Ethylenediaminetetraacetic acid increases identification rate of phosphoproteomics in real biological samples

Journal of Proteome Research

Volumn 9, Issue 3, 2010, Pages 1385-1391

  Nakamura, Tatsuji ^a,b   Myint, Khin Than ^a,b   Oda, Yoshiya ^b,c  

^a EISAI CO LTD   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c EISAI INC   (United States)

Author keywords

Alzheimer's disease; EDTA; Immobilized metal affinity column; Mass spectrometry; Phosphoproteomics; Phosphorylation; Titanium oxide

Indexed keywords

EDETIC ACID; PHOSPHOPROTEIN; TITANIUM DIOXIDE;

ALZHEIMER DISEASE; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; HUMAN; IMMOBILIZED METAL AFFINITY CHROMATOGRAPHY; LIQUID CHROMATOGRAPHY; MALE; MASS SPECTROMETRY; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PHOSPHORYLATION; PROTEOMICS;

ALZHEIMER DISEASE; ANIMALS; BRAIN CHEMISTRY; CHROMATOGRAPHY, AFFINITY; DISEASE MODELS, ANIMAL; EDETIC ACID; HUMANS; MASS SPECTROMETRY; MICE; MICE, INBRED C57BL; MICE, TRANSGENIC; PHOSPHOPROTEINS; PHOSPHORIC ACIDS; PROTEOMICS; TITANIUM;

MUS;

EID: 77949800377     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr900918h     Document Type: Article

References (35)

1. Hunter, T. Signaling-2000 and beyond. Cell 2000, 100, 113-127
2. Mann, M.; Jensen, O. N. Proteomic analysis of post-translational modifications. Nat. Biatechnal. 2003, 21, 255-261
3. Pawson, T.; Scott, J. D. Protein phosphorylation in signaling-50 years and counting. Trends Biochem. Sci. 2005, 30, 286-290
4. de Godoy, L. M.; Olsen, J. V.; Cox, J.; Nielsen, M. L.; Hubner, N. C.; Fröhlich, F.; Walther, T. C.; Mann, M. Comprehensive massspectrometry-based proteome quantification of haploid versus diploid yeast. Nature 2008, 455, 1251-1254
5. Chen, G.; Pramanik, B. N. Application of LC/MS to proteomics studies; current status and future prospects, Drug Discovery Today 2009, 14, 465-471
6. Yates, J.; Ruse, C. I.; Nakorchevsky, A. Proteomics by mass spectrometry: approaches, advances, and applications. Annu. Rev. Biomed. Eng. 2009, 11, 49-79.
7. Smith, J. C.; Figeys, D. Recent developments in mass spectrometrybased quantitative phosphoproteomics. Biochem. Cell Biol. 2008, 86, 137-148
8. Ishihama, Y.; Wei, F. Y.; Aoshima, K.; Sato, T.; Kuromitsu, J.; Oda, Y. Enhancement of the efficiency of phosphoproteomic identification by removing phosphates after phosphopeptide enrichment. I, Proteome Res. 2007, 6, 1139-1144
9. Guo, A.; Villén, J.; Kornhauser, J.; Lee, K. A.; Stokes, M. P.; Rikova, K.; Possemato, A.; Nardone, J.; Innocenti, G.; Wetzel, R.; Wang, Y.; MacNeill, J.; Mitchell, J.; Gygi, S. P.; Rush, J.; Polakiewicz, R. D.; Comb, M. J. Signaling networks assembled by oncogenic EGFR and c-Met. Proc. Natl. Acad. Sci U.S.A. 2008, 105, 692-697
10. Rikova, K.; Guo, A.; Zeng, Q.; Possemato, A.; Yu, J.; Haack, H.; Nardone, J.; Lee, K.; Reeves, C.; Li, Y.; Hu, Y.; Tan, Z.; Stokes, M.; Sullivan, L.; Mitchell, J.; Wetzel, R.; Macneill, J.; Ren, J. M.; Yuan, J.; Bakalarski, C. E.; Villen, J.; Kornhauser, J. M.; Smith, B.; Li, D.; Zhou, X.; Gygi, S. P.; Gu, T. L.; Polakiewicz, R. D.; Rush, J.; Comb, M. J. Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell 2007, 137, 1190-1203
11. Oda, Y.; Nagasu, T.; Chait, B. T. Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome. Nat. Biotechnol. 2001, 19, 379-382
12. 3+) affinity chromatography. Anal Biochem. 1986, 154, 250-254
13. Kokubu, M.; Ishihama, Y.; Sato, T.; Nagasu, T.; Oda, Y. Specificity of immobilized metal affinity-based IMAC/C18 tip enrichment of phosphopeptides for protein phosphorylation analysis. Anal. Chem. 2005, 77, 5144-5154
14. Beausoleil, S. A.; Jedrychowski, M.; Schwartz, D.; Elias, J. E.; Villén, 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, 12130-12135
15. Sano, A.; Nakamura, H. Chemo-affinity of titania for the columnswitching HPLC analysis of phosphopeptides. Anal Sci. 2004, 20, 565-566
16. Larsen, M. R.; Thingholm, T. E.; Jensen, O. N.; Roepstorff, P.; Jørgensen, T. J. Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns. Mol. Cell, Proteomics 2005, 4, 873-886
17. Kyono, Y.; Sugiyama, N.; Imami, K.; Tomifa, M.; Ishihama, Y. Successive and selective release of phosphorylated peptides captured, by hydroxy acid-modified metal oxide chromatography. J. Proteome Res. 2008, 7, 4535-4593
18. Villén, J.; Beausoleil, S. A.; Gerber, S. A.; Gygi, S. P. Large-scale phosphorylation analysis of mouse liver. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 1488-1493
19. Olsen, J. V.; Blagoev, B.; Gnad, F.; Macek, B.; Kumar, C.; Morfensen, P.; Mann, M. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2006, 127, 635-648
20. Nakamura, T.; Kuromitsu, J.; Oda, Y. Evaluation of comprehensive multidimensional separations using reversed-phase, reversedphase liquid chromatography/mass spectrometry for shotgun proteomics. J. Prteome Res. 2008, 7, 1007-1011
21. Tabata, T.; Sato, T.; Kuromitsu, J.; Oda, Y. Pseudo internal standard approach for label-free quantitative proteomics. Anal. Chem. 2007, 79, 8440-8445
22. Sugiyama, N.; Masuda, T.; Shinoda, K.; Nakamura, A.; Tomíta, M.; Ishihama, Y. Phosphopeptide enrichment by aliphatic hydroxy acid-modified metal oxide chromatography for nano-LC-MS/MS in proteomics applications. Mol. Cell. 2007, 6, 1103-1109
23. Kim, J.; Camp, D. G., 2nd; Smith, R. D. Improved detection of multl- phosphorylated peptides in the presence of phosphoric acid in liquid chromatography/mass spectrometry. J. Mass Spectrom. 2004, 39, 208-215
24. Liu, S.; Zhang, C.; Campbell, J. L.; Zhang, H.; Yeung, K. K.; Han, V. K.; Lajoie, G. A Formation of phosphopeptide-metal ion complexes in liquid chromatography/electrospray mass spectrom- etry and their influence on phosphopeptide detection. Rapid Commun Mass. Spectrom. 2005, 19, 2747-2756
25. Qing, Y.; Campuzano, L; Gilar, M. Enhanced nanoLC/MS analysis of phosphopeptides. Waters Application Note 2006, 720001458EN.
26. Winter, D.; Seidler, J.; Ziv, Y.; Shiloh, Y.; Lehmann, W. D. Citrate boosts the performance of phosphopeptide analysis by UPLC-ESIMS/MS. J. Proteome Res. 2009, 8, 418-424
27. Anderson, N. L.; Anderson, N. G. The human plasma proteome; history, character, and diagnostic prospects. Mol. Cell. Proteomics 2002, 1, 845-867
28. Ishihama, Y.; Oda, Y.; Tabata, T.; Sato, T.; Nagasu, T.; Rappsilber, J.; Mann, M. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol. Cell. Priteimics, 2005, 4, 1265-1272
29. Alberts, B.; Bray, D.; Lewis, J.; Raff, M.; Roberts, K.; Watson, J. D. Molecular Biology of the Cell, 3rd ed.; Garland Publishing: New York, 1994; pp 195-222.
30. Mann, M.; Ong, S. E.; Grenborg, M.; Steen, H.; Jensen, O. N.; Pandey, A Analysis of protein phosphorylation using mass spectrometry deciphering the phosphoproteome. Trends Biotechnol 2002, 20, 261-268
31. Donev, R.; Newall, A.; Thome, J.; Sheer, D. A role for SC35 and hnrnpal in the determination of amyloid precursor isoforms. Mol. Psychiatry 2007, 12, 681-690.
32. Hirokawa, N.; Takemura, R. Molecular motors and mechanisms of directional transport in neurons. Nat. Rev. 2005, 6, 201-214
33. Shi, Q.; Prior, M.; He, W.; Tang, X.; Hu, X.; Yan, R. Reduced amyloid deposition in mice overexpressing RTN3 is adversely affected by preformed dystrophic neurites. J. Neurocl. 2009, 29, 9163-9173
34. Neve, R. L.; Selkoe, D. J.; Kurnit, D. M.; Kosik, K. S. A cDNA for a human microtubule associated protein 2 epitope in the Alzheimer neurofibrillary tangle. Mol. Brain Res. 1986, 1, 193-196
35. DeTure, M. A.; Di Noto, L.; Purich, D. L. In vitro assembly of Alzheimer-like filaments. How a small cluster of charged residues in Tau and MAP2 controls filament morphology. J. Biol. Chem. 2002, 277, 34755-34759