Targeted analysis of tyrosine phosphorylation by immuno-affinity enrichment of tyrosine phosphorylated peptides prior to mass spectrometric analysis

Methods

Volumn 56, Issue 2, 2012, Pages 268-274

  Zoumaro Djayoon, Adja D ^a,b   Heck, Albert J R ^a,b   Muñoz, Javier ^a,b  

^a UTRECHT UNIVERSITY   (Netherlands)

^b NETHERLANDS PROTEOMICS CENTRE   (Netherlands)

Author keywords

Immuno affinity purification; Mass spectrometry; Phosphorylation; Tyrosine

Indexed keywords

IMMUNOGLOBULIN G; PEPTIDE ANTIBODY; PHOSPHOTYROSINE ANTIBODY; TYROSINE; UNCLASSIFIED DRUG;

ARTICLE; CONCENTRATION (PARAMETERS); CYTOLYSIS; FEMALE; HELA CELL; HUMAN; HUMAN CELL; HUMAN CELL CULTURE; IMMUNOAFFINITY CHROMATOGRAPHY; INTRACELLULAR SIGNALING; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN PHOSPHORYLATION; PROTEIN PURIFICATION;

ANTIBODY AFFINITY; CHROMATOGRAPHY, LIQUID; ENZYME ACTIVATION; HELA CELLS; HUMANS; IMMUNOASSAY; MASS SPECTROMETRY; MULTIPROTEIN COMPLEXES; PEPTIDES; PHOSPHORYLATION; PHOSPHOTYROSINE; PROTEIN-TYROSINE KINASES; PROTEOLYSIS; SENSITIVITY AND SPECIFICITY; TIME FACTORS; TYROSINE;

EID: 84858441541     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2011.09.003     Document Type: Article

References (60)

1. Eckhart W., Hutchinson M.A., Hunter T. Cell 1979, 18:925-933.
2. Hunter T. Philos. Trans. R. Soc. B-Biol. Sci. 1998, 353:583-605.
3. Manning G., Whyte D.B., Martinez R., Hunter T., Sudarsanam S. Science 2002, 298:1912-1934.
4. Alonso A., Sasin J., Bottini N., Friedberg I., Osterman A., Godzik A., Hunter T., Dixon J., Mustelin T. Cell 2004, 117:699-711.
5. Hunter T. Cell 2000, 100:113-127.
6. Beausoleil S.A., Jedrychowski M., Schwartz D., Elias J.E., Villen J., Li J., Cohn M.A., Cantley L.C., Gygi S.P. Proc. Natl Acad. Sci. USA 2004, 101:12130-12135.
7. Larsen M.R., Thingholm T.E., Jensen O.N., Roepstorff P., Jorgensen T.J. Mol. Cell. Proteomics 2005, 4:873-886.
8. Pinkse M.W., Uitto P.M., Hilhorst M.J., Ooms B., Heck A.J. Anal. Chem. 2004, 76:3935-3943.
9. Andersson L., Porath J. Anal. Biochem. 1986, 154:250-254.
10. Hunter T., Sefton B.M. Proc. Natl Acad. Sci. USA 1980, 77:1311-1315.
11. Lemeer S., Heck A.J. Curr. Opin. Chem. Biol. 2009, 13:414-420.
12. Machida K., Thompson C.M., Dierck K., Jablonowski K., Karkkainen S., Liu B., Zhang H., Nash P.D., Newman D.K., Nollau P., Pawson T., Renkema G.H., Saksela K., Schiller M.R., Shin D.G., Mayer B.J. Mol. Cell 2007, 26:899-915.
13. Blagoev B., Ong S.E., Kratchmarova I., Mann M. Nat. Biotechnol. 2004, 22:1139-1145.
14. Pandey A., Podtelejnikov A.V., Blagoev B., Bustelo X.R., Mann M., Lodish H.F. Proc. Natl Acad. Sci. USA 2000, 97:179-184.
15. Salomon A.R., Ficarro S.B., Brill L.M., Brinker A., Phung Q.T., Ericson C., Sauer K., Brock A., Horn D.M., Schultz P.G., Peters E.C. Proc. Natl Acad. Sci. USA 2003, 100:443-448.
16. Rush J., Moritz A., Lee K.A., Guo A., Goss V.L., Spek E.J., Zhang H., Zha X.M., Polakiewicz R.D., Comb M.J. Nat. Biotechnol. 2005, 23:94-101.
17. Boersema P.J., Foong L.Y., Ding V.M., Lemeer S., van Breukelen B., Philp R., Boekhorst J., Snel B., den Hertog J., Choo A.B., Heck A.J. Mol. Cell. Proteomics 2010, 9:84-99.
18. Rikova K., Guo A., Zeng Q., Possemato A., Yu J., Haack H., Nardone J., Lee K., Reeves C., Li Y., Hu Y., Tan Z., Stokes M., Sullivan L., Mitchell J., Wetzel R., Macneill J., Ren J.M., Yuan J., Bakalarski C.E., Villen J., Kornhauser J.M., Smith B., Li D., Zhou X., Gygi S.P., Gu T.L., Polakiewicz R.D., Rush J., Comb M.J. Cell 2007, 131:1190-1203.
19. Zhang Y., Wolf-Yadlin A., Ross P.L., Pappin D.J., Rush J., Lauffenburger D.A., White F.M. Mol. Cell. Proteomics 2005, 4:1240-1250.
20. Zhang G., Spellman D.S., Skolnik E.Y., Neubert T.A. J. Proteome Res. 2006, 5:581-588.
21. Iwai L.K., Benoist C., Mathis D., White F.M. Quantitative phosphoproteomic analysis of T cell receptor signaling in diabetes prone and resistant mice. J. Proteome Res. 2010, 9:3135-3145.
22. Zhang G., Neubert T.A. Proteomics 2006, 6:571-578.
23. Gobom J., Nordhoff E., Mirgorodskaya E., Ekman R., Roepstorff P. J. Mass Spectrom. 1999, 34:105-116.
24. Schwartz D., Gygi S.P. Nat. Biotechnol. 2005, 23:1391-1398.
25. Linding R., Jensen L.J., Pasculescu A., Olhovsky M., Colwill K., Bork P., Yaffe M.B., Pawson T. Nucleic Acids Res. 2008, 36:D695-699.
26. Linding R., Jensen L.J., Ostheimer G.J., van Vugt M.A., Jorgensen C., Miron I.M., Diella F., Colwill K., Taylor L., Elder K., Metalnikov P., Nguyen V., Pasculescu A., Jin J., Park J.G., Samson L.D., Woodgett J.R., Russell R.B., Bork P., Yaffe M.B., Pawson T. Cell 2007, 129:1415-1426.
27. Ding V.M., Boersema P.J., Foong L.Y., Preisinger C., Koh G., Natarajan S., Lee D.Y., Boekhorst J., Snel B., Lemeer S., Heck A.J., Choo A. PLoS ONE 2011, 6:e17538.
28. Van Hoof D., Munoz J., Braam S.R., Pinkse M.W., Linding R., Heck A.J., Mummery C.L., Krijgsveld J. Cell Stem Cell 2009, 5:214-226.
29. Daub H., Olsen J.V., Bairlein M., Gnad F., Oppermann F.S., Korner R., Greff Z., Keri G., Stemmann O., Mann M. Mol. Cell 2008, 31:438-448.
30. Jensen L.J., Kuhn M., Stark M., Chaffron S., Creevey C., Muller J., Doerks T., Julien P., Roth A., Simonovic M., Bork P., von Mering C. Nucleic Acids Res. 2009, 37:D412-D416.
31. Bergstrom Lind S., Molin M., Savitski M.M., Emilsson L., Astrom J., Hedberg L., Adams C., Nielsen M.L., Engstrom A., Elfineh L., Andersson E., Zubarev R.A., Pettersson U. J. Proteome Res. 2008, 7:2897-2910.
32. Del Rosario A.M., White F.M. Curr. Opin. Genet. Dev. 2010, 20:23-30.
33. Thompson A., Schafer J., Kuhn K., Kienle S., Schwarz J., Schmidt G., Neumann T., Johnstone R., Mohammed A.K., Hamon C. Anal. Chem. 2003, 75:1895-1904.
34. Dormeyer W., van Hoof D., Braam S.R., Heck A.J., Mummery C.L., Krijgsveld J. J. Proteome Res. 2008, 7:2936-2951.
35. Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S. Anal. Chem. 2009, 81:4493-4501.
36. Huang P.H., Miraldi E.R., Xu A.M., Kundukulam V.A., Del Rosario A.M., Flynn R.A., Cavenee W.K., Furnari F.B., White F.M. Mol. BioSyst. 2010, 6:1227-1237.
37. Good D.M., Wirtala M., McAlister G.C., Coon J.J. Mol. Cell. Proteomics 2007, 6:1942-1951.
38. Olsen J.V., Macek B., Lange O., Makarov A., Horning S., Mann M. Nat. Methods 2007, 4:709-712.
39. Frese C.K., Altelaar A.F., Hennrich M.L., Nolting D., Zeller M., Griep-Raming J., Heck A.J., Mohammed S. J. Proteome Res. 2011, 10:2377-2388.
40. Kelstrup C.D., Hekmat O., Francavilla C., Olsen J.V. J. Proteome Res. 2011.
41. Mathivanan S., Periaswamy B., Gandhi T.K., Kandasamy K., Suresh S., Mohmood R., Ramachandra Y.L., Pandey A. BMC Bioinf. 2006, 5(7 Suppl):S19.
42. Cohen P. Nature 1982, 296:613-620.
43. Tan C.S., Pasculescu A., Lim W.A., Pawson T., Bader G.D., Linding R. Science 2009, 325:1686-1688.
44. Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R., Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P. Cell 2010, 143:1174-1189.
45. Wolf-Yadlin A., Kumar N., Zhang Y., Hautaniemi S., Zaman M., Kim H.D., Grantcharova V., Lauffenburger D.A., White F.M. Mol. Syst. Biol. 2006, 2:54.
46. Hinsby A.M., Olsen J.V., Bennett K.L., Mann M. Mol. Cell. Proteomics 2003, 2:29-36.
47. Schmelzle K., Kane S., Gridley S., Lienhard G.E., White F.M. Diabetes 2006, 55:2171-2179.
48. Kim J.E., White F.M. J. Immunol. 2006, 176:2833-2843.
49. Gu T.L., Goss V.L., Reeves C., Popova L., Nardone J., Macneill J., Walters D.K., Wang Y., Rush J., Comb M.J., Druker B.J., Polakiewicz R.D. Blood 2006, 108:4202-4204.
50. Huang P.H., Mukasa A., Bonavia R., Flynn R.A., Brewer Z.E., Cavenee W.K., Furnari F.B., White F.M. Proc. Natl Acad. Sci. USA 2007, 104:12867-12872.
51. Guo A., Villen J., Kornhauser J., Lee K.A., Stokes M.P., Rikova K., Possemato A., Nardone J., Innocenti G., Wetzel R., Wang Y., MacNeill J., Mitchell J., Gygi S.P., Rush J., Polakiewicz R.D., Comb M.J. Proc. Natl Acad. Sci. USA 2008, 105:692-697.
52. Boccalatte F.E., Voena C., Riganti C., Bosia A., D'Amico L., Riera L., Cheng M., Ruggeri B., Jensen O.N., Goss V.L., Lee K., Nardone J., Rush J., Polakiewicz R.D., Comb M.J., Chiarle R., Inghirami G. Blood 2009, 113:2776-2790.
53. Zhang Y., Yoshida Y., Nameta M., Xu B., Taguchi I., Ikeda T., Fujinaka H., Mohamed S.M., Tsukaguchi H., Harita Y., Yaoita E., Yamamoto T. Nephrol. Dial. Transplant. 2010, 25:1785-1795.
54. Tong J., Taylor P., Jovceva E., St-Germain J.R., Jin L.L., Nikolic A., Gu X., Li Z.H., Trudel S., Moran M.F. J. Proteome Res. 2008, 7:1067-1077.
55. Kruger M., Kratchmarova I., Blagoev B., Tseng Y.H., Kahn C.R., Mann M. Proc. Natl Acad. Sci. USA 2008, 105:2451-2456.
56. Schulze W.X., Deng L., Mann M. Mol. Syst. Biol. 2005, 1:2005.0008.
57. Steen H., Pandey A., Andersen J.S., Mann M. Sci. STKE 2002, 2002:116.
58. Steen H., Kuster B., Fernandez M., Pandey A., Mann M. Anal. Chem. 2001, 73:1440-1448.
59. Mertins P., Eberl H.C., Renkawitz J., Olsen J.V., Tremblay M.L., Mann M., Ullrich A., Daub H. Mol. Cell. Proteomics 2008, 7:1763-1777.
60. Wisniewski J.R., Nagaraj N., Zougman A., Gnad F., Mann M. J. Proteome Res. 2010, 9:3280-3289.