Refined phosphopeptide enrichment by phosphate additive and the analysis of human brain phosphoproteome

Proteomics

Volumn 15, Issue 2-3, 2015, Pages 500-507

  Tan, Haiyan ^a   Wu, Zhiping ^a   Wang, Hong ^a,b   Bai, Bing ^a   Li, Yuxin ^a   Wang, Xusheng ^a   Zhai, Bo ^a   Beach, Thomas G ^c   Peng, Junmin ^a  

^a ST JUDE CHILDREN S RESEARCH HOSPITAL   (United States)

^b UNIVERSITY OF TENNESSEE HEALTH SCIENCE CENTER   (United States)

^c SUN HEALTH RESEARCH INSTITUTE   (United States)

Author keywords

Alzheimer's disease; Human brain; LC MS MS; Phosphopeptide enrichment; Phosphorylation; Technology

Indexed keywords

PHOSPHATE; PHOSPHOPEPTIDE; TITANIUM DIOXIDE; PROTEOME; TITANIUM;

ALZHEIMER DISEASE; ARTICLE; COGNITION; GENETIC SUSCEPTIBILITY; HUMAN; IMMUNODETECTION; ION CURRENT; PRIORITY JOURNAL; PROTEIN PHOSPHORYLATION; PROTEOMICS; QUANTITATIVE ANALYSIS; AMINO ACID SEQUENCE; BRAIN; BRAIN CHEMISTRY; CHEMISTRY; ISOLATION AND PURIFICATION; LIQUID CHROMATOGRAPHY; METABOLISM; MOLECULAR GENETICS; PHOSPHORYLATION; PROCEDURES; TANDEM MASS SPECTROMETRY;

ALZHEIMER DISEASE; AMINO ACID SEQUENCE; BRAIN; BRAIN CHEMISTRY; CHROMATOGRAPHY, LIQUID; HUMANS; MOLECULAR SEQUENCE DATA; PHOSPHATES; PHOSPHOPEPTIDES; PHOSPHORYLATION; PROTEOME; PROTEOMICS; TANDEM MASS SPECTROMETRY; TITANIUM;

EID: 84921277367     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201400171     Document Type: Article

References (44)

1. Alzheimer's Association. 2012 Alzheimer's disease facts and figures. Alzheimers Dement. 2012, 8, 131-168.
2. Hardy, J., Selkoe, D. J., The amyloid hypothesis of Alzheimer's disease: progress and problems on the road to therapeutics. Science 2002, 297, 353-356.
3. Ballatore, C., Lee, V. M., Trojanowski, J. Q., Tau-mediated neurodegeneration in Alzheimer's disease and related disorders. Nat. Rev. Neurosci. 2007, 8, 663-672.
4. Kosik, K. S., Joachim, C. L., Selkoe, D. J., Microtubule-associated protein tau (tau) is a major antigenic component of paired helical filaments in Alzheimer disease. Proc. Natl. Acad. Sci. USA 1986, 83, 4044-4048.
5. Sternberger, N. H., Sternberger, L. A., Ulrich, J., Aberrant neurofilament phosphorylation in Alzheimer disease. Proc. Natl. Acad. Sci. USA 1985, 82, 4274-4276.
6. Ulloa, L., Montejo de Garcini, E., Gomez-Ramos, P., Moran, M. A., Avila, J., Microtubule-associated protein MAP1B showing a fetal phosphorylation pattern is present in sites of neurofibrillary degeneration in brains of Alzheimer's disease patients. Brain Res. Mol. Brain Res. 1994, 26, 113-122.
7. Dolan, P. J., Johnson, G. V., The role of tau kinases in Alzheimer's disease. Curr. Opin. Drug Discov. Dev. 2010, 13, 595-603.
8. Wang, J. Z., Xia, Y. Y., Grundke-Iqbal, I., Iqbal, K., Abnormal hyperphosphorylation of tau: sites, regulation, and molecular mechanism of neurofibrillary degeneration. J. Alzheimers Dis. 2013, 33, S123-S139.
9. Macek, B., Mann, M., Olsen, J. V., Global and site-specific quantitative phosphoproteomics: principles and applications. Annu. Rev. Pharm. Toxicol. 2009, 49, 199-221.
10. Ficarro, S. B., McCleland, M. L., Stukenberg, P. T., Burke, D. J. et al., Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat. Biotechnol. 2002, 20, 301-305.
11. Nuhse, T. S., Stensballe, A., Jensen, O. N., Peck, S. C., Large-scale analysis of in vivo phosphorylated membrane proteins by immobilized metal ion affinity chromatography and mass spectrometry. Mol. Cell Proteomics 2003, 2, 1234-1243.
12. Larsen, M. R., Thingholm, T. E., Jensen, O. N., Roepstorff, P., Jorgensen, T. J., Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns. Mol. Cell Proteomics 2005, 4, 873-886.
13. Olsen, J. V., Blagoev, B., Gnad, F., Macek, B. et al., Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2006, 127, 635-648.
14. Iliuk, A., Martinez, J. S., Hall, M. C., Tao, W. A., Phosphorylation assay based on multifunctionalized soluble nanopolymer. Anal. Chem. 2011, 83, 2767-2774.
15. Ballif, B. A., Villen, J., Beausoleil, S. A., Schwartz, D., Gygi, S. P., Phosphoproteomic analysis of the developing mouse brain. Mol. Cell Proteomics 2004, 3, 1093-1101.
16. Beausoleil, S. A., Jedrychowski, M., Schwartz, D., Elias, J. E. et al., Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc. Natl. Acad. Sci. USA 2004, 101, 12130-12135.
17. Motoyama, A., Xu, T., Ruse, C. I., Wohlschlegel, J. A., Yates, J. R., 3rd, Anion and cation mixed-bed ion exchange for enhanced multidimensional separations of peptides and phosphopeptides. Anal. Chem. 2007, 79, 3623-3634.
18. Steen, H., Kuster, B., Fernandez, M., Pandey, A., Mann, M., Tyrosine phosphorylation mapping of the epidermal growth factor receptor signaling pathway. J. Biol. Chem. 2002, 277, 1031-1039.
19. Pandey, A., Podtelejnikov, A. V., Blagoev, B., Bustelo, X. R. et al., Analysis of receptor signaling pathways by mass spectrometry: identification of vav-2 as a substrate of the epidermal and platelet-derived growth factor receptors. Proc. Natl. Acad. Sci. USA 2000, 97, 179-184.
20. Rush, J., Moritz, A., Lee, K. A., Guo, A. et al., Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Nat. Biotechnol. 2005, 23, 94-101.
21. Zhou, H., Watts, J. D., Aebersold, R., A systematic approach to the analysis of protein phosphorylation. Nat. Biotechnol. 2001, 19, 375-378.
22. McLachlin, D. T., Chait, B. T., Analysis of phosphorylated proteins and peptides by mass spectrometry. Curr. Opin. Chem. Biol. 2001, 5, 591-602.
23. Villen, J., Beausoleil, S. A., Gerber, S. A., Gygi, S. P., Large-scale phosphorylation analysis of mouse liver. Proc. Natl. Acad. Sci. USA 2007, 104, 1488-1493.
24. Nagaraj, N., Kulak, N. A., Cox, J., Neuhauser, N. et al., 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 2012, 11, M111 013722.
25. Kettenbach, A. N., Gerber, S. A., Rapid and reproducible single-stage phosphopeptide enrichment of complex peptide mixtures: application to general and phosphotyrosine-specific phosphoproteomics experiments. Anal. Chem. 2011, 83, 7635-7644.
26. Hyman, B. T., Trojanowski, J. Q., Consensus recommendations for the postmortem diagnosis of Alzheimer disease from the National Institute on Aging and the Reagan Institute Working Group on diagnostic criteria for the neuropathological assessment of Alzheimer disease. J. Neuropathol. Exp. Neurol. 1997, 56, 1095-1097.
27. Xu, P., Duong, D. M., Peng, J., Systematical optimization of reverse-phase chromatography for shotgun proteomics. J. Proteome Res. 2009, 8, 3944-3950.
28. Peng, J., Elias, J. E., Thoreen, C. C., Licklider, L. J., Gygi, S. P., Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J. Proteome Res. 2003, 2, 43-50.
29. Elias, J. E., Gygi, S. P., Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 2007, 4, 207-214.
30. Jedrychowski, M. P., Huttlin, E. L., Haas, W., Sowa, M. E. et al., Evaluation of HCD- and CID-type fragmentation within their respective detection platforms for murine phosphoproteomics. Mol. Cell Proteomics 2011, 10, M111.009910.
31. Beausoleil, S. A., Villen, J., Gerber, S. A., Rush, J., Gygi, S. P., A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat. Biotechnol. 2006, 24, 1285-1292.
32. Vizcaino, J. A., Deutsch, E. W., Wang, R., Csordas, A. et al., ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat. Biotechnol. 2014, 32, 223-226.
33. Liao, L., Cheng, D., Wang, J., Duong, D. M. et al., Proteomic characterization of postmortem amyloid plaques isolated by laser capture microdissection. J. Biol. Chem. 2004, 279, 37061-37068.
34. Gozal, Y. M., Duong, D. M., Gearing, M., Cheng, D. et al., Proteomics analysis reveals novel components in the detergent-insoluble subproteome in Alzheimer's disease. J. Proteome Res. 2009, 8, 5069-5079.
35. Thomas, S. N., Cripps, D., Yang, A. J., Proteomic analysis of protein phosphorylation and ubiquitination in Alzheimer's disease. Methods Mol. Biol. 2009, 566, 109-121.
36. Bai, B., Hales, C. M., Chen, P. C., Gozal, Y. et al., U1 small nuclear ribonucleoprotein complex and RNA splicing alterations in Alzheimer's disease. Proc. Natl. Acad. Sci. USA 2013, 110, 16562-16567.
37. Andreev, V. P., Petyuk, V. A., Brewer, H. M., Karpievitch, Y. V. et al., Label-free quantitative LC-MS proteomics of Alzheimer's disease and normally aged human brains. J. Proteome Res. 2012, 11, 3053-3067.
38. Begcevic, I., Kosanam, H., Martinez-Morillo, E., Dimitromanolakis, A. et al., Semiquantitative proteomic analysis of human hippocampal tissues from Alzheimer's disease and age-matched control brains. Clin. Proteomics 2013, 10, 5.
39. Zahid, S., Oellerich, M., Asif, A. R., Ahmed, N., Phosphoproteome profiling of substantia nigra and cortex regions of Alzheimer's disease patients. J. Neurochem. 2012, 121, 954-963.
40. Xia, Q., Cheng, D., Duong, D. M., Gearing, M. et al., Phosphoproteomic analysis of human brain by calcium phosphate precipitation and mass spectrometry. J. Proteome Res. 2008, 7, 2845-2851.
41. 2 beads ratio on phosphopeptide enrichment selectivity. J. Proteome Res. 2009, 8, 5375-5381.
42. Guerreiro, R., Bras, J., Hardy, J., SnapShot: genetics of Alzheimer's disease. Cell 2013, 155, 968, e961.
43. Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B. et al., Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell Proteomics 2004, 3, 1154-1169.
44. Thompson, A., Schafer, J., Kuhn, K., Kienle, S. et al., Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chem. 2003, 75, 1895-1904.