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Playing tag with quantitative proteomics

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Abstract

There is steady need for new proteomic strategies on quantitative measurements that provide essential components for detailing dynamic changes in many cellular functions and processes. Stable isotope labeling is a rapidly evolving field, which can be used either after protein extraction with chemical labeling, or in cell culture with metabolic incorporation. In this review, we explore the most frequently utilized quantitation techniques with particular attention paid to chemical labeling using different isotopic tags, including a recent labeling strategy—soluble polymer-based isotopic labeling (SoPIL)—that achieves efficient labeling in homogeneous conditions. Special care should be devoted to the selection of appropriate quantitation approaches according to the needs of the sample and overall experimental design. We evaluate recent advances in quantitative proteomics using stable isotope labeling and their applications to current insightful biological inquiries.

Chemical modules of isotopic tags for quantitative proteomics.

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Abbreviations

cICAT:

cleavable isotope-coded affinity tag

CILAT:

cleavable isobaric labeled affinity tag

ICAT:

isotope-coded affinity tag

ICPL:

isotope-coded protein label

iTRAQ:

isobaric tag for absolute and relative quantitation

MS:

mass spectrometry

LC:

liquid chromatography

SILAC:

stable isotope labeling with amino acids in cell culture

SoPIL:

soluble polymer-based isotopic labeling

SPE:

solid-phase extraction

References

  1. Aebersold R, Mann M (2003) Nature 422:198–207

    Article  CAS  Google Scholar 

  2. Ong SE, Mann M (2006) Nat Protoc 1:2650–2660

    Article  CAS  Google Scholar 

  3. Tao WA, Aebersold R (2003) Curr Opin Biotechnol 14:110–118

    Article  CAS  Google Scholar 

  4. Tao WA (2007) Expert Rev Proteomics 4:603–607

    Article  CAS  Google Scholar 

  5. Matta A, DeSouza LV, Shukla NK, Gupta SD, Ralhan R, Siu KW (2008) J Proteome Res 7:2078–2087

    Article  CAS  Google Scholar 

  6. Pitteri SJ, Faca VM, Kelly-Spratt KS, Kasarda AE, Wang H, Zhang Q, Newcomb L, Krasnoselsky A, Paczesny S, Choi G, Fitzgibbon M, McIntosh MW, Kemp CJ, Hanash SM (2008) J Proteome Res 7:1481–1489

    Article  CAS  Google Scholar 

  7. Reddy CS, Holzgreve W, Hahn S (2008) Methods Mol Biol 444:311–326

    Article  CAS  Google Scholar 

  8. Luo W, Slebos RJ, Hill S, Li M, Brabek J, Amanchy R, Chaerkady R, Pandey A, Ham AJ, Hanks SK (2008) J Proteome Res 7:3447–3460

    Google Scholar 

  9. Hanash SM, Pitteri SJ, Faca VM (2008) Nature 452:571–579

    Article  CAS  Google Scholar 

  10. Liao H, Wu J, Kuhn E, Chin W, Chang B, Jones MD, O’Neil S, Clauser KR, Karl J, Hasler F, Roubenoff R, Zolg W, Guild BC (2004) Arthritis Rheum 50:3792–3803

    Article  CAS  Google Scholar 

  11. Garbis SD, Tyritzis SI, Roumeliotis T, Zerefos P, Giannopoulou EG, Vlahou A, Kossida S, Diaz J, Vourekas S, Tamvakopoulos C, Pavlakis K, Sanoudou D, Constantinides CA (2008) J Proteome Res 7(8):3146–3158

    Google Scholar 

  12. Chen R, Brentnall TA, Pan S, Cooke K, Moyes KW, Lane Z, Crispin DA, Goodlett DR, Aebersold R, Bronner MP (2007) Mol Cell Proteomics 6:1331–1342

    Article  CAS  Google Scholar 

  13. Sanz-Medel A, Montes-Bayon M, del Rosario Fernandez de la Campa M, Encinar JR, Bettmer J (2008) Anal Bioanal Chem 390:3–16

    Article  CAS  Google Scholar 

  14. Sanz-Medel A (2008) Anal Bioanal Chem 391:885–894

    Article  CAS  Google Scholar 

  15. Old WM, Meyer-Arendt K, Aveline-Wolf L, Pierce KG, Mendoza A, Sevinsky JR, Resing KA, Ahn NG (2005) Mol Cell Proteomics 4:1487–1502

    Article  CAS  Google Scholar 

  16. Wang W, Zhou H, Lin H, Roy S, Shaler TA, Hill LR, Norton S, Kumar P, Anderle M, Becker CH (2003) Anal Chem 75:4818–4826

    Article  CAS  Google Scholar 

  17. Liu H, Sadygov RG, Yates JR 3rd (2004) Anal Chem 76:4193–4201

    Article  CAS  Google Scholar 

  18. Ippel JH, Pouvreau L, Kroef T, Gruppen H, Versteeg G, van den Putten P, Struik PC, van Mierlo CP (2004) Proteomics 4:226–234

    Article  CAS  Google Scholar 

  19. Oda Y, Huang K, Cross FR, Cowburn D, Chait BT (1999) Proc Natl Acad Sci USA 96:6591–6596

    Google Scholar 

  20. Veenstra TD, Martinovic S, Anderson GA, Pasa-Tolic L, Smith RD (2000) J Am Soc Mass Spectrom 11:78–82

    Article  CAS  Google Scholar 

  21. Thelen JJ, Peck SC (2007) Plant Cell 19:3339–3346

    Article  CAS  Google Scholar 

  22. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M (2002) Mol Cell Proteomics 1:376–386

    Article  CAS  Google Scholar 

  23. Zhu H, Pan S, Gu S, Bradbury EM, Chen X (2002) Rapid Commun Mass Spectrom 16:2115–2123

    Article  CAS  Google Scholar 

  24. Mann M (2006) Nat Rev Mol Cell Biol 7:952–958

    Article  CAS  Google Scholar 

  25. Gu S, Pan S, Bradbury EM, Chen X (2003) J Am Soc Mass Spectrom 14:1–7

    Article  CAS  Google Scholar 

  26. Ong SE, Mittler G, Mann M (2004) Nat Methods 1:119–126

    Article  CAS  Google Scholar 

  27. Ong SE, Kratchmarova I, Mann M (2003) J Proteome Res 2:173–181

    Article  CAS  Google Scholar 

  28. Scott L, Lamb J, Smith S, Wheatley DN (2000) Br J Cancer 83:800–810

    Article  CAS  Google Scholar 

  29. Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M (2006) Cell 127:635–648

    Article  CAS  Google Scholar 

  30. Graumann J, Hubner NC, Kim JB, Ko K, Moser M, Kumar C, Cox J, Scholer H, Mann M (2008) Mol Cell Proteomics 7:672–683

    CAS  Google Scholar 

  31. Liang X, Zhao J, Hajivandi M, Wu R, Tao J, Amshey JW, Pope RM (2006) J Proteome Res 5:2632–2641

    Article  CAS  Google Scholar 

  32. Gronborg M, Kristiansen TZ, Iwahori A, Chang R, Reddy R, Sato N, Molina H, Jensen ON, Hruban RH, Goggins MG, Maitra A, Pandey A (2006) Mol Cell Proteomics 5:157–171

    CAS  Google Scholar 

  33. Blagoev B, Mann M (2006) Methods 40:243–250

    Article  CAS  Google Scholar 

  34. Kruger M, Kratchmarova I, Blagoev B, Tseng YH, Kahn CR, Mann M (2008) Proc Natl Acad Sci USA 105:2451–2456

    Google Scholar 

  35. Amanchy R, Kalume DE, Iwahori A, Zhong J, Pandey A (2005) J Proteome Res 4:1661–1671

    Article  CAS  Google Scholar 

  36. McClain DA, Crook ED (1996) Diabetes 45:1003–1009

    Article  CAS  Google Scholar 

  37. Liu F, Iqbal K, Grundke-Iqbal I, Hart GW, Gong CX (2004) Proc Natl Acad Sci USA 101:10804–10809

    Google Scholar 

  38. Wang Z, Pandey A, Hart GW (2007) Mol Cell Proteomics 6:1365–1379

    Article  CAS  Google Scholar 

  39. Ong SE, Mann M (2006) Curr Protoc Protein Sci Dec:14.9

  40. Wisniewski JR, Zougman A, Kruger S, Ziolkowski P, Pudelko M, Bebenek M, Mann M (2008) Proteins (accepted)

  41. Bonenfant D, Towbin H, Coulot M, Schindler P, Mueller DR, van Oostrum J (2007) Mol Cell Proteomics 6:1917–1932

    Article  CAS  Google Scholar 

  42. Dobreva I, Fielding A, Foster LJ, Dedhar S (2008) J Proteome Res 7:1740–1749

    Article  CAS  Google Scholar 

  43. Wang X, Huang L (2008) Mol Cell Proteomics 7:46–57

    Google Scholar 

  44. Hanke S, Besir H, Oesterhelt D, Mann M (2008) J Proteome Res 7:1118–1130

    Article  CAS  Google Scholar 

  45. Spellman DS, Deinhardt K, Darie CC, Chao MV, Neubert TA (2008) Mol Cell Proteomics 7:1067–1076

    Article  CAS  Google Scholar 

  46. Van Hoof D, Pinkse MW, Oostwaard DW, Mummery CL, Heck AJ, Krijgsveld J (2007) Nat Methods 4:677–678

    Article  Google Scholar 

  47. Bendall SC, Hughes C, Stewart MH, Doble B, Bhatia M, Lajoie GA (2008) Mol Cell Proteomics (accepted)

  48. Schnolzer M, Jedrzejewski P, Lehmann WD (1996) Electrophoresis 17:945–953

    Article  CAS  Google Scholar 

  49. Reynolds KJ, Yao X, Fenselau C (2002) J Proteome Res 1:27–33

    Article  CAS  Google Scholar 

  50. Angel PM, Orlando R (2006) Anal Biochem 359:26–34

    Article  CAS  Google Scholar 

  51. Yao X, Afonso C, Fenselau C (2003) J Proteome Res 2:147–152

    Article  CAS  Google Scholar 

  52. Rao KC, Carruth RT, Miyagi M (2005) J Proteome Res 4:507–514

    Article  CAS  Google Scholar 

  53. Bonenfant D, Schmelzle T, Jacinto E, Crespo JL, Mini T, Hall MN, Jenoe P (2003) Proc Natl Acad Sci USA 100:880–885

    Google Scholar 

  54. Wang Y, Ding SJ, Wang W, Jacobs JM, Qian WJ, Moore RJ, Yang F, Camp DG 2nd, Smith RD, Klemke RL (2007) Proc Natl Acad Sci USA 104:8328–8333

    Google Scholar 

  55. Hess S, Chen X (2008) Methods Mol Biol 456:131–140

    Article  Google Scholar 

  56. Liu H, Zhang Y, Meng L, Qin P, Wei J, Jia W, Li X, Cai Y, Qian X (2007) Anal Chem 79:7700–7707

    Article  CAS  Google Scholar 

  57. Storms HF, van der Heijden R, Tjaden UR, van der Greef J (2006) Rapid Commun Mass Spectrom 20:3491–3497

    Article  CAS  Google Scholar 

  58. Wang YK, Ma Z, Quinn DF, Fu EW (2001) Anal Chem 73:3742–3750

    Article  CAS  Google Scholar 

  59. Schmidt A, Kellermann J, Lottspeich F (2005) Proteomics 5:4–15

    Article  CAS  Google Scholar 

  60. Li S, Zeng D (2007) Chem Commun (Camb) 2181–2183

  61. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R (1999) Nat Biotechnol 17:994–999

    Article  CAS  Google Scholar 

  62. Wang S, Zhang X, Regnier FE (2002) J Chromatogr A 949:153–162

    Article  CAS  Google Scholar 

  63. Simons BL, Wang G, Shen RF, Knepper MA (2006) Rapid Commun Mass Spectrom 20:2463–2477

    Article  CAS  Google Scholar 

  64. Zappacosta F, Huddleston MJ, Annan RS (2004) Methods Mol Biol 284:91–110

    CAS  Google Scholar 

  65. DeSouza L, Diehl G, Rodrigues MJ, Guo J, Romaschin AD, Colgan TJ, Siu KW (2005) J Proteome Res 4:377–386

    Article  CAS  Google Scholar 

  66. Jenkins LM, Mazur SJ, Rossi M, Gaidarenko O, Xu Y, Appella E (2008) Mol Cell Proteomics 7:716–727

    CAS  Google Scholar 

  67. Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L (2001) Science 292:929–934

    Article  CAS  Google Scholar 

  68. Stewart JJ, White JT, Yan X, Collins S, Drescher CW, Urban ND, Hood L, Lin B (2006) Mol Cell Proteomics 5:433–443

    CAS  Google Scholar 

  69. Liu Y, He J, Ji S, Wang Q, Pu H, Jiang T, Meng L, Yang X, Ji J (2008) Mol Cell Proteomics 7:1737–1747

  70. Thompson A, Schafer J, Kuhn K, Kienle S, Schwarz J, Schmidt G, Neumann T, Johnstone R, Mohammed AK, Hamon C (2003) Anal Chem 75:1895–1904

    Article  CAS  Google Scholar 

  71. Dayon L, Hainard A, Licker V, Turck N, Kuhn K, Hochstrasser DF, Burkhard PR, Sanchez JC (2008) Anal Chem 80:2921–2931

    Article  CAS  Google Scholar 

  72. Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin DJ (2004) Mol Cell Proteomics 3:1154–1169

    Article  CAS  Google Scholar 

  73. Ow SY, Cardona T, Taton A, Magnuson A, Lindblad P, Stensjo K, Wright PC (2008) J Proteome Res 7:1615–1628

    Article  CAS  Google Scholar 

  74. Ong SE, Mann M (2005) Nat Chem Biol 1:252–262

    Article  CAS  Google Scholar 

  75. Zhang J, Sui J, Ching CB, Chen WN (2008) Proteomics 8:1595–1607

    Article  CAS  Google Scholar 

  76. Maurya P, Meleady P, Dowling P, Clynes M (2007) Anticancer Res 27:1247–1255

    CAS  Google Scholar 

  77. Lu H, Yang Y, Allister EM, Wijesekara N, Wheeler MB (2008) Mol Cell Proteomics 7:1434–1451

    Google Scholar 

  78. Majeran W, Zybailov B, Ytterberg AJ, Dunsmore J, Sun Q, van Wijk KJ (2008) Mol Cell Proteomics (accepted)

  79. Zhou F, Galan J, Geahlen RL, Tao WA (2007) J Proteome Res 6:133–140

    Article  CAS  Google Scholar 

  80. Enoksson M, Li J, Ivancic MM, Timmer JC, Wildfang E, Eroshkin A, Salvesen GS, Tao WA (2007) J Proteome Res 6:2850–2858

    Article  CAS  Google Scholar 

  81. Zhou H, Ranish JA, Watts JD, Aebersold R (2002) Nat Biotechnol 20:512–515

    Article  CAS  Google Scholar 

  82. Oda Y, Owa T, Sato T, Boucher B, Daniels S, Yamanaka H, Shinohara Y, Yokoi A, Kuromitsu J, Nagasu T (2003) Anal Chem 75:2159–2165

    Article  CAS  Google Scholar 

  83. Qiu Y, Sousa EA, Hewick RM, Wang JH (2002) Anal Chem 74:4969–4979

    Article  CAS  Google Scholar 

  84. Shi Y, Xiang R, Crawford JK, Colangelo CM, Horvath C, Wilkins JA (2004) J Proteome Res 3:104–111

    Article  CAS  Google Scholar 

  85. Zhang H, Li XJ, Martin DB, Aebersold R (2003) Nat Biotechnol 21:660–666

    Article  CAS  Google Scholar 

  86. Zhang H, Yi EC, Li XJ, Mallick P, Kelly-Spratt KS, Masselon CD, Camp DG 2nd, Smith RD, Kemp CJ, Aebersold R (2005) Mol Cell Proteomics 4:144–155

    CAS  Google Scholar 

  87. Guo M, Galan J, Tao WA (2007) Chem Commun (Camb) 1251–1253

  88. Galan JA, Guo M, Sanchez EE, Cantu E, Rodriguez-Acosta A, Perez JC, Tao WA (2008) Mol Cell Proteomics 7:785–799

    CAS  Google Scholar 

  89. Boas U, Heegaard PM (2004) Chem Soc Rev 33:43–63

    Article  CAS  Google Scholar 

  90. Glenn JL, Straight R (1978) Toxicon 16:81–84

    Article  CAS  Google Scholar 

  91. Sanchez EE, Galan JA, Powell RL, Reyes SR, Soto JG, Russell WK, Russell DH, Perez JC (2005) Comp Biochem Physiol C Toxicol Pharmacol 141:124–132

    Article  Google Scholar 

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Authors and Affiliations

  1. Departments of Biochemistry, Chemistry, and Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, 47907, USA

    Anton Iliuk, Jacob Galan & W. Andy Tao

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  1. Anton Iliuk
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  2. Jacob Galan
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Correspondence to W. Andy Tao.

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Iliuk, A., Galan, J. & Tao, W.A. Playing tag with quantitative proteomics. Anal Bioanal Chem 393, 503–513 (2009). https://doi.org/10.1007/s00216-008-2386-0

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