Evaluation of shotgun sequencing for proteomic analysis of human plasma using HPLC coupled with either ion trap or Fourier transform mass spectrometry

Journal of Proteome Research

Volumn 2, Issue 4, 2003, Pages 383-393

  Wu, Shiaw Lin ^a   Choudhary, Gargi ^a   Ramström, Margareta ^b   Bergquist, Jonas ^b,c   Hancock, William S ^d  

^a Thermo Finnigan   (United States)

^b UPPSALA UNIVERSITY   (Sweden)

^c SAHLGRENSKA UNIVERSITY HOSPITAL   (Sweden)

^d NORTHEASTERN UNIVERSITY   (United States)

Author keywords

2D LC; Differential quantitation; FTMS; Human growth hormone; Human plasma proteins; ICAT; Ion Trap; LC MS; Multidimensional seperation; Proteomics

Indexed keywords

BLOOD CLOTTING FACTOR; CARRIER PROTEIN; ENZYME; ENZYME INHIBITOR; GLYCOPROTEIN; HUMAN GROWTH HORMONE; IMMUNOGLOBULIN; ION; ISOTOPE; MEMBRANE PROTEIN; PLASMA PROTEIN; RECEPTOR;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; DISULFIDE BOND; FOURIER ANALYSIS; FRAGMENTATION REACTION; GEL ELECTROPHORESIS; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; LABORATORY; MASS; PRIORITY JOURNAL; PROTEOMICS; QUANTITATIVE ANALYSIS; SAMPLING; SCIENTIFIC LITERATURE;

ALGORITHMS; AUTOMATIC DATA PROCESSING; BLOOD PROTEINS; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; FOURIER ANALYSIS; GAS CHROMATOGRAPHY-MASS SPECTROMETRY; HUMAN GROWTH HORMONE; HUMANS; ISOTOPE LABELING; MASS SPECTROMETRY; PEPTIDE FRAGMENTS; PROTEOMICS; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION;

EID: 0041733300     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr034015i     Document Type: Article

References (37)

1. Anderson, N. L.; Anderson, N. G. Proc. Nat. Acad. Sci. 1977, 74, 5421-25.
2. Malmstrom, L.; Malmstrom, J.; Marko-Varga, G.; Westergren-Thorsson, G. J. Proteome Res. 2002, 2, 135-38.
3. Gygi, S. P.; Rist, B.; Gerber, S. A.; Turecek, F.; Gelb, M. H.; Aebersold, R.; Nature Biotechnology 1999, 17, 994-999.
4. Scopes, R. K. Protein Purification: Principles and Practice, 3rd ed.; Springer-Verlag: New York, New York, 1994.
5. Apffel, A.; Chakel, J, A.; Hancock, W. S.; Souders, C.; M'Timkulu, T.; Pungor, E. J. Chromatogr. 1996, 734, 35-42.
6. Wu, S.-L.; Amato, H.; Biringer, R.; Choudhary, G.; Shieh, P.; Hancock, W. S. J. Proteome Res, 2002, 1, 459-465.
7. Battersby, J. E.; Mukku, V. R.; Clark, R. G.; Hancock, W. S. Analytical Chemistry 1995, 67, 447-455.
8. Haynes, P. A.; Yates, J. R., III. Yeast 2000, 17, 81-87.
9. Gygi, S. P.; Rist, B.; Griffin, T. J.; Eng, J.; Aebersold, R. J. Proteome Res. 2002, 2, 47-54.
10. Delinsky, D. C.; Gries, K. D. J. Proteome Res. 2002, 3, 279-84.
11. Adkins, J. N.; Varnum, S. M.; Auberry, K. J.; Moore, R. J.; Angell, N. H.; Smith, R. D.; Springer, D. L.; Pounds, J. G. Mol. Cell Proteomics 2002.
12. Smith, R. D. Int. J. Mass Spectrometry 2000, 200, 509-44.
13. Wetterhall, M.; Palmblad, M.; Hakansson, P.; Markides, K. E.; Bergquist, J. J. Proteome Res. 2002, 4, 361-367.
14. Ramström, M.; Palmblad, M.; Markides, K. E.; Håkansson, P.; Bergquist, J. Proteomics, in press.
15. Palmblad, M.; Håkansson, K.; Håkansson, P.; Feng, X.; et al. Eur. J. Mass Spectrom. 2000, 6, 267-275
16. Nilsson, S.; Wetterhall, M.; Bergquist, J.; Nyholm, L.; Markides, K. E. Rapid. Commun. Mass Spectrom. 2001, 15, 1997-2000
17. Eng, J. K.; McCormack, A. L.; Yates, J. R., III. J. Am. Mass. Spectrom. 1994, 5, 976-989.
18. Ducret, A.; Van Oostveen, I.; Eng, J. K.; Yates, J. R., III.; Aebersold, R. Protein Science 1998, 7, 706-719.
19. Tabb, D. L.; McDonald, W. H.; Yates, J. R. J. Proteome Res. 2002, 1, 21-26.
20. Sadygov, R. G.; Eng, J.; Durr, E.; Saraf, A.; McDonald, H.; MacCoss, M. J.; Yates, J. R., III. J. Proteome Res. 2002, 3, 211-16.
21. ThermoFinnigan Product Bulletin, B-1033, Feb 2002, "Xcalibur BioWorks 3.0".
22. Hancock, W. S.; Choudhary, G.; Wu, S.-L.; Shieh, P. American Laboratory 2000, 32, 20-22.
23. Gygi, S. P.; Corthals, G. L.; Zhang, Y.; Rochon, Y.; Aebersold, R. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 9390-9395.
24. Anderson, N. L.; Anderson, N. G. MoL CellProteomics 2002, 1, 845-867.
25. Swiss Institute of Bioinformatics, see http://us.expasy.org/ch2d.
26. Anderson, N. L.; Anderson, N. G. Electrophoresis 1991, 12, 883-906.
27. Hancock, W. S.; Apffel, A. J.; Chakel, J. A.; Hahnenberger, K.; Choudhary, G.; Traina, J.; Pungor, E. Anal. Chem. 1999, 742A-748A.
28. Udiavar, S.; Apffel, A.; Chakel, J.; Swedberg, S.; Hancock, W. S.; Pungor, E. Anal. Chem. 1998, 70, 3572-3578.
29. Sell, S. Clin. Lab. Medicine 1990, 10, 27-31.
30. Martell, R. E.; Xu, F, J.; Davis, W. Z.; Anselmino, L.; Yu, Y. H.; Daly, L.; Bast, R. C. Int. J. Biol. Markers 1998, 13, 145-9.
31. Gygi, S. P.; Rist, B.; Griffith, T. J.; Eng, J.; Aebersold, R. J. Proteome Res. 2002, 1, 47-54.
32. Reynolds, K. J.; Yao, X.; Feneslau, C. J. Proteome Res. 2002, 1, 27-34.
33. Zhang, R.; Regnier, F. J. Proteome Res. 2002, 2, 139-148.
34. Chelius, D.; Bondarenko, P. J. Proteome Res. 2002, 4, 317-24.
35. Jiang, H.; English, A. M. J. Proteome Res. 2002, 4, 345-50.
36. Liu, P.; Regnier, F. J. Proteome Res. 2002, 5, 443-50.
37. Bergquist, J.; Palmblad, M.; Wetterhall, M.; Håkansson, P.; Markides, K. Mass Spectrom. Rev. 2002, 21, 2-15.