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3 protocols using l lysine

1

Proteome Analysis of SIH Cell Lines

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Complete HL-5 and defined SIH (-arginine; -lysine) growth media and unlabelled L-arginine and L-lysine were from Formedium. Labelled K8 L-lysine and R6 L-arginine were from Cambridge Isotope Laboratories. Complete EDTA-free protease inhibitor cocktail was from Roche. Turbo DNase was from Ambion. Novex NuPAGE 4–12% gradient bis-tris gels with MOPS SDS running buffer and Novex colloidal blue staining kit were from Invitrogen. Trypsin Gold was from Promega. LavaPep peptide quantification kit was from Gel Company. ZipTip C-18 peptide purification microcolumns and high fidelity KOD hot start DNA polymerase were from Merck Millipore. Restriction enzymes, T4 DNA ligase and Antarctic phosphatase were from New England Biolabs. Plasmid miniprep kit and PCR clean-up kit were from Qiagen. Krypton fluorescent protein stain and Nunc Lab-Tek chambered cover glass plates for cell imaging were from Thermo Scientific. All the other reagents were obtained from Sigma-Aldrich.
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2

Quantitative Mass Spectrometry Proteomics

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Complete HL-5 and defined SIH (-arginine; -lysine) growth media and unlabelled L-arginine and L-lysine were from Formedium. Labelled K8 L-lysine and R6 L-arginine were from Cambridge Isotope Laboratories. Complete EDTA-free Protease Inhibitors cocktail was from Roche. Turbo DNase was from Ambion. Novex NuPAGE 4-12% gradient bis-tris gels with MOPS SDS running buffer and Novex colloidal blue staining kit were from Invitrogen. Trypsin Gold was from Promega. LavaPep peptide quantification kit was from Gel Company. ZipTip C-18 peptide purification microcolumns and high fidelity KOD hot start DNA polymerase were from Merck Millipore. Restriction enzymes, T4 DNA ligase and Antarctic Phosphatase were from New England Biolabs. Plasmid miniprep kit and PCR clean-up kit were from Qiagen. Krypton fluorescent protein stain and Nunc Lab-Tek chambered cover glass plates for cell imaging were from Thermo Scientific. All the other reagents were obtained from Sigma Aldrich.
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3

Yeast Cell Culture and Preparation

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All chemicals were purchased from Sigma‐Aldrich (Darmstadt, Germany), unless otherwise indicated. Cells were cultured at 30 °C with 200 RPM shaking in 50 mL CELLreactor™ filter top tubes (Greiner Bio‐On, Kremsmünster, Austria). Strains were grown overnight by inoculation in 5‐mL synthetic glucose media without uracil and lysine and supplemented with the dipeptide Lys‐Lys. Media were prepared by dissolving 2% w/v glucose and 0.69% w/v yeast nitrogen base (YNB) without amino acids (Formedium, Norfolk, UK). Media were supplemented with 0.19% w/v Kaiser synthetic mixture without uracil and lysine 51, that is, a mixture containing 18 mg·L−1 adenine, 76 mg·L−1 myo‐inositol, 8 mg·L−1 para‐aminobenzoic acid, and 76 mg·L−1 of all 20 standard amino acids (l‐leucine was added at 380 mg·L−1) except l‐lysine (Formedium). Finally, 200 mg·L−1 Lys‐Lys was added. Subcultures were grown and diluted for two to three consecutive days such that the OD600 never exceeded 1. Cells were centrifuged at 3000 g for 5 min at 4 °C, supernatant was decanted, and cells were suspended in ice‐cold 100 mm potassium phosphate, 10 mm glucose, pH 6.0. This step was performed twice before suspension of the cells to an OD600 of 5.
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