Systematic comparison of a two-dimensional ion trap and a three-dimensional ion trap mass spectrometer in proteomics

Molecular and Cellular Proteomics

Volumn 4, Issue 2, 2005, Pages 214-223

  Mayya, Viveka ^a   Rezaul, Karim ^a   Cong, Yu Sheng ^a   Han, David ^a  

^a UNIVERSITY OF CONNECTICUT HEALTH CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; HUMAN; HUMAN CELL; INTERMETHOD COMPARISON; ION TRAP MASS SPECTROMETRY; LEUKEMIA CELL LINE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEOMICS; QUALITY CONTROL; SCORING SYSTEM; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; TANDEM MASS SPECTROMETRY;

COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; HUMANS; IONS; JURKAT CELLS; MASS SPECTROMETRY; PEPTIDES; PROTEINS; PROTEOME; PROTEOMICS; SOFTWARE; TIME FACTORS;

EID: 14944346000     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.T400015-MCP200     Document Type: Article

References (27)

1. Aebersold, R., and Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198-207
2. Yates, J. R., III (2004) Mass spectral analysis in proteomics. Annu. Rev. Biophys. Biomol. Struct. 33, 297-316
3. Dongre, A.R., Eng, J. K., and Yates, J. R., III (1997) Emerging tandem-mass spectrometry techniques for the rapid identification of proteins. Trends Biotechnol. 15, 418-425
4. Jonscher, K. R., and Yates, J. R., III (1997) The quadrupole ion trap mass spectrometer - a small solution to a big challenge. Anal. Biochem. 244, 1-15
5. Aebersold, R., and Goodlett, D. R. (2001) Mass spectrometry in proteomics. Chem. Rev. 101, 269-295
6. Sadygov, R. G., Eng, J., Durr, E., Saraf, A., McDonald, H., MacCoss, M. J., and Yates, J. R., III (2002) Code developments to improve the efficiency of automated MS/MS spectra interpretation. J. Proteome Res. 1, 211-215
7. Eng, J. K., McCormack, A. L., and Yates, J. R., III (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am. Soc. Mass Spectrom. 5, 976-989
8. Washburn, M. P., Wolters, D., and Yates, J. R., III (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol. 19, 242-247
9. Peng, J., and Gygi, S. P. (2001) Proteomics: the move to mixtures. J. Mass Spectrom. 36, 1083-1091
10. Schwartz, J. C., Senko, M. W., and Syka, J. E. (2002) A two-dimensional quadrupole ion trap mass spectrometer. J. Am. Soc. Mass Spectrom. 13, 659-669
11. Shevchenko, A., Wilm, M., Vorm, O., and Mann, M. (1996) Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal. Chem. 68, 850-858
12. Gatlin, C. L., Kleemann, G. R., Hays, L. G., Link, A. J., and Yates, J. R., III (1998) Protein identification at the low femtomole level from silver-stained gels using a new fritless electrospray interface for liquid chromatography-microspray and nanospray mass spectrometry. Anal. Biochem. 263, 93-101
13. Han, D. K., Eng, J., Zhou, H., and Aebersold, R. (2001) Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat. Biotechnol. 19, 946-951
14. Peng, J., Elias, J. E., Thoreen, C. C., Licklider, L. J., and Gygi, S. P. (2003) Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC MS/MS) for large-scale protein analysis: the yeast proteome. J. Proteome Res. 2, 43-50
15. Elias, J. E., Gibbons, F. D., King, O. D., Roth, F. P., and Gygi, S. P. (2004) Intensity-based protein identification by machine learning from a library of tandem mass spectra. Nat. Biotechnol. 22, 214-219
16. Spahr, C. S., Davis, M. T., McGinley, M. D., Robinson, J. H., Bures, E. J., Beierle, J., Mort, J., Courchesne, P. L., Chen, K., Wahl, R. C., Yu, W., Luethy, R., and Patterson, S. D. (2001) Towards defining the urinary proteome using liquid chromatography-tandem mass spectrometry. I. Profiling an unfractionated tryptic digest. Proteomics 1, 93-107
17. Yi, E. C., Marelli, M., Lee, H., Purvine, S. O., Aebersold, R., Aitchison, J. D., and Goodlett, D. R. (2002) Approaching complete peroxisome characterization by gas-phase fractionation. Electrophoresis 23, 3205-3216
18. Goodlett, D. R., Bruce, J. E., Anderson, G. A., Rist, B., Pasa-Tolic, L., Fiehn, O., Smith, R. D., and Aebersold, R. (2000) Protein identification with a single accurate mass of a cysteine-containing peptide and constrained database searching. Anal. Chem. 72, 1112-1118
19. Patterson, S. D. (2004) How much of the proteome do we see with discovery-based proteomics methods and how much do we need to see? Curr. Proteomics 1, 3-12
20. Florens, L., Washburn, M. P., Raine, J. D., Anthony, R. M., Grainger, M., Haynes, J. D., Moch, J. K., Muster, N., Sacci, J. B., Tabb, D. L., Witney, A. A., Wolters, D., Wu, Y., Gardner, M. J., Holder, A. A., Sinden, R. E., Yates, J. R., and Carucci, D. J. (2002) A proteomic view of the Plasmodium falciparum life cycle. Nature 419, 520-526
21. Link, A. J., Eng, J., Schieltz, D. M., Carmack, E., Mize, G. J., Morris, D. R., Garvik, B. M., and Yates, J. R., III (1999) Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol. 17, 676-682
22. Syka, J. E., Marto, J. A., Bai, D. L., Horning, S., Senko, M. W., Schwartz, J. C., Ueberheide, B., Garcia, B., Busby, S., Muratore, T., Shabanowitz, J., and Hunt, D. F. (2004) Novel linear quadrupole ion trap/FT mass spectrometer: performance characterization and use in the comparative analysis of histone H3 post-translational modifications. J. Proteome Res. 3, 621-626
23. Olsen, J. V., Ong, S. E., and Mann, M. (2004) Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Mol. Cell. Proteomics 3, 608-614
24. Le Blanc, J. C., Hager, J. W., Ilisiu, A. M., Hunter, C., Zhong, F., and Chu, I. (2003) Unique scanning capabilities of a new hybrid linear ion trap mass spectrometer (Q TRAP) used for high sensitivity proteomics applications. Proteomics 3, 859-869
25. Beausoleil, S. A., Jedrychowski, M., Schwartz, D., Elias, J. E., Villen, J., Li, J., Cohn, M. A., Cantley, L. C., and Gygi, S. P. (2004) Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc. Natl. Acad. Sci. U. S. A. 101, 12130-12135
26. Olsen, J. V., and Mann, M. (2004) Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation. Proc. Natl. Acad. Sci. U. S. A. 101, 13417-13422
27. Syka, J. E., Coon, J. J., Schroeder, M. J., Shabanowitz, J., and Hunt, D. F. (2004) Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 101, 9528-9533