Direct analysis of protein complexes using mass spectrometry

Nature Biotechnology

Volumn 17, Issue 7, 1999, Pages 676-682

  Link, Andrew J ^a,b   Eng, Jimmy ^a   Schieltz, David M ^a   Carmack, Edwin ^a   Mize, Gregory J ^c   Morris, David R ^c   Garvik, Barbara M ^d   Yates III, John R ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b Millennium Predictive Medicine Inc   (United States)

^c UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^d Fred Hutchinson Cancer Research Center   (United States)

Author keywords

Mass spectrometry; Multidimensional chromatography; Protein identification; Ribosome; Yeast genome

Indexed keywords

PROTEIN;

ANALYTIC METHOD; ARTICLE; COMPLEX FORMATION; GENE SEQUENCE; LIQUID CHROMATOGRAPHY; MACROMOLECULE; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; RIBOSOME SUBUNIT; SACCHAROMYCES CEREVISIAE; YEAST;

ALGORITHMS; AMINO ACID SEQUENCE; CHROMATOGRAPHY, LIQUID; HUMANS; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; RIBOSOMAL PROTEINS; RIBOSOMES; SACCHAROMYCES CEREVISIAE; SENSITIVITY AND SPECIFICITY;

SACCHAROMYCES CEREVISIAE;

EID: 0033051101     PISSN: 10870156     EISSN: None     Source Type: Journal    
DOI: 10.1038/10890     Document Type: Article

References (32)

1. Pugh, B.F. Mechanisms of transcription complex assembly. Curr. Opin. Cell Biol. 8, 303-311 (1996).
2. Wool, I.G., Chan, Y.-L. & Gluck, A. Structure and evolution of mammalian ribosomal proteins. Biochem. Cell Biol. 73, 933-947 (1995).
3. Mager, W.H. et al. A new nomenclature for the cytoplasmic ribosomal proteins of Saccharomyces cerevisiae. Nucleic. Acids Res. 25, 4872-4875 (1997).
4. Phizicky, E.M. & Fields, S. Protein-protein interactions: methods for detection and analysis. Microbiol. Rev. 59, 94-123 (1995).
5. Neubauer, G. et al. Identification of the proteins of the yeast U1 small nuclear ribonucleoprotein complex by mass spectrometry. Proc. Natl. Acad. Sci. USA 94, 385-390 (1997).
6. Eng, J.K., McCormack, A.L. & Yates, J.R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Amer. Soc. Mass Spectrom., 5, 976-989 (1994).
7. Link, A.J., Carmack, E. & Yates, J.R. A strategy for the identification of proteins localized to subcellular spaces: applications to E. coli periplasmic proteins. Int. J. Mass Spectrom. Ion Proc. 160, 303-316 (1997).
8. McCormack, A.L. et al. Direct analysis and identification of proteins in mixtures by LC/MS/MS and database searching at the low-femtomole level. Anal. Chem. 69, 767-776 (1997).
9. Giddings, J.C. Concepts and comparisons in multidimensional separation. J. High Resol. Chromatogr. Commun. 10, 319-323 (1987).
10. Lundell, N. & Markides, K. Two-dimensional liquid Chromatography of peptides: an optimization of strategy. Chromatographia 34, 369-375 (1992).
11. O'Farrell, P.H. High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 250, 4007-4021 (1975).
12. Takahashi, N., Ishioka, N., Takahashi, Y. & Putnam, F.W. Automated tandem high-performance liquid Chromatographic system for separation of extremely complex peptide mixtures. J. Chromatogr. 326, 407-418 (1985).
13. Opiteck, G.J., Lewis, K.C. & Jorgenson, J.W. Comprehensive on-line LC/LC/MS of proteins. Anal. Chem. 69, 1518-1524 (1997).
14. Yates, J.R., Eng, J.K., McCormack, A.L. & Schieltz, D. Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal. Chem. 67, 1426-1436 (1995).
15. Otaka, E. & Osawa, S. Yeast ribosomal proteins: V. Correlation of several nomenclatures and proposal of a standard nomenclature. Mol. Gen. Genet. 181, 176-182 (1981).
16. Mager, W.H. & Planta, R.J. Coordinate expression of ribosomal protein genes in yeast as a function of cellular growth rate. Mol. Cell. Biol. 104, 181-187 (1991).
17. Warner, J. Synthesis of ribosomes in Saccharomyces cerevisiae. Microbiol. Rev. 53, 256-271 (1989).
18. Link, A.J., Hays, L.G., Carmack, E.B. & Yates, J.R. Identifying the major proteome components of Haemophilus influenzae type-strain NCTC 8143. Electrophoresis 18, 1314-1334 (1997).
19. Gatlin, C.L., Kleemann, G.R., Hays, L.G., Link, A.J. & Yates, J.R. 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 (1998).
20. Cherry, J.M. et al. Genetic and physical maps of Saccharomyces cerevisiae. Nature 387, 67-73 (1997).
21. Ron, D. et al. Cloning of an intracellular receptor for protein kinase C: a homolog of the β subunit of G proteins. Proc. Natl. Acad. Sci. USA 91, 839-343 (1994).
22. Chantrel, Y., Gaisne, M., Lions, C. & Verdiere, J. The transcriptional regulator Hap1p (Cyp1p) is essential for anaerobic or heme-deficient growth of Saccharomyces cerevisiae: genetic and molecular characterization of an extragenic suppressor that encodes a WD repeat protein. Genetics 148, 559-569 (1998).
23. Battaner, E. & Vazquez, D. Preparation of active 60S and 40S subunits from yeast ribosomes. Methods Enzymol. 20, 446-449 (1971).
24. Warner, J.R. & Gorenstein, C. in Methods in cell biology. (ed. Prescott, D.M.) 45-60 (Academic, New York; 1978).
25. Jones, E.W. Tackling the protease problem in Saccharomyces cerevisiae. Methods. Enzymol. 194, 428-453 (1991).
26. Raue, H.A., Mager, W.H. & Planta, R.J. Structural and functional analysis of yeast ribosomal proteins. Methods Enzymol. 194, 453-477 (1991).
27. Wessel, D. & Flügge, U.I. A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. Anal. Biochem. 138, 141-143 (1984).
28. Drubin, D.G., Miller, K.G. & Botstein, D. Yeast actin-binding proteins: evidence for a role in morphogenesis. J. Cell Biol. 107, 2551-2561 (1988).
29. Ruan, H., Brown, C.Y. & Morris, D.R. in mRNA formation and function. (ed. Richter, J.D.) 305-321 (Academic, New York; 1997).
30. Saccharomyces genome database at http://genome-www.stanford.edu/Saccharomyces/.
31. Güldener, U., Heck, S., Fiedler, T., Beinhauer, J. & Hegemann, J.H. A new efficient gene disruption cassette for repeated use in budding yeast. Nucleic Acids Res. 24, 2519-2524 (1996).
32. Direct Analysis of Large Protein Complexes (DALPC) at http://thompson.mbt.washington.edu/dalpc/.