Evaluating preparative isoelectric focusing of complex peptide mixtures for tandem mass spectrometry-based proteomics: A case study in profiling chromatin-enriched subcellular fractions in Saccharomyces cerevisiae

Analytical Chemistry

Volumn 77, Issue 10, 2005, Pages 3198-3207

  Xie, Hongwei ^a   Bandhakavi, Sricharan ^a   Griffin, Timothy J ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ELECTROSPRAYING; FREE-FLOW ELECTROPHORESIS; PEPTIDE MIXTURES; SEQUENCE MATCHING;

DATABASE SYSTEMS; ELECTROPHORESIS; FRACTIONATION; MASS SPECTROMETRY; MIXTURES; PROBABILITY;

POLYPEPTIDES;

PEPTIDE;

AMINO ACID SEQUENCE; ARTICLE; CAPILLARY CHROMATOGRAPHY; CASE STUDY; CELL FRACTIONATION; CHROMATIN; DATA BASE; DNA FINGERPRINTING; ELECTROPHORESIS; ISOELECTRIC FOCUSING; LIQUID CHROMATOGRAPHY; ONLINE ANALYSIS; PROBABILITY; PROTEOMICS; SACCHAROMYCES CEREVISIAE; SCORING SYSTEM; TANDEM MASS SPECTROMETRY;

AMINO ACID SEQUENCE; CHROMATIN; DATABASES, PROTEIN; ELECTROPHORESIS; HYDROGEN-ION CONCENTRATION; ISOELECTRIC FOCUSING; ISOELECTRIC POINT; PEPTIDES; PROTEINS; PROTEOMICS; SACCHAROMYCES CEREVISIAE; SUBCELLULAR FRACTIONS; TANDEM MASS SPECTROMETRY;

EID: 18844404358     PISSN: 00032700     EISSN: None     Source Type: Journal    
DOI: 10.1021/ac0482256     Document Type: Article

References (24)

1. Link, A. J.; Eng, J.; Schieltz, D. M.; Carmack, E.; Mize, G. J.; Morris, D. R.; Garvik, B. M.; Yates, J. R., III. Nat. Biotechnol. 1999, 17, 676-682.
2. Washburn, M. P.; Wolters, D.; Yates, J. R., III. Nat. Biotechnol. 2001, 19, 242-247.
3. Peng, J.; Elias, J. E.; Thoreen, C. C.; Licklider, L. J.; Gygi, S. P. J. Proteome Res. 2003, 2, 43-50.
4. Gygi, S. P.; Corthals, G. L.; Zhang, Y.; Rochon, Y.; Aebersold, R. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 9390-9395.
5. Cargile, B. J.; Talley, D. L.; Stephenson, J. L., Jr. Electrophoresis 2004, 25, 936-945.
6. Cargile, B. J.; Bundy, J. L.; Freeman, T. W.; Stephenson, J. L., Jr. J. Proteome Res. 2004, 3, 112-119.
7. Cargile, B. J.; Bundy, J. L.; Stephenson, J. L., Jr. J. Proteome Res. 2004, 3, 1082-1085.
8. Loseva, O. I.; Gavryushkin, A. V.; Osipov, V. V.; Vanyakin, E. N. Electrophoresis 1998, 19, 1127-1134.
9. Moritz, R. L.; Ji, H.; Schutz, F.; Connolly, L. M.; Kapp, E. A.; Speed, T. P.; Simpson, R. J. Anal. Chem 2004, 76, 4811-4824.
10. Keller, A.; Nesvizhskii, A. I.; Kolker, E.; Aebersold, R. Anal. Chem 2002, 74, 5383-5392.
11. Donovan, S.; Harwood, J.; Drury, L. S.; Diffley, J. F. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 5611-5616.
12. Liang, C.; Stillman, B. Genes Dev. 1997, 11, 3375-3386.
13. Yi, E. C.; Lee, H.; Aebersold, R.; Goodlett, D. R. Rapid Commun. Mass Spectrom. 2003, 17, 2093-2098.
14. Eng, J.; McCormack, A. L.; Yates, J. R., III. J. Am. Soc. Mass Spectrom. 1994, 5, 976-989.
15. Han, D. K.; Eng, J.; Zhou, H.; Aebersold, R. Nat. Biotechnol. 2001, 19, 946-951.
16. Bjellqvist, B.; Hughes, G. J.; Pasquali, C.; Paquet, N.; Ravier, F.; Sanchez, J. C.; Frutiger, S.; Hochstrasser, D. Electrophoresis 1993, 14, 1023-1031.
17. Shimura, K.; Kamiya, K.; Matsumoto, H.; Kasai, K. Anal. Chem 2002, 74, 1046-1053.
18. Christie, K. R.; Weng, S.; Balakrishnan, R.; Costanzo, M. C.; Dolinski, K.; Dwight, S. S.; Engel, S. R.; Feierbach, B.; Fisk, D. G.; Hirschman, J. E.; Hong, E. L.; Issel-Tarver, L.; Nash, R.; Sethuraman, A.; Starr, B.; Theesfeld, C. L.; Andrada, R.; Binkley, G.; Dong, Q.; Lane, C.; Schroeder, M.; Botstein, D.; Cherry, J. M. Nucleic Acids Res. 2004, 32 (Database issue), D311-314.
19. Huh, W. K.; Falvo, J. V.; Gerke, L. C.; Carroll, A. S.; Howson, R. W.; Weissman, J. S.; O'Shea, E. K. Nature 2003, 425, 686-691.
20. Kumar, A.; Agarwal, S.; Heyman, J. A.; Matson, S.; Heidtman, M.; Piccirillo, S.; Umansky, L.; Drawid, A.; Jansen, R.; Liu, Y.; Cheung, K. H.; Miller, P.; Gerstein, M.; Roeder, G. S.; Snyder, M. Genes Dev. 2002, 16, 707-719.
21. Shiio, Y.; Eisenman, R. N.; Ti, E. C.; Donohoe, S.; Goodlett, D. R.; Aebersold, R. J. Am. Soc. Mass Spectrom. 2003, 14, 696-703.
22. Strittmatter, E. F.; Kangas, L. J.; Petritis, K.; Mottaz, H. M.; Anderson, G. A.; Shen, Y.; Jacobs, J. M.; Camp, D. G., II; Smith, R. D. J. Proteome Res. 2004, 3, 760-769.
23. Cargile, B. J.; Stephenson, J. L., Jr. Anal. Chem 2004, 76, 267-275.
24. Resing, K. A.; Meyer-Arendt, K.; Mendoza, A. M.; Aveline-Wolf, L. D.; Jonscher, K. R.; Pierce, K. G.; Old, W. M.; Cheung, H. T.; Russell, S.; Wattawa, J. L.; Goehle, G. R.; Knight, R. D.; Ahn, N. G. Anal. Chem 2004, 76, 3556-3568.