A comparative study of electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) versus SCX-IMAC-based methods for phosphopeptide isolation/enrichment

Journal of Proteome Research

Volumn 7, Issue 11, 2008, Pages 4869-4877

  Gan, Chee Sian ^a   Guo, Tiannan ^a,b   Zhang, Huoming ^a   Lim, Sal Kiang ^c   Sze, Siu Kwan ^a  

^a NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^b DIVISION OF MEDICAL ONCOLOGY   (Singapore)

^c INSTITUTE OF MEDICAL BIOLOGY   (Singapore)

Author keywords

A431 carcinoma cells; EGFR signaling; ERLIC; IMAC; Phosphopeptide enrichment; SCX; WAX

Indexed keywords

EPIDERMAL GROWTH FACTOR; EPIDERMAL GROWTH FACTOR RECEPTOR; PHOSPHOPEPTIDE;

ARTICLE; CANCER CELL CULTURE; CHROMATOGRAPHY; CONTROLLED STUDY; ELECTROSTATIC REPULSION HYDROPHILIC INTERACTION CHROMATOGRAPHY; HUMAN; HUMAN CELL; IMMOBILIZED METAL AFFINITY CHROMATOGRAPHY; INTERMETHOD COMPARISON; ION EXCHANGE CHROMATOGRAPHY; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN MOTIF; AFFINITY CHROMATOGRAPHY; BIOLOGICAL MODEL; CARCINOMA; CHEMISTRY; COMPARATIVE STUDY; ENZYME SPECIFICITY; EVALUATION; INSTRUMENTATION; ION EXCHANGE; ISOLATION AND PURIFICATION; METABOLISM; METHODOLOGY; PATHOLOGY; STATIC ELECTRICITY; TUMOR CELL LINE;

CARCINOMA; CELL LINE, TUMOR; CHROMATOGRAPHY; CHROMATOGRAPHY, AFFINITY; EPIDERMAL GROWTH FACTOR; HUMANS; ION EXCHANGE; MODELS, BIOLOGICAL; PHOSPHOPEPTIDES; STATIC ELECTRICITY; SUBSTRATE SPECIFICITY;

EID: 58149387660     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr800473j     Document Type: Article

References (34)

1. Hubbard, M. J.; Cohen, P. On target with a new mechanism for the regulation of protein phosphorylation. Trends Biochem. Sci. 1993, 18 (5), 172-7.
2. Linding, R.; Jensen, L. J.; Pasculescu, A.; Olhovsky, M.; Colwill, K.; Bork, P.; Yaffe, M. B.; Pawson, T. NetworKIN: a resource for exploring cellular phosphorylation networks. Nucleic Acids Res. 2008, 36 (Database issue), D695-9.
3. Amanchy, R.; Periaswamy, B.; Mathivanan, S.; Reddy, R.; Tattlkota, S. G.; Pandey, A. A curated compendium of phosphorylation motifs. Nat. Biotechnol. 2007, 25 (3), 285-6.
4. Gnad, F.; Ren, S.; Cox, J.; Olsen, J. V.; Macek, B.; Oroshi, M.; Mann, M. PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. Genome Biol. 2007, 8 (11), R250.
5. Smith, J. C.; Figeys, D. Recent developments in mass spectrometry-based quantitative phosphoproteomics. Biochem. Cell. Biol. 2008, 86 (2), 137-48.
6. Yarden, Y.; Shilo, B. Z. Snapshot: EGFR signaling pathway. Cell 2007, 131 (5), 1018.
7. Olsen, J. V.; Blagoev, B.; Gnad, F.; Macek, B.; Kumar, C.; Mortensen, P.; Mann, M. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2006, 127 (3), 635-48.
8. Johns, T. G.; Perera, R. M.; Vernes, S. C.; Vitali, A. A.; Cao, D. X.; Cavenee, W. K.; Scott, A. M.; Furnari, F. B. The efficacy of epidermal growth factor receptor-specific antibodies against glioma xenografts is influenced by receptor levels, activation status, and heterodimerization. Clin. Cancer Res. 2007, 13 (6), 1911-25.
9. Tao, W. A.; Wollscheid, B.; O'Brien, R.; Eng, J. K.; Li, X. J.; Bodenmiller, B.; Watts, J. D.; Hood, L.; Aebersold, R. Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry. Nat. Methods 2005, 2 (8), 591-8.
10. 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. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Nat. Biotechnol. 2005, 23 (1), 94-101.
11. Ficarro, S. B.; McCleland, M. L.; Stukenberg, P. T.; Burke, D. J.; Ross, M. M.; Shabanowitz, J.; Hunt, D. F.; White, F. M. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat. Biotechnol. 2002, 20 (3), 301-5.
12. Beausoleil, S. A.; Jedrychowski, M.; Schwartz, D.; Elias, J. E.; Villen, J.; Li, J.; Cohn, M. A.; Cantley, L. C.; Gygi, S. P. Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc. Natl. Acad. Sci. U.S.A 2004, 101 (33), 12130-5.
13. 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 (7), 873-86.
14. Villen, J.; Beausoleil, S. A.; Gerber, S. A.; Gygi, S. P. Large-scale phosphorylation analysis of mouse liver. Proc. Natl. Acad. Sci. U.SA. 2007, 104 (5), 1488-93.
15. Bodenmiller, B.; Mueller, L. N.; Mueller, M.; Domon, B.; Aebersold, R. Reproducible isolation of distinct, overlapping segments of the phosphoproteome. Nat. Methods 2007, 4 (3), 231-7.
16. Gruhler, A.; Olsen, J. V.; Mohammed, S.; Mortensen, P.; Faergeman, N. J.; Mann, M.; Jensen, O. N. Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol. Cell. Proteomics 2005, 4 (3), 310-27.
17. Zhang, Y.; Wolf-Yadlin, A.; Ross, P. L.; Pappin, D. J.; Rush, J.; Lauffenburger, D. A.; White, F. M. Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules. Mol. Cell. Proteomics 2005, 4 (9), 1240-50.
18. Alpert, A. J. Electrostatic repulsion hydrophilic interaction chromatography for isocratic separation of charged solutes and selective isolation of phosphopeptides. Anal. Chem. 2008, 80 (1), 62-76.
19. Sze, S. K.; de Heijn, D. P.; Lai, R. C.; Khia Way Tan, E.; Zhao, H.; Yeo, K. S.; Low, T. Y.; Lian, Q.; Lee, C. N.; Mitchell, W.; El Oakley, R. M.; Lim, S. K. Elucidating the secretion proteome of human embryonic stem cell-derived mesenchymal stem cells. Mol. Cell. Proteomics 2007, 6 (10), 1680-9.
20. Kersey, P. J.; Duarte, J.; Williams, A.; Karavidopoulou, Y.; Birney, E.; Apweiler, R. The International Protein Index: an integrated database for proteomics experiments. Proteomics 2004, 4 (7), 1985-8.
21. 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 (3), 207-14.
22. Schwartz, D.; Gygi, S. P. An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets. Nat. Biotechnol. 2005, 23 (11), 1391-8.
23. Mi, H.; Lazareva-Ulitsky, B.; Loo, R.; Kejariwal, A.; Vandergriff, J.; Rabkin, S.; Guo, N.; Muruganujan, A.; Doremieux, O.; Campbell, M. J.; Kitano, H.; Thomas, P. D. The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Res. 2005, 33 (Database issue), D284-8.
24. Shannon, P.; Markiel, A.; Ozier, O.; Baliga, N. S.; Wang, J. T.; Ramage, D.; Amin, N.; Schwikowski, B.; Ideker, T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13 (11), 2498-504.
25. Ulintz, P. J.; Bodenmiller, B.; rews, P. C.; Aebersold, R.; Nesvizhskii, A. I. Investigating MS2/MS3 matching statistics: a model for coupling consecutive stage mass spectrometry data for increased peptide identification confidence. Mol. Cell. Proteomics 2008, 7 (1), 71-87.
26. 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 (10), 1285-92.
27. Wilson-Grady, J. T.; Villen, J.; Gygi, S. P. Phosphoproteome analysis of fission yeast. J. Proteome Res. 2008, 7 (3), 1088-97.
28. Smith, J. C.; Duchesne, M. A.; Tozzi, P.; Ethier, M.; Figeys, D. A differential phosphoproteomic analysis of retinoic acid-treated P19 cells. J. Proteome Res. 2007, 6 (8), 3174-86.
29. Alpert, A.; Mitulović, G.; Mechtler, K. Isolation of Tryptic Phosphopeptides by ERLIC (Electrostatic Repulsion-Hydrophilic Interaction Chromatography) ABRF Conference, 2008, poster P31-S.
30. Zhang, X.; Ye, J.; Jensen, O. N.; Roepstorff, P. Highly efficient phosphopeptide enrichment by calcium phosphate precipitation combined with subsequent IMAC enrichment. Mol. Cell. Proteomics 2007, 6 (11), 2032-42.
31. Hunter, T.; Sefton, B. M. Transforming gene product of Rous sarcoma virus phosphorylates tyrosine. Proc. Natl. Acad. Sci. U.SA. 1980, 77 (3), 1311-5.
32. Li, X.; Gerber, S. A.; Rudner, A. D.; Beausoleil, S. A.; Haas, W.; Villen, J.; Elias, J. E.; Gygi, S. P. Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae. J. Proteome Res. 2007, 6 (3), 1190-7.
33. Sato, T.; Fujita, N.; Yamada, A.; Ooshio, T.; Okamoto, R.; Irie, K.; Takai, Y. Regulation of the assembly and adhesion activity of E-cadherin by nectin and afadin for the formation of adherens junctions in Madin-Darby canine kidney cells. J. Biol Chem. 2006, 281 (8), 5288-99.
34. Hunt, D. F.; Yates, J. R., 3rd; Shabanowitz, J.; Winston, S.; Hauer, C. R. Protein sequencing by tandem mass spectrometry. Proc. Natl. Acad. Sci. U.SA. 1986, 83 (17), 6233-7.