SILAM Mouse Diets

Amino acid specific labeled SILAM diets for mice (suitable for proteomics studies)

• ¹³C-lysine labeled mice feed has been developed in cooperation with the group of Prof. Matthias Mann, Max-Planck-Institute of Biochemistry. [1] The ¹³C-lysine-labeled “heavy” diet is based on an artifical formulatin including Silantes-produced ¹³C-lysine and components from Envigo (formerly Harlan).
• In addition to ¹³C-lysine-labeled feed, other stable isotope-labeled amino acid formulations are also available upon request.

¹⁵N labeled SILAM diets for mice (suitable for proteomics and metabolomics studies)

• Silantes has developed a ¹⁵N-diet in cooperation with the group of Professor Chris Turck, Max-Planck-Institute of Psychiatry. [2] The ¹⁵N-labeled “heavy” diet is based on a hydrolysate of the bacterium Cupriavidus necator (formerly Ralstonia eutropha) as ¹⁵N-protein source and components from Envigo (formerly Harlan). Feeding experiments showed that the mice accepted bacterial-based protein better than algae-based protein.

¹³C labeled SILAM diets for mice (suitable for proteomics and metabolomics studies)
Silantes has developed two diets for ¹³C-labeling of mice:

• Partially ¹³C-labeled SILAM mouse diet based on bacterial Cupriavidus necator (formerly Ralstonia eutropha) biomass with a ¹³C isotopic enrichment of > 20 atom %
• Uniformly ¹³C-labeled SILAM mouse diet based on algal Arthrospira maxima (“Spirulina”) biomass with a ¹³C isotopic enrichment of > 98 atom %.
  Preliminary studies by us have shown that the partially ¹³C-labeled mouse reference material can be used for the relative quantification of amino acids in human plasma samples. We envision that this approach can be extended to the relative quantification of other small molecules of interest in metabolomics research.
  Read the Silantes Study Partially 13C-labeled SILAM Mouse Diet.

A short outline of the procedure of metabolic labeling workflow

Feeding strategies vary depending on the research question. Pulsed feeding with stable isotope-labeled SILAM feed is commonly used to analyze global protein or metabolite turnover or for biomarker discovery.

Full labeling over several generations, on the other hand, leads to uniformly labeled tissue, which can be used as a reference standard for relative protein quantification.

Differences in protein or metabolite levels are determined using the SILAM “spike-in” approach.

References:

Relevant documents:

• Silantes SILAM Lysine labeled Diet and Tissue
• In-vivo SILAM Mouse Tissues Lyophilized
• Silantes SILAM 15N labeled Diet and Tissue
• Silantes SILAM 13C labeled Diet

Use cases of the SILAM amino acid mouse diet Silantes in scientific publications:

• Silantes Lys6-SILAM diet (Complete labeling of oocytes): Harasimov, K., Gorry, R. L., Welp, L. M., Penir, S. M., Horokhovskyi, Y., Cheng, S., Takaoka, K., Stützer, A., Frombach, A., Tavares, A. L. T., Raabe, M., Haag, S., Saha, D., Grewe, K., Schipper, V., Rizzoli, S. O., Urlaub, H., Liepe, J., & Schuh, M. (2024). The maintenance of oocytes in the mammalian ovary involves extreme protein longevity. Nature Cell Biology, 26(7), 1124–1138. https://doi.org/10.1038/s41556-024-01442-7
• Silantes Lys6-SILAM diet (Time dependent labeling of sceletal mucle tissue): Bock, T., Türk, C., Aravamudhan, S. et al. PERM1 interacts with the MICOS-MIB complex to connect the mitochondria and sarcolemma via ankyrin B. Nat Commun 12, 4900 (2021). https://doi.org/10.1038/s41467-021-25185-3
• Silantes Lys8-SILAM diet (Time dependent labeling of liver, skeletal muscle, cartilage, mucosa, and blood): Rolfs, Z., Frey, B.L., Shi, X. et al. An atlas of protein turnover rates in mouse tissues. Nat Commun 12, 6778 (2021). https://doi.org/10.1038/s41467-021-26842-3
• Silantes Lys6-SILAM diet (Time dependent labeling of spinal cord tissue): Meschkat, M., Steyer, A.M., Weil, MT. et al. White matter integrity in mice requires continuous myelin synthesis at the inner tongue. Nat Commun 13, 1163 (2022). https://doi.org/10.1038/s41467-022-28720-y
• Silantes Lys6-SILAM diet (Complete labeling of heart tissue): Aravamudhan, S., Türk, C., Bock, T., Keufgens, L., Nolte, H., Lang, F., Krishnan, R. K., König, T., Hammerschmidt, P., Schindler, N., Brodesser, S., Rozsivalova, D. H., Rugarli, E., Trifunovic, A., Brüning, J., Langer, T., Braun, T., & Krüger, M. (2021). Phosphoproteomics of the developing heart identifies perm1 – an outer mitochondrial membrane protein. Journal of Molecular and Cellular Cardiology, 154, 41–59. https://doi.org/10.1016/j.yjmcc.2021.01.010
• Silantes Lys6-SILAM diet (Time dependent labeling of kidney tissue): Rinschen, M. M., Gödel, M., Grahammer, F., Zschiedrich, S., Helmstädter, M., Kretz, O., Zarei, M., Braun, D. A., Dittrich, S., Pahmeyer, C., Schroder, P., Teetzen, C., Gee, H., Daouk, G., Pohl, M., Kuhn, E., Schermer, B., Küttner, V., Boerries, M., Huber, T. B. (2018). A multi-layered quantitative in vivo expression atlas of the podocyte unravels kidney disease candidate genes. Cell Reports, 23(8), 2495–2508. https://doi.org/10.1016/j.celrep.2018.04.059
• Silantes Lys6-SILAM diet (Time dependent labling of kidney tissue): Rinschen, M. M., Palygin, O., El-Meanawy, A., Domingo-Almenara, X., Palermo, A., Dissanayake, L. V., Golosova, D., Schafroth, M. A., Guijas, C., Demir, F., Jaegers, J., Gliozzi, M. L., Xue, J., Hoehne, M., Benzing, T., Kok, B. P., Saez, E., Bleich, M., Himmerkus, N., Staruschenko, A. (2022). Accelerated lysine metabolism conveys kidney protection in salt-sensitive hypertension. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-31670-0
• Silantes Lys6-SILAM diet (Time dependent labeling of epithelial cells and mucus along the gastrointestinal tract): Arike, L., Seiman, A., van der Post, S., Rodriguez Piñeiro, A. M., Ermund, A., Schütte, A., Bäckhed, F., Johansson, M. E. V., Hansson, G. C. (2020). Protein turnover in epithelial cells and mucus along the gastrointestinal tract is coordinated by the spatial location and microbiota. Cell Reports, 30(4). https://doi.org/10.1016/j.celrep.2019.12.068
• Silantes Lys6-SILAM diet (Time dependent labeling of brain tissue): Andrews, B., Murphy, A. E., Stofella, M., Maslen, S., Almeida-Souza, L., Skehel, J. M., Skene, N. G., Sobott, F., Frank, R. A. W. (2022). Multidimensional Dynamics of the proteome in the neurodegenerative and aging mammalian brain. Molecular and Cellular Proteomics, 21(2), 100192. https://doi.org/10.1016/j.mcpro.2021.100192
• Silantes Lys6-SILAM diet (Time dependent labeling of muscle tissue): Kallabis S, Abraham L, Müller S, Dzialas V, Türk C, Wiederstein JL, Bock T, Nolte H, Nogara L, Blaauw B, Braun T, Krüger M. High-throughput proteomics fiber typing (ProFiT) for comprehensive characterization of single skeletal muscle fibers. Skelet Muscle. 2020 Mar 23;10(1):7. doi: 10.1186/s13395-020-00226-5. PMID: 32293536; PMCID: PMC7087369

Use cases of the SILAM 13C and 15N mouse diet from Silantes in scientific publications:

• Silantes 15N SILAM diet (Imaging using NanoSims, time dependent proteomics of retina tissue): Bonnin, E. A., Fornasiero, E. F., Lange, F., Turck, C. W., & Rizzoli, S. O. (2021). NanoSIMS observations of mouse retinal cells reveal strict metabolic controls on nitrogen turnover. BMC Molecular and Cell Biology, 22(1). https://doi.org/10.1186/s12860-020-00339-1
• Silantes 15N SILAM diet (time dependent targeted metabolomics and proteomics): Weckmann, K., Deery, M. J., Howard, J. A., Feret, R., Asara, J. M., Dethloff, F., Filiou, M. D., Labermaier, C., Maccarrone, G., Lilley, K. S., Mueller, M., & Turck, C. W. (2018). Ketamine’s effects on the glutamatergic and GABAergic systems: A proteomics and metabolomics study in mice. Complex Psychiatry, 5(1), 42–51. https://doi.org/10.1159/000493425
• Silantes 15N-SILAM diet (time dependent targeted metabolomics and proteomics, brain tissue, hippocampus tissue, blood tissue, plasma): Zhang, Y., Filiou, M. D., Reckow, S., Gormanns, P., Maccarrone, G., Kessler, M. S., Frank, E., Hambsch, B., Holsboer, F., Landgraf, R., & Turck, C. W. (2011). Proteomic and metabolomic profiling of a trait anxiety mouse model implicate affected pathways. Molecular & Cellular Proteomics, 10(12). https://doi.org/10.1074/mcp.m111.008110
• Silantes 15N-SILAM diet (complete labeling of brain tissue, proteomics): Klingener, Michael, et al. “N-Cadherin Promotes Recruitment and Migration of Neural Progenitor Cells from the SVZ Neural Stem Cell Niche into Demyelinated Lesions.” The Journal of Neuroscience, vol. 34, no. 29, 16 July 2014, pp. 9590–9606, https://doi.org/10.1523/jneurosci.3699-13.2014.
• Silantes 15N-SILAM diet (time dependent labeling in slowly proliferative tissues, proteomics): John Hasper, Kevin Welle, Jennifer Hryhorenko, Sina Ghaemmaghami, Abigail Buchwalter Turnover and replication analysis by isotope labeling (TRAIL) reveals the influence of tissue context on protein and organelle lifetimes. Mol Syst Biol. (2023) 19: e11393 https://doi.org/10.15252/msb.202211393

Relevant blog articles:

• Quantitative Proteomics Explained: Techniques, Applications, and Challenges
• Quantitative Proteomics: Comparing the Big Three – iTRAQ, TMT, and SILAC
• Quantitative Proteomics: Label-Free versus Label-Based Methods
• Understanding the Role of Mass Spectrometry in Metabolomics
• Understanding Proteomics: A Comprehensive Guide to the Various Types
• A Proteomics and Metabolomics Study using 15N-SILAM mouse diet

Relevant webinars:

• Proteomics using SILAC presented by Prof. Dr. Marcus Krüger
• Multiplexing with isotopic labels for DDA and DIA in MaxQuant presented by Dr. Jürgen Cox
• Stable Isotope Labeling of Mammals presented by Dr. Christoph Turck