Evaluation of comprehensive multidimensional separations using reversed-phase, reversed-phase liquid chromatography/mass spectrometry for shotgun proteomics

Journal of Proteome Research

Volumn 7, Issue 3, 2008, Pages 1007-1011

  Nakamura, Tatsuji ^a   Kuromitsu, Junro ^a   Oda, Yoshiya ^a  

^a EISAI CO LTD   (Japan)

Author keywords

LC MS; Peptide identification; Polymeric column; Shotgun proteomics

Indexed keywords

ACETONITRILE; POLYMER; SILANE DERIVATIVE; SILICON DIOXIDE;

ACIDIFICATION; ALKALINITY; ARTICLE; CATION EXCHANGE; COLUMN CHROMATOGRAPHY; COMPLEX FORMATION; MASS SPECTROMETRY; MEASUREMENT; NANOTECHNOLOGY; PH; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; REVERSED PHASE LIQUID CHROMATOGRAPHY; SEPARATION TECHNIQUE; TWO DIMENSIONAL GEL ELECTROPHORESIS; ANIMAL; BRAIN; C57BL MOUSE; EVALUATION; LIQUID CHROMATOGRAPHY; METABOLISM; METHODOLOGY; MOUSE; ULTRAVIOLET SPECTROPHOTOMETRY;

ANIMALS; BRAIN; CHROMATOGRAPHY, LIQUID; HYDROGEN-ION CONCENTRATION; MASS SPECTROMETRY; MICE; MICE, INBRED C57BL; NANOTECHNOLOGY; PROTEOMICS; SPECTROPHOTOMETRY, ULTRAVIOLET;

EID: 44449172641     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr7005878     Document Type: Article

References (21)

1. Peng, J.; Gygi, S. P. Proteomics: the move to mixtures. J Mass Spectrom. 2001, 36, 1083-1091.
2. Wu, C. C.; Yates, J. R., III. The application of mass spectrometry to membrane proteomics. Nat. Biotechnol. 2003, 21, 262-267.
3. Qian, W. J.; Jacobs, J. M.; Liu, T.; Camp, D. G., II; Smith, R. D. Advances and challenges in liquid chromatography-mass spec-trometry-based proteomics profiling for clinical applications. Mol. Cell. Proteomics 2006, 5, 1727-1744.
4. Giddings, J. C. Two-dimensional separations: concept and promise. Anal. Chem. 1984, 56, 1258A-1264A.
5. Wu, C. C.; MacCoss, M. J. Shotgun proteomics: tools for the analysis of complex biological systems. Curr. Opin. Mol. Ther. 2002, 4, 242-250.
6. Wang, H.; Hanash, S. Multi-dimensional liquid phase based separations in proteomics. J Chromatogr., B: Anal. Technol. Biomed. Life Sci. 2003, 787, 11-18.
7. Frahm, J. L.; Howard, B. E.; Heber, S.; Muddiman, D. C. Accessible proteomics space and its implications for peak capacity for zero-,one- and two-dimensional separations coupled with FT-ICR and TOF mass spectrometry. J. Mass Spectrom. 2006, 41, 281-288.
8. Wong, V.; Shalliker, R. A. Isolation of the active constituents in natural materials by 'heart-cutting' isocratic reversed-phase two-dimensional liquid chromatography. J. Chromatogr., A 2004, 1036, 15-24.
9. Dobrev, P. I.; Havlicek, L.; Vagner, M.; Malbeck, J.; Kaminek, M. Purification and determination of plant hormones auxin and abscisic acid using solid phase extraction and two-dimensional high performance liquid chromatography. J. Chromatogr., A 2005, 1075, 159-166.
10. Patton, W. F. A thousand points of light: the application of fluorescence detection technologies to two-dimensional gel electrophoresis and proteomics. Electrophoresis 2000, 21, 1123-1144.
11. Wittmann-Liebold, B.; Graack, H. R.; Pohl, T. Two-dimensional gel electrophoresis as tool for proteomics studies in combination with protein identification by mass spectrometry. Proteomics 2006, 6, 4688-4703.
12. Link, A. J.; Eng, J.; Schieltz, D. M.; Carmack, E.; Mize, G. J.; Morris, D. R.; Garvik, B. M.; Yates, J. R., III. Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol. 1999, 17, 676-682.
13. Washburn, M. P.; Wolters, D.; Yates, J. R., III. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 2001, 19, 242-247.
14. Sasagawa, T.; Ericsson, L. H.; Teller, D. C; Titani, K.; Walsh, K. A. Separation of peptides on a polystyrene resin column. J. Chromatogr. 1984, 307, 29-38.
15. Mohammad, J.; Jaderlund, B.; Lindblom, H. New polymer-based prepacked column for the reversed-phase liquid chromatographic separation of peptides over the pH range 2-12. J. Chromatogr., A 1999, 852, 255-259.
16. Linde, S; Welinder, B. S. Silica versus polymer-based stationary phases for reversed-phase high-performance liquid chromatographic analyses of rat insulin biosynthesis. A comparison of resolution and recovery. J. Chromatogr. 1991, 548, 195-206.
17. McCalley, D. V. Comparison of an organic polymeric column and a silica-based reversed-phase for the analysis of basic peptides by high-performance liquid chromatography. J. Chromatogr., A 2005,1073, 137-145.
18. Gilar, M.; Olivova, P.; Daly, A. E.; Gebler, J. C. Orthogonality of separation in two-dimensional liquid chromatography. Anal. Chem. 2005, 77, 6426-6434.
19. Ruiz, R; Ruiz-Angel, M. J.; Garcia-Alvarez-Coque, M. C; Rafols, C; Roses, M; Bosch, E. Hydrophobic and cation exchange mechanisms in the retention of basic compounds in a polymeric column. J. Chromatogr., A 2004, 1028, 139-148.
20. Oda, Y.; Huang, K.; Cross, F. R.; Cowburn, D.; Chait, B. T. Accurate quantitation of protein expression and site-specific phosphorylation. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 6591-6596.
21. Ishihama, Y.; Sato, T.; Tabata, T.; Miyamoto, N.; Sagane, K.; Nagasu, T.; Oda, Y. Quantitative mouse brain proteomics using culture-derived isotope tags as internal standards. Nat. Biotechnol. 2005, 23, 617-621.