Stable isotope labeling by amino acids in cell culture
Stable isotope labeling by/with amino acids in cell culture (SILAC) is a technique based on mass spectrometry that detects differences in protein abundance among samples using non-radioactive isotopic labeling.[1][2][3][4] It is a popular method for quantitative proteomics
Procedure
Two populations of cells are cultivated in
Applications
A SILAC approach involving incorporation of tyrosine labeled with nine carbon-13 atoms (13C) instead of the normal carbon-12 (12C) has been utilized to study tyrosine kinase substrates in signaling pathways.[6] SILAC has emerged as a very powerful method to study cell signaling, post translation modifications such as phosphorylation,[6][7] protein–protein interaction and regulation of gene expression. In addition, SILAC has become an important method in secretomics, the global study of secreted proteins and secretory pathways.[8] It can be used to distinguish between proteins secreted by cells in culture and serum contaminants.[9] Standardized protocols of SILAC for various applications have also been published.[10][11]
Pulsed SILAC
Pulsed SILAC (pSILAC) is a variation of the SILAC method where the labelled amino acids are added to the growth medium for only a short period of time. This allows monitoring differences in de novo protein production rather than raw concentration.[12]
NeuCode SILAC
Traditionally the level of multiplexing in SILAC was limited due to the number of SILAC isotopes available. Recently, a new technique called NeuCode (neutron encoding) SILAC, has augmented the level of multiplexing achievable with metabolic labeling (up to 4).[13] The NeuCode amino acid method is similar to SILAC but differs in that the labeling only utilizes heavy amino acids. The use of only heavy amino acids eliminates the need for 100% incorporation of amino acids needed for SILAC. The increased multiplexing capability of NeuCode amino acids is from the use of mass defects from extra neutrons in the stable isotopes. These small mass differences however need to be resolved on high-resolution mass spectrometers.
References
Further reading
- Ong SE, Kratchmarova I, Mann M (2003). "Properties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC)". Journal of Proteome Research. 2 (2): 173–181. PMID 12716131.
- Ong SE, Mann M (2006). "A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC)". Nature Protocols. 1 (6): 2650–2660. S2CID 10651610.
- Ong SE, Mann M (2007). "Stable isotope labeling by amino acids in cell culture for quantitative proteomics". Quantitative Proteomics by Mass Spectrometry. Methods in Molecular Biology. Vol. 359. pp. 37–52. PMID 17484109.