# Chemical Sciences: A Manual for CSIR-UGC National Eligibility Test for Lectureship and JRF/SILAC

SILAC (stable isotope labeling by amino acids in cell culture) is a technique based on mass spectrometry that detects differences in protein abundance among samples using non-radioactive isotopic labeling. It is a popular method for quantitative proteomics.

## Procedure

Two populations of cells are cultivated in cell culture. One of the cell populations is fed with growth medium containing normal amino acids. In contrast, the second population is fed with growth medium containing amino acids labeled with stable (non-radioactive) heavy isotopes. For example, the medium can contain arginine labeled with six carbon-13 atoms ($^{13}$C) instead of the normal carbon-12 ($^{12}$C). When the cells are growing in this medium, they incorporate the heavy arginine into all of their proteins. Therefore, all of the arginine containing peptides are now 6 Da heavier than their normal counterparts. The trick is that the proteins from both cell populations can be combined and analyzed together by mass spectrometry. Pairs of chemically identical peptides of different stable-isotope composition can be differentiated in a mass spectrometer owing to their mass difference. The ratio of peak intensities in the mass spectrum for such peptide pairs reflects the abundance ratio for the two proteins.

## Applications

A SILAC approach involving incorporation of tyrosine labeled with nine carbon-13 atoms ($^{13}$C) instead of the normal carbon-12 ($^{12}$C) has been utilized to study tyrosine kinase substrates in signaling pathways. SILAC has emerged as a very powerful method to study cell signaling, post translation modifications such as phosphorylation, protein-protein interaction and regulation of gene expression. Standardized protocols of SILAC for various application have also been published.

## 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.

## References
### Bibliography

* 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): 173–81. doi:10.1021/pr0255708. PMID 12716131.{{cite journal}}: CS1 maint: multiple names: authors list (link)
* Ong SE, Mann M (2006). "A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC)". Nature Protocols. 1 (6): 2650–60. doi:10.1038/nprot.2006.427. PMID 17406521.
* Ong SE, Mann M (2007). "Stable isotope labeling by amino acids in cell culture for quantitative proteomics". Methods in Molecular Biology. 359: 37–52. doi:10.1007/978-1-59745-255-7_3. PMID 17484109.

### Notes

* ↑ Jiang H, English, AM (2002). "Quantitative Analysis of the Yeast Proteome by Incorporation of Isotopically Labeled Leucine". Journal of Proteome Research. 1 (4): 345–50. doi:10.1021/pr025523f. PMID 12645890.{{cite journal}}: CS1 maint: multiple names: authors list (link)
* ↑ Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M (2002). "Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics". Molecular & Cellular Proteomics. 1 (5): 376–86. doi:10.1074/mcp.M200025-MCP200. PMID 12118079.{{cite journal}}: CS1 maint: multiple names: authors list (link)
* ↑ Zhu H, Pan S, Gu S, Bradbury EM, Chen X (2002). "Amino acid residue specific stable isotope labeling for quantitative proteomics". Rapid Communications in Mass Spectrometry. 16 (22): 2115–23. doi:10.1002/rcm.831. PMID 12415544.{{cite journal}}: CS1 maint: multiple names: authors list (link)
* 1 2 Ibarrola N, Molina H, Iwahori A, Pandey A (2004). "A novel proteomic approach for specific identification of tyrosine kinase substrates using 13C tyrosine". The Journal of Biological Chemistry. 279 (16): 15805–13. doi:10.1074/jbc.M311714200. PMID 14739304.{{cite journal}}: CS1 maint: multiple names: authors list (link)
* ↑ Ibarrola N, Kalume DE, Gronborg M, Iwahori A, Pandey A (2003). "A Proteomic Approach for Quantitation of Phosphorylation Using Stable Isotope Labeling in Cell Culture". Analytical Chemistry. 75 (22): 6043–49. doi:10.1021/ac034931f. PMID 14615979.{{cite journal}}: CS1 maint: multiple names: authors list (link)
* ↑ Amanchy R, Kalume DE, Pandey A (2005). "Stable isotope labeling with amino acids in cell culture (SILAC) for studying dynamics of protein abundance and posttranslational modifications". Science's STKE. 2005 (16): pl2. doi:10.1126/stke.2672005pl2. PMID 14739304.{{cite journal}}: CS1 maint: multiple names: authors list (link)
* ↑ Harsha HC, Molina H, Pandey A (2008). "Quantitative proteomics using stable isotope labeling with amino acids in cell culture". Nature Protocols. 3 (3): 505–16. doi:10.1038/nprot.2008.2. PMID 18323819.{{cite journal}}: CS1 maint: multiple names: authors list (link)
* ↑ Schwanhäusser, Björn (2009-01). "Global analysis of cellular protein translation by pulsed SILAC". Proteomics. 9 (1): 205–9. doi:10.1002/pmic.200800275. PMID 19053139. Retrieved 2009-03-17. {{cite journal}}: Check date values in: |date= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)