L-Lysine

RELEVANT DOCUMENTS: • Stable Isotope labeled Compounds for in-vitro SILAC Experiments: https://silantes-products.com/product_catalogue/Silantes_in-vitro_SILAC.pdf • Stable Isotope labeled Compounds for in-vitro SILAC: cell type-specific labeling using amino acid precursors (CTAP): https://silantes-products.com/product_catalogue/Silantes_SILAC_CTAP_with_DAP.pdf RELEVANT MANUALS: • Silantes Powder RPMI and DMEM for SILAC Preparation of sterile liquid Cell Culture Media: https://silantes-products.com/product_catalogue/Silantes_SILAC_RPMI_DMEM_Powder_Application_Note.pdf USE CASES OF THE SILAC AMINO ACIDS FROM SILANTES IN SCIENTIFIC PUBLICATIONS: • Hao, B., Li, X., Jia, X., Wang, Y., Zhai, L., Li, D., Liu, J., Zhang, D., Chen, Y., Xu, Y., Lee, S., Xu, G., Chen, X., Dang, Y., Liu, B., & Tan, M. (2020). The novel cereblon modulator CC-885 inhibits mitophagy via selective degradation of BNIP3L. Acta Pharmacologica Sinica, 41(9), 1246–1254. https://doi.org/10.1038/s41401-020-0367-9 • Lößner, C., Warnken, U., Pscherer, A., & Schnölzer, M. (2011). Preventing arginine-to-proline conversion in a cell-line-independent manner during cell cultivation under stable isotope labeling by amino acids in cell culture (SILAC) conditions. Analytical Biochemistry, 412(1), 123–125. https://doi.org/10.1016/j.ab.2011.01.011 • Sigismondo, G., Arseni, L., Palacio-Escat, N., Hofmann, T. G., Seiffert, M., & Krijgsveld, J. (2023c). Multi-layered chromatin proteomics identifies cell vulnerabilities in DNA repair. Nucleic Acids Research, 51(2), 687–711. https://doi.org/10.1093/nar/gkac1264 • Pateetin, P., Hutvagner, G., Bajan, S., Padula, M. P., McGowan, E. M., & Boonyaratanakornkit, V. (2021). Triple SILAC identified progestin-independent and dependent PRA and PRB interacting partners in breast cancer. Scientific Data, 8(1). https://doi.org/10.1038/s41597-021-00884-0 • Lopez-Serra, P., Marcilla, M., Villanueva, A., Ramos-Fernandez, A., Palau, A., Leal, L., Wahi, J. E., Setien-Baranda, F., Szczesna, K., Moutinho, C., Martinez-Cardus, A., Heyn, H., Sandoval, J., Puertas, S., Vidal, A., Sanjuan, X., Martinez-Balibrea, E., Viñals, F., Perales, J. C., . . . Esteller, M. (2014). A DERL3-associated defect in the degradation of SLC2A1 mediates the Warburg effect. Nature Communications, 5(1). https://doi.org/10.1038/ncomms4608 • Ong, S., Kratchmarova, I., & Mann, M. (2002). Properties of 13C-Substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC). Journal of Proteome Research, 2(2), 173–181. https://doi.org/10.1021/pr0255708 • Lößner, C., Warnken, U., Pscherer, A., & Schnölzer, M. (2011b). Preventing arginine-to-proline conversion in a cell-line-independent manner during cell cultivation under stable isotope labeling by amino acids in cell culture (SILAC) conditions. Analytical Biochemistry, 412(1), 123–125. https://doi.org/10.1016/j.ab.2011.01.011 • Malet, J. K., Impens, F., Carvalho, F., Hamon, M. A., Cossart, P., & Ribet, D. (2018b). Rapid remodeling of the host epithelial cell proteome by the listeriolysin O (LLO) pore-forming toxin. Molecular & Cellular Proteomics, 17(8), 1627–1636. https://doi.org/10.1074/mcp.ra118.000767 • Rogers, L. C., Kremer, J. C., Brashears, C. B., Lin, Z., Hu, Z., Bastos, A. C., Baker, A., Fettig, N., Zhou, D., Shoghi, K. I., Dehner, C. A., Chrisinger, J. S., Bomalaski, J. S., Garcia, B. A., Oyama, T., White, E. P., & Van Tine, B. A. (2023). Discovery and targeting of a noncanonical mechanism of sarcoma resistance to ADI-PEG20 mediated by the microenvironment. Clinical Cancer Research, 29(16), 3189–3202. https://doi.org/10.1158/1078-0432.ccr-22-2642 • Geiger, T., Wisniewski, J. R., Cox, J., Zanivan, S., Kruger, M., Ishihama, Y., & Mann, M. (2011). Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics. Nature Protocols, 6(2), 147–157. https://doi.org/10.1038/nprot.2010.192 • Hao, B., Sun, M., Zhang, M., Zhao, X., Zhao, L., Li, B., Zhai, L., Liu, P., Hu, H., Xu, J., & Tan, M. (2020). Global characterization of proteome and lysine methylome features in EZH2 wild-type and mutant lymphoma cell lines. Journal of Proteomics, 213, 103614. https://doi.org/10.1016/j.jprot.2019.103614 RELEVANT BLOG ARTICLES: • Quantitative Proteomics Explained: Techniques, Applications, and Challenges: https://www.silantes.com/guide-to-quantitative-proteomics-techniques-applications-and-challenges/ • Quantitative Proteomics: Comparing the Big Three – iTRAQ, TMT, and SILAC: https://www.silantes.com/itraq-tmt-silac/ • Quantitative Proteomics: Label-Free versus Label-Based Methods: https://www.silantes.com/label-vs-label-free-quantitative-proteomics/ Understanding the Role of Mass Spectrometry in Metabolomics: https://www.silantes.com/mass-spectrometry-metabolomics/ • Understanding Proteomics: A Comprehensive Guide to the Various Types: https://www.silantes.com/types-of-proteomics/ RELEVANT WEBINARS: • Proteomics using SILAC presented by Prof. Dr. Marcus Krüger: https://www.youtube.com/watch?v=TY6iV8_43iA • Multiplexing with isotopic labels for DDA and DIA in MaxQuant presented by Dr. Jürgen Cox: https://www.youtube.com/watch?v=-Yddv7ehYsk • Stable Isotope Labeling of Mammals presented by Dr. Christoph Turck: https://www.youtube.com/watch?v=BQWvLdILjCA STRATEGIC CONSIDERATION: Offer SILAC media at a low price (at the retail price) in order to generate many customers here, who can then be used as leads for SILAC amino acids. DECISION TO DISCONTINUE DEUTERATED ARG UND ASP: A decision was made to perform deuterated Ralstonia/Cupriavidus necator fermentations without CyPh expression in the future due to problems with isotopic purity of deuterated fermentations: Deuterium atoms at the β-C (CH2 group) exchange completely. In addition, an exchange is also observed at the α-C, which partially results in the decrease of isotopic purity at this position as well as the decrease of enantiomeric purity (racemization). There, an exchange from D to H of about 10-12% was observed, of which simply statistically about half will be D, the other half L form. This is also in agreement with literature describing the problem and expecting about 5% D form after our hydrolysis time for Asp. Other amino acids also racemize readily, but much more slowly and so this is not as much of a problem in the process. There are also mechanism suggestions as to why this happens. So no new deuterated Arg/Asp will be added in the future. There are still some fractions that have already been purified. If there is concrete, high customer interest in deuterated Arg/Asp in the future, we can try isotope exchange and test enantiomeric purity analysis. Otherwise, it is not worth the effort given the problems/conditions mentioned.