The expanding field of SILAC

Analytical and Bioanalytical Chemistry

Volumn 404, Issue 4, 2012, Pages 967-976

  Ong, Shao En ^a  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

Mass spectrometry; Proteomics; Quantification; SILAC; Stable isotopes

Indexed keywords

CELL POPULATIONS; MASS RESOLUTION; METABOLIC LABELING; NEW APPLICATIONS; PEPTIDE IDENTIFICATION; POST-TRANSLATIONAL MODIFICATIONS; PROTEIN QUANTIFICATION; PROTEOMICS; QUANTIFICATION; SILAC; STABLE ISOTOPES; STABLE-ISOTOPE LABELING;

AMINO ACIDS; CELL CULTURE; CELL PROLIFERATION; ISOTOPES; MASS SPECTROMETRY; MOLECULAR BIOLOGY;

PROTEINS;

AMINO ACID; PROTEIN;

ANIMAL; CHEMISTRY; EVALUATION; HUMAN; ISOTOPE LABELING; METHODOLOGY; REVIEW;

AMINO ACIDS; ANIMALS; HUMANS; ISOTOPE LABELING; PROTEINS;

EID: 84865595374     PISSN: 16182642     EISSN: 16182650     Source Type: Journal    
DOI: 10.1007/s00216-012-5998-3     Document Type: Review

References (79)

1. J Peng SP Gygi 2001 J Mass Spectrom 36 10 1083 91 10.1002/jms.229 1:CAS:528:DC%2BD3MXotFOqt7Y%3D
2. MW Senko SC Beu FW Mclafferty 1995 J Am Soc Mass Spectrom 6 4 229 33 10.1016/1044-0305(95)00017-8 1:CAS:528:DyaK2MXlt1Oqu7Y%3D
3. A Michalski J Cox M Mann 2011 J Proteome Res 10 4 1785 93 10.1021/pr101060v 1:CAS:528:DC%2BC3MXisVyksLw%3D
4. J Cox M Mann 2011 Annu Rev Biochem 80 273 99 10.1146/annurev-biochem- 061308-093216 1:CAS:528:DC%2BC3MXptVCnsL4%3D
5. M Gstaiger R Aebersold 2009 Nature reviews Genetics 10 9 617 27 1:CAS:528:DC%2BD1MXhtVWhsLzP
6. SP Gygi B Rist SA Gerber F Turecek MH Gelb R Aebersold 1999 Nat Biotechnol 17 10 994 9 10.1038/13690 1:CAS:528:DyaK1MXmvVelsLs%3D
7. SE Ong M Mann 2005 Nat Chem Biol 1 5 252 62 10.1038/nchembio736 1:CAS:528:DC%2BD2MXhtVamtrfI
8. PL Ross YN Huang JN Marchese B Williamson K Parker S Hattan, et al. 2004 Mol Cell Proteomics 3 12 1154 69 10.1074/mcp.M400129-MCP200 1:CAS:528: DC%2BD2MXhvFartg%3D%3D
9. A Thompson J Schafer K Kuhn S Kienle J Schwarz G Schmidt, et al. 2003 Anal Chem 75 8 1895 904 10.1021/ac0262560 1:CAS:528:DC%2BD3sXhslSmtbw%3D
10. KA Neilson NA Ali S Muralidharan M Mirzaei M Mariani G Assadourian, et al. 2011 Proteomics 11 4 535 53 10.1002/pmic.201000553 1:CAS:528: DC%2BC3MXhsVSnu74%3D
11. Y Oda K Huang FR Cross D Cowburn BT Chait 1999 Proc Natl Acad Sci U S A 96 12 6591 6 10.1073/pnas.96.12.6591 1:CAS:528:DyaK1MXks1Wlu70%3D
12. TP Conrads K Alving TD Veenstra ME Belov GA Anderson DJ Anderson, et al. 2001 Anal Chem 73 9 2132 9 10.1021/ac001487x 1:CAS:528:DC%2BD3MXhslSrsbk%3D
13. H Jiang AM English 2002 J Proteome Res 1 4 345 50 10.1021/pr025523f 1:CAS:528:DC%2BD38Xjs12gsr4%3D
14. SE Ong B Blagoev I Kratchmarova DB Kristensen H Steen A Pandey, et al. 2002 Mol Cell Proteomics 1 5 376 86 10.1074/mcp.M200025-MCP200 1:CAS:528:DC%2BD38XlslWhsrk%3D
15. H Zhu S Pan S Gu EM Bradbury X Chen 2002 Rapid Commun Mass Spectrom 16 22 2115 23 10.1002/rcm.831 1:CAS:528:DC%2BD38XovFOmsLk%3D
16. JV Olsen SE Ong M Mann 2004 Mol Cell Proteomics 3 6 608 14 10.1074/mcp.T400003-MCP200 1:CAS:528:DC%2BD2cXltFCktrw%3D
17. A Gruhler JV Olsen S Mohammed P Mortensen NJ Faergeman M Mann, et al. 2005 Mol Cell Proteomics 4 3 310 27 10.1074/mcp.M400219-MCP200 1:CAS:528:DC%2BD2MXisFSms78%3D
18. B Soufi C Kumar F Gnad M Mann I Mijakovic B Macek 2010 J Proteome Res 9 7 3638 46 10.1021/pr100150w 1:CAS:528:DC%2BC3cXnsVansrk%3D
19. A Gruhler WX Schulze R Matthiesen M Mann ON Jensen 2005 Mol Cell Proteomics 4 11 1697 709 10.1074/mcp.M500190-MCP200 1:CAS:528:DC%2BD2MXht1Cgtb7E
20. A Cuomo T Bonaldi 2010 Methods Mol Biol 662 59 78 10.1007/978-1-60761- 800-3-3 1:CAS:528:DC%2BC3cXhtlKju7bJ
21. MD Sury JX Chen M Selbach 2010 Mol Cell Proteomics 9 10 2173 83 10.1074/mcp.M110.000323 1:CAS:528:DC%2BC3cXhtlegt7vF
22. J Fredens K Engholm-Keller A Giessing D Pultz MR Larsen P Hojrup, et al. 2011 Nat Methods 8 10 845 7 10.1038/nmeth.1675 1:CAS:528:DC%2BC3MXhtV2gsbvP
23. M Larance AP Bailly E Pourkarimi RT Hay G Buchanan S Coulthurst, et al. 2011 Nat Methods 8 10 849 51 10.1038/nmeth.1679 1:CAS:528:DC%2BC3MXhtV2gt7jN
24. M Kruger M Moser S Ussar I Thievessen CA Luber F Forner, et al. 2008 Cell 134 2 353 64 10.1016/j.cell.2008.05.033
25. L Ting R Rad SP Gygi W Haas 2011 Nat Methods 8 11 937 40 10.1038/nmeth.1714 1:CAS:528:DC%2BC3MXht1CrtrvI
26. CD Wenger MV Lee AS Hebert GC McAlister DH Phanstiel MS Westphall, et al. 2011 Nat Methods 8 11 933 5 10.1038/nmeth.1716 1:CAS:528:DC%2BC3MXht1CrtrvJ
27. Mertins P, Udeshi ND, Clauser KR, Mani DR, Patel J, Ong SE et al (2011) Mol Cell Proteomics. doi: 10.1074/mcp.M111.014423
28. PA Everley J Krijgsveld BR Zetter SP Gygi 2004 Mol Cell Proteomics 3 7 729 35 10.1074/mcp.M400021-MCP200 1:CAS:528:DC%2BD2cXlvFensL4%3D
29. KS Park DP Mohapatra H Misonou JS Trimmer 2006 Science 313 5789 976 9 10.1126/science.1124254 1:CAS:528:DC%2BD28XotFCitb8%3D
30. GL Christensen CD Kelstrup C Lyngso U Sarwar R Bogebo SP Sheikh, et al. 2010 Mol Cell Proteomics 9 7 1540 53 10.1074/mcp.M900550-MCP200 1:CAS:528:DC%2BC3cXhtlGisbrM
31. AM Hinsby JV Olsen M Mann 2004 J Biol Chem 279 45 46438 47 10.1074/jbc.M404537200 1:CAS:528:DC%2BD2cXptFaqt78%3D
32. K Xiao J Sun J Kim S Rajagopal B Zhai J Villen, et al. 2010 Proc Natl Acad Sci U S A 107 34 15299 304 10.1073/pnas.1008461107 1:CAS:528: DC%2BC3cXhtFSnsb%2FI
33. JV Olsen B Blagoev F Gnad B Macek C Kumar P Mortensen, et al. 2006 Cell 127 3 635 48 10.1016/j.cell.2006.09.026 1:CAS:528:DC%2BD28Xht1WgtbzO
34. KT Rigbolt TA Prokhorova V Akimov J Henningsen PT Johansen I Kratchmarova, et al. 2011 Sci Signal 4 164 rs3 10.1126/scisignal.2001570
35. MR Larsen TE Thingholm ON Jensen P Roepstorff TJ Jorgensen 2005 Mol Cell Proteomics 4 7 873 86 10.1074/mcp.T500007-MCP200 1:CAS:528:DC%2BD2MXmtFKktbg%3D
36. J Villen SP Gygi 2008 Nat Protoc 3 10 1630 8 10.1038/nprot.2008.150
37. SA Wagner P Beli BT Weinert ML Nielsen J Cox M Mann, et al. 2011 Mol Cell Proteomics 10 10 M111.013284 10.1074/mcp.M111.013284
38. C Choudhary C Kumar F Gnad ML Nielsen M Rehman TC Walther, et al. 2009 Science 325 5942 834 40 10.1126/science.1175371 1:CAS:528:DC%2BD1MXps1Ogt70%3D
39. BR Martin C Wang A Adibekian SE Tully BF Cravatt 2011 Nat Methods 9 1 84 9 10.1038/nmeth.1769
40. SE Ong G Mittler M Mann 2004 Nat Methods 1 2 119 26 10.1038/nmeth715 1:CAS:528:DC%2BD2MXisVGhurc%3D
41. SM Sweet M Li PM Thomas KR Durbin NL Kelleher 2010 J Biol Chem 285 43 32778 86 10.1074/jbc.M110.145094 1:CAS:528:DC%2BC3cXht12nu7%2FL
42. BM Zee RS Levin B Xu G LeRoy NS Wingreen BA Garcia 2010 J Biol Chem 285 5 3341 50 10.1074/jbc.M109.063784 1:CAS:528:DC%2BC3cXovVekug%3D%3D
43. DM Desiderio S Yamada FS Tanzer J Horton J Trimble 1981 J Chromatogr 217 437 52 10.1016/S0021-9673(00)88096-6 1:CAS:528:DyaL38Xks1ensA%3D%3D
44. P Picotti B Bodenmiller LN Mueller B Domon R Aebersold 2009 Cell 138 4 795 806 10.1016/j.cell.2009.05.051 1:CAS:528:DC%2BD1MXhsVCjs7vM
45. MF Festing DG Altman 2002 ILAR J 43 4 244 58 1:CAS:528: DC%2BD38Xnt1SitLk%3D
46. Y Ishihama T Sato T Tabata N Miyamoto K Sagane T Nagasu, et al. 2005 Nat Biotechnol 23 5 617 21 10.1038/nbt1086 1:CAS:528:DC%2BD2MXjvV2ntbs%3D
47. KH Yu CG Barry D Austin CM Busch V Sangar AK Rustgi, et al. 2009 J Proteome Res 8 3 1565 76 10.1021/pr800904z 1:CAS:528:DC%2BD1MXmvVWmtQ%3D%3D
48. T Geiger J Cox P Ostasiewicz JR Wisniewski M Mann 2010 Nat Methods 7 5 383 5 10.1038/nmeth.1446 1:CAS:528:DC%2BC3cXkt1aqtb8%3D
49. M Monetti N Nagaraj K Sharma M Mann 2011 Nat Methods 8 8 655 8 10.1038/nmeth.1647 1:CAS:528:DC%2BC3MXos1Onu7g%3D
50. Ong SE, Mortensen P, Mann M (2005) Comparing in-solution and in-gel enzymatic digestion efficiencies using SILAC. Proceedings of the 53rd ASMS Conference on Mass Spectrometry and Allied Topics, San Antonio, Texas, June 5-9
51. G Zhang D Fenyo TA Neubert 2009 J Proteome Res 8 3 1285 92 10.1021/pr8006107 1:CAS:528:DC%2BD1MXkvVOmtQ%3D%3D
52. S Hanke H Besir D Oesterhelt M Mann 2008 J Proteome Res 7 3 1118 30 10.1021/pr7007175 1:CAS:528:DC%2BD1cXhvV2lsrk%3D
53. Zeiler M, Straube WL, Lundberg E, Uhlen M, Mann M (2012) Mol Cell Proteomics 11(3):0111009613
54. RJ Austin RE Kuestner DK Chang KR Madden DB Martin 2011 J Proteome Res 10 11 5251 9 10.1021/pr200551e 1:CAS:528:DC%2BC3MXhtlSqtrrF
55. A Pandey AV Podtelejnikov B Blagoev XR Bustelo M Mann HF Lodish 2000 Proc Natl Acad Sci U S A 97 1 179 84 10.1073/pnas.97.1.179 1:CAS:528: DC%2BD3cXjvVCqsg%3D%3D
56. B Blagoev I Kratchmarova SE Ong M Nielsen LJ Foster M Mann 2003 Nat Biotechnol 21 3 315 8 10.1038/nbt790 1:CAS:528:DC%2BD3sXhsFajs7o%3D
57. JA Ranish EC Yi DM Leslie SO Purvine DR Goodlett J Eng, et al. 2003 Nat Genet 33 3 349 55 10.1038/ng1101 1:CAS:528:DC%2BD3sXhsV2kurk%3D
58. B Blagoev SE Ong I Kratchmarova M Mann 2004 Nat Biotechnol 22 9 1139 45 10.1038/nbt1005 1:CAS:528:DC%2BD2cXntFCgtbs%3D
59. WX Schulze M Mann 2004 J Biol Chem 279 11 10756 64 10.1074/jbc.M309909200 1:CAS:528:DC%2BD2cXhvFChtrk%3D
60. M Vermeulen KW Mulder S Denissov WW Pijnappel FM van Schaik RA Varier, et al. 2007 Cell 131 1 58 69 10.1016/j.cell.2007.08.016 1:CAS:528: DC%2BD2sXht1CntLnN
61. G Mittler F Butter M Mann 2009 Genome Res 19 2 284 93 10.1101/gr.081711.108 1:CAS:528:DC%2BD1MXhvVSju7k%3D
62. F Butter M Scheibe M Morl M Mann 2009 Proc Natl Acad Sci U S A 106 26 10626 31 10.1073/pnas.0812099106 1:CAS:528:DC%2BD1MXos1SmsL0%3D
63. SE Ong M Schenone AA Margolin X Li K Do MK Doud, et al. 2009 Proc Natl Acad Sci U S A 106 12 4617 22 10.1073/pnas.0900191106 1:CAS:528: DC%2BD1MXktFOgsb4%3D
64. K Sharma C Weber M Bairlein Z Greff G Keri J Cox, et al. 2009 Nat Methods 6 10 741 4 10.1038/nmeth.1373 1:CAS:528:DC%2BD1MXhtFaju73O
65. H Daub JV Olsen M Bairlein F Gnad FS Oppermann R Korner, et al. 2008 Mol Cell 31 3 438 48 10.1016/j.molcel.2008.07.007 1:CAS:528:DC%2BD1cXhtVSrsrnL
66. M Bantscheff D Eberhard Y Abraham S Bastuck M Boesche S Hobson, et al. 2007 Nat Biotechnol 25 9 1035 44 10.1038/nbt1328 1:CAS:528:DC%2BD2sXhtVWksLvF
67. JM Pratt J Petty I Riba-Garcia DH Robertson SJ Gaskell SG Oliver, et al. 2002 Mol Cell Proteomics 1 8 579 91 10.1074/mcp.M200046-MCP200 1:CAS:528:DC%2BD38XotlCntLo%3D
68. IV Hinkson JE Elias 2011 Trends Cell Biol 21 5 293 303 10.1016/j.tcb.2011.02.002 1:CAS:528:DC%2BC3MXlvFWjs7c%3D
69. MK Doherty C Whitehead H McCormack SJ Gaskell RJ Beynon 2005 Proteomics 5 2 522 33 10.1002/pmic.200400959 1:CAS:528:DC%2BD2MXhs1Oiur4%3D
70. MK Doherty DE Hammond MJ Clague SJ Gaskell RJ Beynon 2009 J Proteome Res 8 1 104 12 10.1021/pr800641v 1:CAS:528:DC%2BD1cXhtlSnur7L
71. E Milner E Barnea I Beer A Admon 2006 Mol Cell Proteomics 5 2 357 65 1:CAS:528:DC%2BD28XitVagsb0%3D
72. YW Lam AI Lamond M Mann JS Andersen 2007 Curr Biol 17 9 749 60 10.1016/j.cub.2007.03.064 1:CAS:528:DC%2BD2sXkslCiu7k%3D
73. SB Cambridge F Gnad C Nguyen JL Bermejo M Kruger M Mann 2011 J Proteome Res 10 12 5275 84 1:CAS:528:DC%2BC3MXhsVSks7zI
74. KP Jayapal S Sui RJ Philp YJ Kok MG Yap TJ Griffin, et al. 2010 J Proteome Res 9 5 2087 97 10.1021/pr9007738 1:CAS:528:DC%2BC3cXjvFWmurc%3D
75. B Schwanhausser M Gossen G Dittmar M Selbach 2009 Proteomics 9 1 205 9 10.1002/pmic.200800275
76. M Selbach B Schwanhausser N Thierfelder Z Fang R Khanin N Rajewsky 2008 Nature 455 7209 58 63 10.1038/nature07228 1:CAS:528:DC%2BD1cXhtVKrsbnK
77. B Schwanhausser D Busse N Li G Dittmar J Schuchhardt J Wolf, et al. 2011 Nature 473 7347 337 42 10.1038/nature10098
78. DL Swaney GC McAlister JJ Coon 2008 Nat Methods 5 11 959 64 10.1038/nmeth.1260 1:CAS:528:DC%2BD1cXhtlSkt77F
79. Graumann J, Scheltema RA, Zhang Y, Cox J, Mann M (2012) Mol Cell Proteomics 11(3):M111013185