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5 protocols using purelab purification system

1

Lipid Extraction and Standards

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The following chemicals were purchased from Fisher Scientific (Ottawa, ON, Canada): LC-grade chloroform, methanol, acetonitrile, formic acid, acetic acid and ammonium acetate. For solutions preparation, deionized water (PURELAB Purification System, ELGA Labwater, ON, Canada) was employed. Phospholipids, sphingolipids and glycolipids standards were used (Avanti Polar Lipids Inc., Alabaster, AL, USA).
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2

Quantification of Isotopically Labeled Thyroid Hormone

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Acetonitrile (Ultra Chromasolv, LCMS grade), triethylammonium bicarbonate (TEAB) buffer (1 M), ethylenediamine-tetraacetic acid (EDTA, anhydrous), HSA (lyophilized powder, 97–99%), and porcine trypsin were from Sigma-Aldrich (St. Louis, MO). Methanol (Optima, LCMS grade), formic acid (Optima, LCMS grade), and iodoacetamide (IAA) were from Fisher Scientific (Pittsburgh, PA). Purified human Hb was purchased from MP Biomedicals, LLC (Santa Ana, CA). Isotopically labeled T3 (iT3) with sequence AL-[15N,13C-Val]-LIAFAQYLQQCPFEDH-[15N,13C-Val]-K was custom-made (>95%, BioMer Technology, Pleasanton, CA), and the carbamidomethylated iT3 (IAA-iT3)[18 (link)] was used as an internal standard to monitor retention time and mass drifts. Water was prepared with a PureLab purification system (18.2 mΩ cm resistivity at 25 °C; Elga LabWater, Woodridge, IL).
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3

Comprehensive Lipid Standard Preparation

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HPLC grade acetonitrile, chloroform and methanol were purchased from Fisher Scientific, Canada; deionized water was obtained from PURELAB Purification System (ELGA Labwater, ON, Canada). HPLC grade acetic acid, formic acid, ammonium formate and ammonium acetate were purchased from Sigma-Aldrich (ON, Canada). Each lipid class was purchased as individual from Avanti Polar Lipids (Alabaster, AL, USA) and used to make a complex lipid standard mixture consisting SQDG 16:0/16:0, MGDG 16:3(7Z,10Z,13Z)/18:3(9Z,12Z,15Z), PA 18:1(9Z)/18:1(9Z), PG 18:0/20:4(5Z,8Z,11Z,14Z), PC 18:0/20:4(5Z,8Z,11Z,14Z), PE 18:0/20:4(5Z,8Z,11Z,14Z), diether PC O-18:0/O-18:0, plasmalogen PC P-18:0/20:4(5Z,8Z,11Z,14Z), plasmalogen PE P-18:0/20:4(5Z,8Z,11Z,14Z), MMPE 16:0/16:0 and DMPE 16:0/16:0, LPA 20:4(5Z,8Z,11Z,14Z), LPC 18:1(9Z), LPE 18:0, plasmalogen LPE P-18:0; PI 18:0/20:4(5Z,8Z,11Z,14Z); DLCL 18:2(9Z,12Z)/18:2(9Z,12Z), and SM d18:1/18:0. Aliquots of the prepared standard mixture were used for method development.
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4

Hemoglobin Quantification Using Labeled T3

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Acetonitrile (Ultra Chromasolv, LCMS grade), triethylammonium bicarbonate (TEAB) buffer (1 M), ethylenediamine-tetraacetic acid (EDTA, anhydrous), and porcine trypsin were from Sigma-Aldrich (St. Louis, MO). Methanol (Optima, LCMS grade), formic acid (Optima, LCMS grade), and iodoacetamide (IAA) were from Fisher Scientific (Pittsburgh, PA). Purified human hemoglobin was from MP Biomedicals, LLC (Santa Ana, CA). Isotopically labeled T3 (iT3) with sequence AL-[15N,13C-Val]-LIAFAQYLQQCPFEDH-[15N,13C-Val]-K was custom-made (>95%, BioMer Technology, Pleasanton, CA), and the carbamidomethylated iT3 (IAA-iT3)[14 (link)] was used as an internal standard to monitor retention time and mass drifts, as well as drift in instrument performance. Water was prepared with a PureLab purification system (18.2 mΩ cm resistivity at 25 °C; Elga LabWater, Woodridge, IL).
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5

Proteomics Workflow for T3 Peptide Quantification

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Triethylammonium bicarbonate buffer (TEAB), ethylenediamine-tetraacetic acid (EDTA, anhydrous), ammonium sulfate, porcine trypsin, HSA (lyophilized powder, 97–99%), acetonitrile (Ultra CHROMASOLV®, LC-MS grade), acetic acid (LCMS grade), L-glutathione (reduced), L-cysteine, L-homocysteine, iodine, iodoacetamide (IAA), ammonium sulfate, dimethyl sulfoxide (DMSO), hydrogen peroxide (30% aqueous solution) were from Sigma-Aldrich (St. Louis, MO). Methanol (Optima®, LCMS grade), tris(2-carboxyethyl)phosphine (TCEP), formic acid (Optima®, LCMS Grade), were from Fisher Scientific (Pittsburgh, PA). Purified water (18.2 mΩ cm resistivity at 25°C) was prepared with a PureLab purification system (Elga LabWater, Woodridge, IL). The following chemicals were custom synthesized: T3 peptide with sequence ALVLIAFAQYLQQCPFEDHVK (>97%, Biomatik, Wilmington, DE), isotopically modified T3 with sequence AL-[15N, 13C-Val]-LIAFAQYLQQCPFEDH-[15N, 13C-Val]-K (>95%, BioMer Technology, Pleasanton, CA).
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