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Toward a Comprehensive Characterization of a Human Cancer Cell Phosphoproteome

Zhou, Houjiang, Di Palma, Serena, Preisinger, Christian, Peng, Mao, Polat, Ayse Nur, Heck, Albert J. R., Mohammed, Shabaz·2013·Journal of Proteome Research
DOI 10.1021/pr300630k
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Abstract

Mass spectrometry (MS)-based phosphoproteomics has achieved extraordinary success in qualitative and quantitative analysis of cellular protein phosphorylation. Considering that an estimated level of phosphorylation in a cell is placed at well above 100,000 sites, there is still much room for improvement. Here, we attempt to extend the depth of phosphoproteome coverage while maintaining realistic aspirations in terms of available material, robustness, and instrument running time. We developed three strategies, where each provided a different balance between these three key parameters. The first strategy simply used enrichment by Ti(4+)-IMAC followed by reversed chromatography LC-MS (termed 1D). The second strategy incorporated an additional fractionation step through the use of HILIC (2D). Finally, a third strategy was designed employing first an SCX fractionation, followed by Ti(4+)-IMAC enrichment and additional fractionation by HILIC (3D). A preliminary evaluation was performed on the HeLa cell line. Detecting 3700 phosphopeptides in about 2 h, the 1D strategy was found to be the most sensitive but limited in comprehensivity, mainly due to issues with complexity and dynamic range. Overall, the best balance was achieved using the 2D based strategy, identifying close to 17,000 phosphopeptides with less than 1 mg of material in about 48 h. Subsequently, we confirmed the findings with the K562 cell sample. When sufficient material was available, the 3D strategy increased phosph…

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  • Phosphorylation at corresponding sites in SNX1, SNX3, SNX12, and SNX17 has been reported in various cancer types.

    “phosphorylation at corresponding sites in SNX1, SNX3, SNX12, and SNX17 has been reported in various cancer types (47, 48, 49, 50, 51, 52)”

    From Phosphorylation of SNX17 impedes activation of Retriever-mediated sorting (2025) · cites this paper as [51]

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Research works printed but not linked: 59

  1. Pawson T., 2005, Trends Biochem. Sci., 30, 286, 10.1016/j.tibs.2005.04.013 · DOI
  2. Hunter T., 2009, Curr. Opin. Cell Biol., 21, 140, 10.1016/j.ceb.2009.01.028 · DOI
  3. Brognard J., 2011, Curr. Opin. Genet. Dev., 21, 4, 10.1016/j.gde.2010.10.012 · DOI
  4. Harsha H. C., 2010, Mol. Oncol., 4, 482, 10.1016/j.molonc.2010.09.004 · DOI
  5. Huttlin E. L., 2010, Cell, 143, 1174, 10.1016/j.cell.2010.12.001 · DOI · Paper page
  6. Olsen J. V., 2006, Cell, 127, 635, 10.1016/j.cell.2006.09.026 · DOI
  7. Cox J., 2011, Annu. Rev. Biochem., 80, 273, 10.1146/annurev-biochem-061308-093216 · DOI · Paper page
  8. Olsen J. V., 2010, Sci. Signaling, 3, ra3, 10.1126/scisignal.2000475 · DOI
  9. Ballif B. A., 2008, J. Proteome Res., 7, 311, 10.1021/pr0701254 · DOI
  10. Ballif B. A., 2004, Mol. Cell. Proteomics, 3, 1093, 10.1074/mcp.M400085-MCP200 · DOI
  11. Fonslow B. R., 2012, J. Proteome Res., 11, 2697, 10.1021/pr300200x · DOI
  12. Leitner A., 2010, Anal. Chem., 82, 2726, 10.1021/ac902560z · DOI
  13. Zhou H., 2011, Mol. Cell. Proteomics, 10, M110 006452, 10.1074/mcp.M110.006452 · DOI
  14. Dephoure N., 2008, Proc. Natl. Acad. Sci. U.S.A., 105, 10762, 10.1073/pnas.0805139105 · DOI · Paper page
  15. Van Hoof D., 2009, Cell Stem Cell, 5, 214, 10.1016/j.stem.2009.05.021 · DOI
  16. Brill L. M., 2009, Cell Stem Cell, 5, 204, 10.1016/j.stem.2009.06.002 · DOI
  17. Rigbolt K. T., 2011, Sci. Signaling, 4, rs3, 10.1126/scisignal.2001570 · DOI · Paper page
  18. Phanstiel D. H., 2011, Nat. Methods, 8, 821, 10.1038/nmeth.1699 · DOI
  19. Andersson L., 1986, Anal. Biochem., 154, 250, 10.1016/0003-2697(86)90523-3 · DOI
  20. Posewitz M. C., 1999, Anal. Chem., 71, 2883, 10.1021/ac981409y · DOI
  21. Zhou H., 2006, J. Proteome Res., 5, 2431, 10.1021/pr060162f · DOI
  22. Zhou H., 2008, J. Proteome Res., 7, 3957, 10.1021/pr800223m · DOI
  23. Pinkse M. W., 2004, Anal. Chem., 76, 3935, 10.1021/ac0498617 · DOI
  24. Pinkse M. W., 2008, J. Proteome Res., 7, 687, 10.1021/pr700605z · DOI
  25. Beausoleil S. A., 2004, Proc. Natl. Acad. Sci. U.S.A., 101, 12130, 10.1073/pnas.0404720101 · DOI
  26. Gauci S., 2009, Anal. Chem., 81, 4493, 10.1021/ac9004309 · DOI
  27. Alpert A. J., 2010, Anal. Chem., 82, 5253, 10.1021/ac100651k · DOI
  28. Dai J., 2007, J. Proteome Res., 6, 250, 10.1021/pr0604155 · DOI
  29. Han G., 2008, Proteomics, 8, 1346, 10.1002/pmic.200700884 · DOI
  30. Alpert A. J., 2008, Anal. Chem., 80, 62, 10.1021/ac070997p · DOI
  31. McNulty D. E., 2008, Mol. Cell. Proteomics, 7, 971, 10.1074/mcp.M700543-MCP200 · DOI
  32. Motoyama A., 2007, Anal. Chem., 79, 3623, 10.1021/ac062292d · DOI
  33. Benschop J. J., 2007, Mol. Cell. Proteomics, 6, 1198, 10.1074/mcp.M600429-MCP200 · DOI
  34. Kettenbach A. N., 2011, Sci. Signaling, 4, rs5, 10.1126/scisignal.2001497 · DOI
  35. Koch A., 2011, Sci. Signaling, 4, rs6, 10.1126/scisignal.2001588 · DOI
  36. Kettenbach A. N., 2011, Anal. Chem., 83, 7635, 10.1021/ac201894j · DOI
  37. Lemeer S., 2009, Curr. Opin. Chem. Biol., 13, 414, 10.1016/j.cbpa.2009.06.022 · DOI
  38. Ficarro S. B., 2011, Mol. Cell. Proteomics, 10, O111 011064, 10.1074/mcp.O111.011064 · DOI
  39. Hennrich M. L., 2011, Anal. Chem., 83, 7137, 10.1021/ac2015068 · DOI
  40. Cantin G. T., 2008, J. Proteome Res., 7, 1346, 10.1021/pr0705441 · DOI
  41. Boersema P. J., 2009, J Mass Spectrom, 44, 861, 10.1002/jms.1599 · DOI
  42. Jedrychowski M. P., 2011, Mol. Cell. Proteomics, 10, M111 009910, 10.1074/mcp.M111.009910 · DOI
  43. Nagaraj N., 2010, J. Proteome Res., 9, 6786, 10.1021/pr100637q · DOI
  44. Chi A., 2007, Proc. Natl. Acad. Sci. U.S.A., 104, 2193, 10.1073/pnas.0607084104 · DOI
  45. Swaney D. L., 2009, Proc. Natl. Acad. Sci. U.S.A., 106, 995, 10.1073/pnas.0811964106 · DOI
  46. Di Palma S., 2011, Anal. Chem., 83, 3440, 10.1021/ac103312e · DOI
  47. Di Palma S., 2011, J. Proteome Res., 10, 3814, 10.1021/pr200367p · DOI
  48. Yu Z., 2009, Anal. Chim. Acta, 636, 34, 10.1016/j.aca.2009.01.033 · DOI
  49. Raijmakers R., 2008, Mol. Cell. Proteomics, 7, 1755, 10.1074/mcp.M800093-MCP200 · DOI
  50. Frese C. K., 2011, J. Proteome Res., 10, 2377, 10.1021/pr1011729 · DOI
  51. Taus T., 2011, J. Proteome Res., 10, 5354, 10.1021/pr200611n · DOI
  52. Schwartz D., 2005, Nat. Biotechnol., 23, 1391, 10.1038/nbt1146 · DOI
  53. Mohammed S., 2010, Curr. Opin. Biotechnol., 22, 9, 10.1016/j.copbio.2010.09.005 · DOI
  54. Hornbeck P. V., 2011, Nucleic Acids Res., 40, D261, 10.1093/nar/gkr1122 · DOI
  55. Diella F., 2008, Nucleic Acids Res., 36, D240, 10.1093/nar/gkm772 · DOI
  56. Dhillon A. S., 2002, Arch. Biochem. Biophys., 404, 3, 10.1016/S0003-9861(02)00244-8 · DOI
  57. Horita M., 2000, J. Exp. Med., 191, 977, 10.1084/jem.191.6.977 · DOI
  58. Faderl S., 1999, New Engl. J. Med., 341, 164, 10.1056/NEJM199907153410306 · DOI
  59. Fabbro D., 2012, Nat. Chem. Biol., 8, 228, 10.1038/nchembio.900 · DOI

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Metadata

Authors
Zhou, H., Di Palma, S., Preisinger, C., Peng, M., Polat, A. N., Heck, A. J. R., & Mohammed, S.
Affiliations
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
Venue
Journal of Proteome Research
Publisher
American Chemical Society (ACS)
Published
2012-12-18
Volume
12
Issue
1
Pages
260-271
ISSN
  • 1535-3893
  • 1535-3907
DOI
10.1021/pr300630k
Cited by
438
References
5
Language
en

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