Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring

Molecular and Cellular Proteomics

Volumn 7, Issue 8, 2008, Pages 1489-1500

  Lange, Vinzenz ^a,b   Malmström, Johan A ^a   Didion, John ^c   King, Nichole L ^c   Johansson, Björn P ^d   Schäfer, Juliane ^a,b   Rameseder, Jonathan ^a   Wong, Chee Hong ^e   Deutsch, Eric W ^c   Brusniak, Mi Youn ^c   Bühlmann, Peter ^a,b   Björck, Lars ^a,d   Domon, Bruno ^a   Aebersold, Ruedi ^a,b,c,f  

^a ETH ZURICH   (Switzerland)

^b Competence Center for Systems Physiology and Metabolic Diseases ^*  (Switzerland)

^c INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^d LUND UNIVERSITY   (Sweden)

^e BIOINFORMATICS INSTITUTE   (Singapore)

^f UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

COLLAGEN LIKE SURFACE PROTEIN A; COMPLEMENT COMPONENT C5A; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; LIPOPROTEIN; M PROTEIN; MEMBRANE PROTEIN; PEPTIDASE; PROTEINASE; PROTEOME; SERINE PROTEINASE; VIRULENCE FACTOR;

ARTICLE; BACTERIUM CULTURE; COMPUTER PROGRAM; CONTROLLED STUDY; NONHUMAN; NUCLEOTIDE SEQUENCE; PEPTIDE MAPPING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEOMICS; QUANTITATIVE ANALYSIS; RELIABILITY; SENSITIVITY ANALYSIS; STREPTOCOCCUS PYOGENES; TANDEM MASS SPECTROMETRY; VALIDATION STUDY;

HUMANS; PEPTIDES; PROTEOME; PROTEOMICS; SOFTWARE; STREPTOCOCCUS PYOGENES; VIRULENCE FACTORS;

STREPTOCOCCUS PYOGENES;

EID: 43049090085     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M800032-MCP200     Document Type: Article

References (37)

1. Ideker, T., Thorsson, V., Ranish, J. A., Christmas, R., Buhler, J., Eng, J. K., Bumgarner, R., Goodlett, D. R., Aebersold, R., and Hood, L. (2001) Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292, 929-934
2. Ong, S. E., and Mann, M. (2005) Mass spectrometry-based proteomics turns quantitative. Nat. Chem. Biol. 1, 252-262
3. Aebersold, R., and Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198-207
4. Gerber, S. A., Rush, J., Stemman, O., Kirschner, M. W., and Gygi, S. P. (2003) Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. U. S. A. 100, 6940-6945
5. Aebersold, R. (2003) Constellations in a cellular universe. Nature 422, 115-116
6. Domon, B., and Aebersold, R. (2006) Mass spectrometry and protein analysis. Science 312, 212-217
7. Kuster, B., Schirle, M., Mallick, P., and Aebersold, R. (2005) Scoring proteomes with proteotypic peptide probes. Nat. Rev. Mol. Cell Biol. 6, 577-583
8. Mallick, P., Schirle, M., Chen, S. S., Flory, M. R., Lee, H., Martin, D., Ranish, J., Raught, B., Schmitt, R., Werner, T., Kuster, B., and Aebersold, R. (2007) Computational prediction of proteotypic peptides for quantitative proteomics. Nat. Biotechnol. 25, 125-131
9. Desiere, F., Deutsch, E. W., King, N. L., Nesvizhskii, A. I., Mallick, P., Eng, J., Chen, S., Eddes, J., Loevenich, S. N., and Aebersold, R. (2006) The PeptideAtlas project. Nucleic Acids Res. 34, D655-D658
10. King, N. L., Deutsch, E. W., Ranish, J. A., Nesvizhskii, A. I., Eddes, J. S., Mallick, P., Eng, J., Desiere, F., Flory, M., Martin, D. B., Kim, B., Lee, H., Raught, B., and Aebersold, R. (2006) Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas. Genome Biol. 7, R106
11. Desiere, F., Deutsch, E. W., Nesvizhskii, A. I., Mallick, P., King, N. L., Eng, J. K., Aderem, A., Boyle, R., Brunner, E., Donohoe, S., Fausto, N., Hafen, E., Hood, L., Katze, M. G., Kennedy, K. A., Kregenow, F., Lee, H., Lin, B., Martin, D., Ranish, J. A., Rawlings, D. J., Samelson, L. E., Shiio, Y., Watts, J. D., Wollscheid, B., Wright, M. E., Yan, W., Yang, L, Yi, E. C., Zhang, H., and Aebersold, R. (2004) Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol. 6, R9
12. Deutsch, E. W., Eng, J. K., Zhang, H., King, N. L., Nesvizhskii, A. I., Lin, B., Lee, H., Yi, E. C., Ossola, R., and Aebersold, R. (2005) Human Plasma PeptideAtlas. Proteomics 5, 3497-3500
13. Domon, B., and Aebersold, R. (2006) Challenges and opportunities in proteomics data analysis. Mol. Cell. Proteomics 5, 1921-1926
14. Wolf-Yadlin, A., Hautaniemi, S., Lauffenburger, D. A., and White, F. M. (2007) Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. Proc. Natl. Acad. Sci. U. S. A. 104, 5860-5865
15. Stahl-Zeng, J., Lange, V., Ossola, R., Eckhardt, K., Krek, W., Aebersold, R., and Domon, B. (2007) High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol. Cell. Proteomics 6, 1809-1817
16. Qu, J., Jusko, W. J., and Straubinger, R. M. (2006) Utility of cleavable isotope-coded affinity-tagged reagents for quantification of low-copy proteins induced by methylprednisolone using liquid chromatography/ tandem mass spectrometry. Anal. Chem. 78, 4543-4552
17. Cunningham, M. W. (2000) Pathogenesis of group A streptococcal infections. Clin. Microbiol. Rev. 13, 470-511
18. Carapetis, J. R., Steer, A. C., Mulholland, E. K., and Weber, M. (2005) The global burden of group A streptococcal diseases. Lancet Infect. Dis. 5, 685-694
19. Musser, J. M., and DeLeo, F. R. (2005) Toward a genome-wide systems biology analysis of host-pathogen interactions in group A Streptococcus. Am. J. Pathol. 167, 1461-1472
20. Johansson, B. P., Levander, F., von Pawel-Rammingen, U., Berggard, T., Bjorck, L., and James, P. (2005) The protein expression of Streptococcus pyogenes is significantly influenced by human plasma. J. Proteome Res. 4, 2302-2311
21. Wessel, D., and Flugge, U. I. (1984) A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. Anal. Biochem. 138, 141-143
22. Malmstrom, J., Lee, H., Nesvizhskii, A. I., Shteynberg, D., Mohanty, S., Brunner, E., Ye, M., Weber, G., Eckerskom, C., and Aebersold, R. (2006) Optimized peptide separation and identification for mass spectrometry based proteomics via free-flow electrophoresis. J. Proteome Res. 5, 2241-2249
23. Heller, M., Ye, M., Michel, P. E., Morier, P., Stalder, D., Junger, M. A., Aebersold, R., Reymond, F., and Rossier, J. S. (2005) Added value for tandem mass spectrometry shotgun proteomics data validation through isoelectric focusing of peptides. J. Proteome Res. 4, 2273-2282
24. Yi, E. C., Lee, H., Aebersold, R., and Goodlett, D. R. (2003) A microcapillary trap cartridge-microcapillary high-performance liquid chromatography electrospray ionization emitter device capable of peptide tandem mass spectrometry at the attomole level on an ion trap mass spectrometer with automated routine operation. Rapid Commun. Mass Spectrom. 17, 2093-2098
25. Eng, J. K., Mccormack, A. L., and Yates, J. R. (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
26. Keller, A., Nesvizhskii, A. I., Kolker, E., and Aebersold, R. (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74, 5383-5392
27. Nesvizhskii, A. I., Keller, A., Kolker, E., and Aebersold, R. (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75, 4646-4658
28. Schmidt, A., Kellermann, J., and Lottspeich, F. (2005) A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 5, 4-15
29. Keller, A., Eng, J., Zhang, N., Li, X. J., and Aebersold, R. (2005) A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol. Syst. Biol. 1, 2005 0017
30. Tang, H., Arnold, R. J., Alves, P., Xun, Z., Clemmer, D. E., Novotny, M. V., Reilly, J. P., and Radivojac, P. (2006) A computational approach toward label-free protein quantification using predicted peptide detectability. Bioinformatics 22, e481-e488
31. Lu, P., Vogel, C., Wang, R., Yao, X., and Marcotte, E. M. (2007) Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat. Biotechnol. 25, 117-124
32. Pandiripally, V., Gregory, E., and Cue, D. (2002) Acquisition of regulators of complement activation by Streptococcus pyogenes serotype M1. Infect. Immun. 70, 6206-6214
33. Shet, A., Kaplan, E., Johnson, D., and Cleary, P. P. (2004) Human immunogenicity studies on group A streptococcal C5a peptidase (SCPA) as a potential vaccine against group A streptococcal infections. Indian J. Med. Res. 119, (suppl.) 95-98
34. Unwin, R. D., Griffiths, J. R., Leverentz, M. K., Grallert, A., Hagan, I. M., and Whetton, A. D. (2005) Multiple reaction monitoring to identify sites of protein phosphorylation with high sensitivity. Mol. Cell. Proteomics 4, 1134-1144
35. Cox, D. M., Zhong, F., Du, M., Duchoslav, E., Sakuma, T., and McDermott, J. C. (2005) Multiple reaction monitoring as a method for identifying protein posttranslational modifications. J. Biomol. Tech. 16, 83-90
36. Liao, H., Wu, J., Kuhn, E., Chin, W., Chang, B., Jones, M. D., O'Neil, S., Clauser, K. R., Karl, J., Hasler, F., Roubenoff, R., Zolg, W., and Guild, B. C. (2004) Use of mass spectrometry to identify protein biomarkers of disease severity in the synovial fluid and serum of patients with rheumatoid arthritis. Arthritis Rheum. 50, 3792-3803
37. Anderson, L., and Hunter, C. L. (2006) Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol. Cell. Proteomics 5, 573-588