Protein profiling of sickle cell versus control rbc core membrane skeletons by icat technology and tandem mass spectrometry

Cellular and Molecular Biology Letters

Volumn 11, Issue 3, 2006, Pages 326-337

  Chou, Jose ^a,b,c   Choudhary, Pankaj K ^a,b,c   Goodman, Steven R ^a,b,c,d  

^a Department of Molecular and Cell Biology ^*  (United States)

^b Institute of Biomedical Sciences and Technology   (United States)

^c UNIVERSITY OF TEXAS AT DALLAS   (United States)

^d UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

Cleavable ICAT; Ion trap mass spectrometry; Proteomics; RBC membrane skeleton; Sickle cell

Indexed keywords

ACTIN; ERYTHROCYTE BAND 4.1 PROTEIN; FODRIN; MEMBRANE PROTEIN; SPECTRIN;

ANALYSIS OF VARIANCE; ARTICLE; CELL MEMBRANE; CONTROLLED STUDY; ERYTHROCYTE; ERYTHROCYTE MEMBRANE; HUMAN; HUMAN CELL; PROTEIN ANALYSIS; SICKLE CELL; TANDEM MASS SPECTROMETRY;

EID: 33749367026     PISSN: 14258153     EISSN: 16891392     Source Type: Journal    
DOI: 10.2478/s11658-006-0026-2     Document Type: Article

References (24)

1. Kakhniashvili, D.G., Bulla, L.A. Jr and Goodman, S.R. The human erythrocyte proteome: analysis by ion trap mass spectrometry. Mol. Cell. Proteomics 3 (2004) 501-509.
2. Aebersold, R. and Mann, M. Mass spectrometry-based proteomics. Nature 422 (2003) 198-207.
3. Shao-En, O., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Hanno Steen, Pandey, A. and Mann M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1 (2002) 376-386.
4. Patterson, S.D. and Aebersold, R.H. Proteomics: the first decade and beyond. Nat. Genet. 33 (2003) 311-323.
5. Yi, E.C., Li, X.J., Cooke, K., Lee, H., Raught, B., Page, A., Aneliunas, V., Hieter, P., Goodlett, D.R., and Aebersold R. Increased quantitative proteome coverage with (13)C/(12)C-based, acid-cleavable isotope-coded affinity tag reagent and modified data acquisition scheme. Proteomics 5 (2005) 380-387.
6. Li, J., Steen, H. and Gygi, S.P. Protein profiling with cleavable isotope-coded affinity tag (cICAT) reagents the yeast salinity stress response. Mol. Cell. Proteomics 2 (2003) 1198-1204.
7. Molloy, M.P., Donohoe, S., Brzezinski, E.E., Kilby, G.W., Stevenson, T.I., Baker, J.D., Goodlett, R.D. and Gage, D.A. Large-scale evaluation of quantitative reproducibility and proteome coverage using acid cleavable isotope coded affinity tag mass spectrometry for proteomic profiling. Proteomics 5 (2005) 1204-1208.
8. Eng, J.K., McCormack, A. L., and Yates, J. R. 3rd. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5 (1994) 976-998.
9. Keller, A., Nesvihzkii, A., Li, X., Pedroli, P., Eng, J., Hubbley, R., Mallick, P., Zhang, N., Shannon, P., Deutsch, E., Watts, J. and Aebersold R. Computatinonal tools for high throughput proteomics. ISB Symposium, 2003.
10. Keller, A., Nesvizhskii, A.I., Kolker E. and Aebersold R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74 (2002) 5383-5392.
11. Li, X.J., Zhang, H., Ranish, J.A. and Aebersold R. Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry. Anal. Chem. 75 (2003) 6648-6657.
12. Nesvizhskii A.I, Keller A., Kolker E. and Aebersold R. A Statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75 (2003) 4646-4658.
13. Searle, S.R., Casella, G. and McCulloch Variance Components, John Wiley, New York, 1992, 168-231.
14. Pinheiro, J.C. and Bates, D. M. Mixed-Effects Models in S and S-PLUS, Springer Verlag, New York, 2000, 57-96.
15. Lehman, E.L. Elements of Large Sample Theory, Springer Verlag, New York, 1998, 277-362.
16. Gygi, S.P., Rist, B., Gerber, S.A., Turecek, F., Gelb, M. and Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17 (1999) 994-999.
17. Zhang, R., Sioma, C.S., Wang, S. and Regnier, F.E. Fractionation of. isotopically labeled peptides in quantitative proteomics. Anal. Chem. 73 (2001) 5142-5149.
18. Oda, Y., Owa, T., Sato, T. and Boucher, B. Quantitative chemical proteomics for identifying candidate drug targets. Anal. Chem. 75 (2003) 2159-2165.
19. 13C-isotope-coded affinity tag and multidimensional chromatography. Mol. Cell Proteomics 2 (2003) 299-314.
20. Gygi, S.P., Corthals, G.L., Zhang, Y., Rochon, Y. and Aebersold, R. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc. Natl. Acad. Sci. USA 97 (2000) 9390-9395.
21. Wilkins, M.R., Gasteiger, E., Sanchez, J.C., Bairoch, A. and Hochstrasser, D.F. Electrophoresis 19 (1998)1501-1505.
22. Santoni, V., Molloy, M. and Rabilloud, T. Membrane proteins and proteomics: Un amour impossible? Electrophoresis 21 (2000) 1054-1070.
23. Molloy, M.P., Phadke, N.D., Chen, H., Tyldesley, R. Garfin D.E., Maddock, J.R. and Andrews P.C. Profiling the alkaline membrane proteome of Caulobacter crescentus with two-dimensional electrophoresis and mass spectrometry. Proteomics 2 (2002) 899-910.
24. Kakhniashvili, D.G., Griko, N.B., Bulla, L.A. Jr and Goodman, S.R. The proteomics of sickle cell disease: profiling of erythrocyte membrane proteins by 2D-DIGE and tandem mass spectrometry. Exp. Biol. Med. 230 (2005) 787-792.