Abstract
Here I describe the history of the Stable Isotope Labeling by Amino Acids in Cell culture (SILAC) technology. Although published in 2002, it had already been developed and used in my laboratory for a number of years. From the beginning, it was applied to challenging problems in cell signaling that were considered out of reach for proteomics at the time. It was also used to pioneer proteomic interactomics, time series and dynamic posttranslational modification studies. While initially developed for metabolically accessible systems, such as cell lines, it was subsequently extended to whole animal labeling as well as to clinical applications—in the form or spike-in or super-SILAC. New formats and applications for SILAC labeling continue to be developed, for instance for protein-turnover studies.
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References
Ong SE, Blagoev B, Kratchmarova I et al (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1:376–386
Mann M, Hendrickson RC, Pandey A (2001) Analysis of proteins and proteomes by mass spectrometry. Annu Rev Biochem 70:437–473
Steen H et al (2002) Tyrosine phosphorylation mapping of the epidermal growth factor receptor signaling pathway. J Biol Chem 277(2):1031–1039
Ong SE, Kratchmarova I, Mann M (2003) Properties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC). J Proteome Res 2(2):173–181
Bendall SC et al (2008) Prevention of amino acid conversion in SILAC experiments with embryonic stem cells. Mol Cell Proteomics 7(9):1587–1597
Park SK et al (2009) A computational approach to correct arginine-to-proline conversion in quantitative proteomics. Nat Methods 6(3):184–185
Bicho CC et al (2010) A genetic engineering solution to the “arginine conversion problem” in stable isotope labeling by amino acids in cell culture (SILAC). Mol Cell Proteomics 9(7):1567–1577
Julka S, Regnier F (2004) Quantification in proteomics through stable isotope coding: a review. J Proteome Res 3(3):350–363
Martinovic S et al (2002) Selective incorporation of isotopically labeled amino acids for identification of intact proteins on a proteome-wide level. J Mass Spectrom 37(1):99–107
Gygi SP et al (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17(10):994–999
Lasonder E et al (2002) Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature 419(6906):537–542
Andersen JS et al (2003) Proteomic characterization of the human centrosome by protein correlation profiling. Nature 426(6966):570–574
Mann M (2006) Functional and quantitative proteomics using SILAC. Nat Rev Mol Cell Biol 7(12):952–958
Choudhary C et al (2009) Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 325(5942):834–840
Walther TC, Mann M (2010) Mass spectrometry-based proteomics in cell biology. J Cell Biol 190(4):491–500
Blagoev B et al (2003) A proteomics strategy to elucidate functional protein–protein interactions applied to EGF signaling. Nat Biotechnol 21(3):315–318
Olsen JV et al (2006) Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127(3):635–648
Mortensen P et al (2010) MSQuant, an open source platform for mass spectrometry-based quantitative proteomics. J Proteome Res 9(1):393–403
Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26(12):1367–1372
de Godoy LM et al (2008) Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 455(7217):1251–1254
Nagaraj N et al (2012) System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench-top Orbitrap. Mol Cell Proteomics 11(3):M111.013722
Mann M et al (2013) The coming age of complete, accurate, and ubiquitous proteomes. Mol Cell 49(4):583–590
Geiger T et al (2011) Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics. Nat Protoc 6(2):147–157
Geiger T et al (2010) Super-SILAC mix for quantitative proteomics of human tumor tissue. Nat Methods 7(5):383–385
Meissner F et al (2013) Direct proteomic quantification of the secretome of activated immune cells. Science 340(6131):475–478
Deeb SJ et al (2012) Super-SILAC allows classification of diffuse large B-cell lymphoma subtypes by their protein expression profiles. Mol Cell Proteomics 11(5):77–89
Zielinska DF et al (2010) Precision mapping of an in vivo N-glycoproteome reveals rigid topological and sequence constraints. Cell 141(5):897–907
Blagoev B et al (2004) Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat Biotechnol 22(9):1139–1145
Hubner NC et al (2010) Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions. J Cell Biol 189(4):739–754
Mittler G, Butter F, Mann M (2009) A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements. Genome Res 19(2):284–293
Vermeulen M et al (2010) Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell 142(6):967–980
Butter F et al (2012) Proteome-wide analysis of disease-associated SNPs that show allele-specific transcription factor binding. PLoS Genet 8(9):e1002982
Doherty MK et al (2009) Turnover of the human proteome: determination of protein intracellular stability by dynamic SILAC. J Proteome Res 8(1):104–112
Schwanhausser B et al (2009) Global analysis of cellular protein translation by pulsed SILAC. Proteomics 9(1):205–209
Selbach M et al (2008) Widespread changes in protein synthesis induced by microRNAs. Nature 455(7209):58–63
Jorgensen C et al (2009) Cell-specific information processing in segregating populations of Eph receptor ephrin-expressing cells. Science 326(5959):1502–1509
Nagaraj N et al (2011) Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol 7:548
Beck M et al (2011) The quantitative proteome of a human cell line. Mol Syst Biol 7:549
Michalski A et al (2011) Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer. Mol Cell Proteomics 10(9):M111.011015
Rose CM et al (2013) Neutron encoded labeling for peptide identification. Anal Chem 85(10):5129–5137
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Mann, M. (2014). Fifteen Years of Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC). In: Warscheid, B. (eds) Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC). Methods in Molecular Biology, vol 1188. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1142-4_1
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DOI: https://doi.org/10.1007/978-1-4939-1142-4_1
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