Hydrophilic interaction chromatography reduces the complexity of the phosphoproteome and improves global phosphopeptide isolation and detection

Molecular and Cellular Proteomics

Volumn 7, Issue 5, 2008, Pages 971-980

  McNulty, Dean E ^a   Annan, Roland S ^a  

^a GLAXOSMITHKLINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PHOSPHOPEPTIDE; PROTEOME;

ARTICLE; CATION EXCHANGE; CELL LYSATE; CONTROLLED STUDY; DERIVATIZATION; ENANTIOSELECTIVITY; HELA CELL; HUMAN; HUMAN CELL; HYDROPHILIC INTERACTION CHROMATOGRAPHY; HYDROPHILICITY; LIQUID CHROMATOGRAPHY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ISOLATION; PROTEIN PHOSPHORYLATION; PROTEOMICS; REVERSED PHASE LIQUID CHROMATOGRAPHY; CHEMISTRY; ISOLATION AND PURIFICATION; METHODOLOGY;

CHROMATOGRAPHY, LIQUID; HELA CELLS; HUMANS; PHOSPHOPEPTIDES; PROTEOME; PROTEOMICS;

EID: 43849091451     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M700543-MCP200     Document Type: Article

References (34)

1. de Godoy, L. M., Olsen, J. V., de Souza, G. A., Li, G., Mortensen, P., and Mann, M. (2006) Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system. Genome Biol. 6, R50
2. Horth, P., Miller, C. A., Preckel, T., and Wenz, C. (2006) Efficient fractionation and improved protein identification by peptide OFFGEL electrophoresis. Mol. Cell. Proteomics 5, 1968-1974
3. Giorgianni, F., Desiderio, D. M., and Beranova-Giorgianni, S. (2003) Proteome analysis using isoelectric focusing in immobilized pH gradient gels followed by mass spectrometry. Electrophoresis 24, 253-259
4. Washburn, M. P., Wolters, D., and Yates, J. R., III (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242-247
5. Lecchi, P., Gupte, A. R., Perez, R. E., Stockert, L. V., and Abramson, F. P. (2006) Size-exclusion chromatography in multidimensional separation schemes for proteome analysis. J. Biochem. Biophys. Methods 56, 141-152
6. Blagoev, B., Kratchmarova, I., Ong, S. E., Nielsen, M., Foster, L. J., and Mann, M. (2003) A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat. Biotechnol. 21, 315-318
7. Beausoleil, S. A., Jedrychowski, M., Schwartz, D., Elias, J. E., Villen, J., Li, J., Cohn, M. A., Cantley, L C., and Gygi, S. P. (2004) Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc. Natl. Acad. Sci. U. S. A. 101, 12130-12135
8. Beausoleil, S. A., Villen, J., Gerber, S. A., Rush, J., and Gygi, S. P. (2006) A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat. Biotechnol. 24, 1285-1292
9. Olsen, J. V., Blagoev, B., Gnad, F., Macek, B., Kumar, C., Mortensen, P., and Mann, M. (2006) Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127, 635-648
10. Nuwaysir, L. M., and Stults, J. T. (1993) Electrospray ionization mass spectrometry of phosphopeptides isolated by on-line immobilized metalion affinity chromatography. J. Am. Soc. Mass Spectrom. 4, 662-667
11. Posewitz, M. C., and Tempst, P. (1999) Immobilized gallium(III) affinity chromatography of phosphopeptides. Anal. Chem. 71, 2883-2892
12. Pinkse, M. W., Uitto, P. M., Hilhorst, M. J., Ooms, B., and Heck, A. J. (2006) Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide pre-columns. Anal. Chem. 76, 3935-3943
13. Larsen, M. R., Thingholm, T. E., Jansen, O. N., Roepstorff, P., and Jorgensen, T. J. (2005) Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns. Mol. Cell. Proteomics 4, 873-886
14. Ficarro, S. B., McCleland, M. L., Stukenberg, P. T., Burke, D. J., Ross, M. M., Shabanowitz, J., Hunt, D. F., and White, F. M. (2002) Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat Biotechnol. 20, 301-305
15. Kim, J. E., Tannenbaum, S. R., and White, F. M. (2005) Global phosphoproteome of HT-29 human colon adenocarcinoma cells. J. Proteome Res. 4, 1339-1346
16. Yang, F., Stenoien, D. L., Strittmatter, E. F., Wang, J., Ding, L, Lipton, M. S., Monroe, M. E., Nicora, C. D., Gristenko, M. A., Tang, K., Fang, R., Adkins, J. N., Camp, D. G., II, Chen, D. J., and Smith, R. D. (2006) Phosphoproteome profiling of human skin fibroblast cells in response to low and high-dose irradiation. J. Proteome Res. 5, 1252-1260
17. Alpert, A. J. (1990) Hydrophilic-interaction chromatography for the separation of peptides, nucleic acids and other polar compounds. J. Chromatogr. 499, 177-196
18. Yoshida, T., and Okada, T. (1999) Peptide separation in normal-phase liquid chromatography: study of selectivity and mobile phase effects on various columns. J. Chromatogr. A 840, 1-9
19. Gilar, M., Olivova, P., Daly, A. E., and Gebler, J. C. (201)5) Orthogonality of separation in two-dimensional liquid chromatography. Anal. Chem. 77, 6426-6434
20. Muszynska, G., Dobrowolska, G., Medin, A., Ekman, P., and Porath, J. O. (1992) Interaction of immobilized iron(III) ions with phosphorylated amino acids, peptides and proteins. J. Chromatogr. 804, 19-28
21. Yoshida, T. (1998) Calculation of peptide retention coefficients in normal-phase liquid chromatography. J. Chromatogr. A 808, 105-112
22. Kokubu, M., Ishihama, Y., Sato, T., Nagasu, T., and Oda, Y. (2006) Specificity of immobilized metal affinity-based IMAC/C18 tip enrichment of phosphopeptides for protein phosphorylation analysis. Anal. Chem. 77, 5144-5154
23. Ndassa, Y. M., Orsi, C., Marto, J. A., Chen, S., and Ross, M. M. (2006) Improved immobilized metal affinity chromatography for large-scale phosphoproteomics applications. J. Proteome Res. 5, 2789-2799
24. Nuhse, T. S., Stensballe, A., Jensen, O. N., and Peck, S. C. (2006) Large-scale analysis of in vivo phosphorylated membrane proteins by immobilized metal ion affinity chromatography and mass spectrometry. Mol. Cell. Proteomics 2,1234-1243
25. Villen, J., Beausoleil, S. A., and Gerber, S. A. (2006) Large-scale phosphorylation analysis of mouse liver. Proc. Natl. Acad. Sci. U. S. A. 104, 1488-1493
26. Thingholm, T. E., Jensen, O. N., Robinson, P. J., and Larsen, M. R. (November 26, 2007) SIMAC, a phosphoproteomics strategy for the rapid separation of monophosphorylated from multiply phosphorylated peptides. Mol. Cell. Proteomics 10.1074/mcp.M700362-MCP200
27. Syka, J. E., Coon, J. J., Schroeder, M. J., Shabanowitz, J., and Hunt, D. F. (2004) Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 101, 9528-9533
28. Bodenmiller, B., Mueller, L. N., Mueller, M., Domon, B., and Aebersold, R. (2006) Reproducible isolation of distinct, overlapping segments of the phosphoproteome. Nat. Methods 4, 231-237
29. Karlsson, G., Winge, S., and Sandberg, H. (2005) Separation of monosaccharides by hydrophilic interaction chromatography with evaporative light scattering detection. J. Chromatogr. A 1092, 246-249
30. Takegawa, Y., Deguchi, K., Ito, H., Keira, T., Nakagawa, H., and Nishimura, S. (2006) Simple separation of isomeric sialylated N-glycopeptides by a zwitterionic type of hydrophilic interaction chromatography. J. Sep. Sci. 29, 2533-2540
31. Garcia, B. A., Pesavento, J. J., Mizzen, C. A., and Kelleher, N. L. (2007) Pervasive combinatorial modification of histone H3 in human cells. Nat. Methods 4, 487-489
32. Boersema, P. J., Divecha, N., Heck, A. J., and Mohammed, S. (2007) Evaluation and optimization of ZIC-HILIC-RP as an alternative MudPIT strategy. J. Proteome Res. 6, 937-946
33. 2-based phosphoproteomics applied to study endogenous phosphorylation in Drosophila melanogaster. J. Proteome Sci. 7, 687-697
34. Chi, A., Huttenhower, C., Geer, L. Y., Coon, J. J., Syka, J. E., Bai, D. L., Shabanowitz, J., Burke, D. J., Troyanskaya, O. G., and Hunt, D. F. (2007) Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc. Natl. Acad. Sci. U. S. A 104, 2193-2198