A fully automated phosphopeptide purification system for large-scale phosphoproteome analysis

Journal of Biochemistry

Volumn 147, Issue 5, 2010, Pages 689-696

  Iwase, Yuka ^a   Honma, Satomi ^a   Matsuzaki, Megumi ^a   Miyakawa, Yukiko ^b   Kanno, Takuma ^b   Ishii, Kohei ^a   Furuichi, Naotaka ^b   Furukawa, Kazuhiro ^a   Horigome, Tsuneyoshi ^a,b  

^a Graduate School of Science and Technology   (Japan)

^b NIIGATA UNIVERSITY   (Japan)

Author keywords

phosphopeptide; phosphoproteome; phosphorylation; proteomics; titania

Indexed keywords

2 PROPANOL; PHOSPHOPEPTIDE; SODIUM CHLORIDE; TITANIUM; TRIFLUOROACETIC ACID; PHOSPHOPROTEIN;

ARTICLE; AUTOMATION; HUMAN; IMMOBILIZED METAL AFFINITY CHROMATOGRAPHY; INTERMETHOD COMPARISON; ION TRAP MASS SPECTROMETRY; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN PURIFICATION; PROTEOMICS; REVERSED PHASE LIQUID CHROMATOGRAPHY; ANIMAL; CHEMISTRY; CYTOSOL; DEVICES; ISOLATION AND PURIFICATION; PROCEDURES; REPRODUCIBILITY; XENOPUS;

ANIMALS; AUTOMATION; CYTOSOL; MASS SPECTROMETRY; PHOSPHOPEPTIDES; PHOSPHOPROTEINS; PROTEOMICS; REPRODUCIBILITY OF RESULTS; XENOPUS;

EID: 77953706157     PISSN: 0021924X     EISSN: 17562651     Source Type: Journal    
DOI: 10.1093/jb/mvp211     Document Type: Article

References (19)

1. Thingholm, T.E., Jensen, O.N., and Larsen, M.R. (2009) Analytical strategies for phosphoproteomics. Proteomics 9, 1451-1468
2. Hoffert, J.D., and Knepper, M.A. (2008) Taking aim at shotgun phosphoproteomics. Anal. Biochem. 375, 1-10
3. Paradela, A., and Albar, J.P. (2008) Advances in the analysis of protein phosphorylation. J. Proteome Res. 7, 1809-1818
4. 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. Biotech. 20, 301-305
5. Gruhler, A., Olsen, J.V., Mohammed, S., Mortensen, P., Faergeman, N.J., Mann, M., and Jensen, O.N. (2005) Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol. Cell. Proteomics 4, 310-327
6. Ficarro, S.B., Salomon, A.R., Brill, L.M., Mason, D.E., Stettler-Gill, M., Brock, A., and Peters, E.C. (2005) Automated immobilized metal affinity chromatography/ nano-liquid chromatography/electrospray ionization mass spectrometry platform for profiling protein phosphorylation sites. Rapid Commun. Mass Spectrom. 19, 57-71
7. Cantin, G.T., Shock, T.R., Park, S.K., Madhani, H.D., and Yates, J.R. (2007) Optimizing TiO2-based phosphopeptide enrichment for automated multidimensional liquid chromatography coupled to tandem mass spectrometry. Anal. Chem. 79, 4666-4673
8. Larsen, M.R., Thingholm, T.E., Jensen, O.N., Roepstorff, P., and Jorgensen, T.J.D. (2005) Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns. Mol. Cell. Proteomics 4, 873-886
9. Sugiyama, N., Masuda, T., Shinoda, K., Nakamura, A., Tomita, M., and Ishihama, Y. (2007) Phosphopeptide enrichment by aliphatic hydroxy acid-modified metal oxide chromatography for nanoLC-MS/MS in proteomics applications. Mol. Cell. Proteomics 6, 1103-1109
10. Kokubo, M., Ishihama, Y., Sato, T., Nagasu, T., and Oda, Y. (2005) Specificity of immobilized metal affinity-based IMAC/C18 tip enrichment of phosphopeptides for protein phosphorylation analysis. Anal. Chem. 77, 5144-5154
11. Takano, M., Takeuchi, M., Ito, H., Furukawa, K., and Horigome, T. (2002) The binding of lamin B receptor to chromatin is regulated by phosphorylation in the RS region. Eur. J. Biochem. 269, 943-953
12. Zhou, W., Merrick, B.A., Khaledi, M.G., and Tomer, K.B. (2000) Detection and sequencing of phosphopeptides affinity bound to immobilized metal ion beads by matrix-assisted laser desorption/ionization mass spectrometry. Am. Soc. Mass Spectrom. 11, 273-282
13. Kuyama, H., Toda, C., Watanabe, M., Tanaka, K., and Nishimura, O. (2003) An efficient chemical method for dephosphorylation of phosphopeptides. Rapid Commun. Mass Spectrom. 17, 1493-1496
14. Imanishi, S.Y., Kochin, V., Ferraris, S.E., de Thonel, A., Pallari, H.M., Corthals, G.L., and Eriksson, J.E. (2007) Reference-facilitated phosphoproteomics. Mol. Cell. Proteomics 6, 1380-1391
15. Pinkse, M.W.H., Uitto, P.M., Hilhorst, M.J., Ooms, B., and Heck, A.J.R. (2004) Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-nanoLC-ESI-MS/MS and titanium oxide precolumns. Anal. Chem. 76, 3935-3943
16. Imami, K., Sugiyama, N., Kyono, Y., Tomita, M., and Ishihama, Y. (2008) Automated phosphoproteome analysis for cultured cancer cells by two-dimensional nanoLC-MS using a calcined titania/C18 biphasic column. Anal. Sci. 24, 161-166
17. Pinkse, M.W.H., Mohammed, S., Gouw, J.W., van Breukelen, B., Vos, H.R., and Heck, A.J.R. (2008) Highly robust, automated, and sensitive online TiO2- based phosphoproteomics applied to study endogenous phosphorylation in Drosophila melanogaster. J. Proteome Res. 7, 687-697
18. Mohammed, S., Kraiczek, K., Pinkse, M.W.H., Lemeer, S., Benschop, J.J., and Heck, A.J.R. (2008) Chip-based enrichment and nanoLC-MS/MS analysis of phosphopeptides from whole lysates. J. Proteome Res. 7, 1565-1571
19. Dephoure, N., Zhou, C., Villén, J., Beausoleil, S.A., Bakalarski, C.E., Elledge, S.J., and Gygi, S.P. (2008) A quantitative atlas of mitotic phosphorylation. Proc. Natl Acad. Sci. USA 105, 10762-10767