µL of 1 mM 2,3,3-D3-2HG) was treated with HCl (120 µL of 4.5 N) at 100 °C for 30 min to form 2-HG-lactone-D3. This solution was evaporated to complete dryness and re-dissolved in water to yield a final concentration of 100 μM 2-HG-D3 and 2-HG-lactone-D3 (in sum) that was used as stable isotope-labeled standard.
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9

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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10

Metabolite Extraction and Derivatization

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Chloroform, methanol, potassium hydroxide, sodium bicarbonate, sodium hydroxide were purchased from MERK (Damstadt, Germany). The internal standard 2,3,3,3-d4-alanine, the derivatization reagent methylChloroformate (MCF), and pyridine were obtained from Sigma-Aldrich (St. Louis, USA). Anhydrous sodium sulphate and were obtained from Fluka (Steinheim, Germany). Sulphuric acid was brought from ROMIL Pure Chemistry (Lameira, England). All chemicals used in this research were of analytical grade.
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