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3 protocols using l lysine 13c615n2 2hcl

1

Cell Culture and Proteomic Profiling

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KBM7 cells were cultured in Iscove’s modified Dulbecco’s medium, human embryonic kidney (HEK) 293ET, and HeLa M cells in RPMI 1640 (all from Sigma-Aldrich). In all cases, the medium was supplemented with 10% fetal calf serum (vol/vol), 2 mM l-glutamine, 100 U/ml penicillin, and 100 µg/ml streptomycin (all from Sigma-Aldrich). Each cell line was regularly screened for absence of mycoplasma contamination by DAPI staining and treated with Micoplasma Removal Agent (MP Biomedicals).
For proteomics, cells were grown in SILAC medium (Thermo Fisher Scientific) supplemented with 10% (vol/vol) dialyzed fetal calf serum (10,000 molecular weight cut-off; Invitrogen), penicillin/streptomycin, and either “heavy” amino acids (l-arginine-13C615N4:HCl [50 mg/l] and l-lysine-13C615N2:2HCl [100 mg/l]; Cambridge Isotope Laboratories) or the equivalent “light” amino acids. Cells were grown in SILAC medium over seven doublings to achieve metabolic labeling.
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2

HeLa and Fibroblast Culture Protocol

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HeLaM cells [56 (link)] and patient fibroblasts [9 (link)] were grown in Dulbecco’s Modified Eagle’s Medium (DMEM, Sigma) supplemented with 10% (v/v) foetal calf serum (Sigma), 2 mM L-glutamine, 50 units/ml penicillin, and 50 μg/ml streptomycin. The BAC-transgenic HeLa cell line expressing SPG15-GFP under its own promoter had to be regularly sorted by FACS due to loss of expression. HeLa cells expressing the reporter constructs composed of the cytoplasmic tail of CIMPR (CD8-CIMPR) or sortilin (CD8-sortilin) coupled to the transmembrane and lumenal domain of CD8 were kind gifts from Matthew Seaman [43 (link)].
For proteomics, HeLa cells were grown in SILAC medium supplemented with 10% (v/v) dialysed foetal calf serum (10,000 MW cutoff; Invitrogen), penicillin/streptomycin (Sigma), and either “Heavy” amino acids (L-arginine-13C615N4:HCl [50 mg/L] and L-lysine-13C615N2:2HCl [100 mg/L]; Cambridge Isotope Laboratories) or the equivalent “Light” amino acids. Cells were grown for at least 7 days to achieve metabolic labelling, and the average incorporation efficiency was approximately 95%, as determined by mass spectrometry.
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3

SILAC Labeling of PC12 Cells

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For SILAC experiments, PC12 cells were cultured in SILAC medium for 3 wk to achieve metabolic labeling. The medium consisted of DMEM (Thermo Fisher) supplemented with 5% (vol/vol) fetal bovine serum (10,000 MW cutoff; Invitrogen), plus 10% (vol/vol) dialyzed horse serum (10,000 MW cutoff; Dundee Cell), and either “heavy” amino acids (l-arginine-13C615N4:HCl (50 mg/l) and l-lysine-13C615N2:2HCl (100 mg/l) or “light” amino acids (Cambridge Isotope Laboratories). The average incorporation efficiency was ∼94%, as determined by mass spectrometry.
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