Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein

Molecular and Cellular Proteomics

Volumn 4, Issue 9, 2005, Pages 1265-1272

  Ishihama, Yasushi ^a,b   Oda, Yoshiya ^a   Tabata, Tsuyoshi ^a   Sato, Toshitaka ^a   Nagasu, Takeshi ^a   Rappsilber, Juri ^b,c   Mann, Matthias ^b  

^a EISAI CO LTD   (Japan)

^b UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

^c FIRC INSTITUTE OF MOLECULAR ONCOLOGY   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

CELL PROTEIN; PEPTIDE; SERUM ALBUMIN;

AMINO ACID SEQUENCE; ANIMAL CELL; ARTICLE; CALCULATION; CANCER CELL CULTURE; CELL LYSATE; CELL STRAIN HCT116; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; GENE EXPRESSION; HUMAN; HUMAN CELL; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONTENT; PROTEIN EXPRESSION; PROTEOMICS; QUANTITATIVE ANALYSIS; STAINING;

ANIMALS; CELL EXTRACTS; CELL LINE, TUMOR; CHROMATOGRAPHY, LIQUID; CLONE CELLS; COLONIC NEOPLASMS; GENE EXPRESSION; HUMANS; MASS SPECTROMETRY; MICE; NEUROBLASTOMA; PEPTIDES; PROTEINS; PROTEOMICS; SEQUENCE ANALYSIS, PROTEIN; SERUM ALBUMIN;

EID: 26844559000     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M500061-MCP200     Document Type: Article

References (34)

1. Aebersold, R., and Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198-207
2. Oda, Y., Huang, K., Cross, F. R., Cowburn, D., and Chait, B. T. (1999) Accurate quantitation of protein expression and site-specific phosphorylation. Proc. Natl. Acad. Sci. U. S. A. 96, 6591-6596
3. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., and Aebersold, R. (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17, 994-999
4. Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A., and Mann, M. (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1, 376-386
5. MacCoss, M. J., Wu, C. C., Liu, H., Sadygov, R., and Yates, J. R., III (2003) A correlation algorithm for the automated quantitative analysis of shotgun proteomics data. Anal. Chem. 75, 6912-6921
6. Foster, L. J., De Hoog, C. L., and Mann, M. (2003) Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors. Proc. Natl. Acad. Sci. U. S. A. 100, 5813-5818
7. Blagoev, B., Kratchmarova, I., Ong, S. E., Nielsen, M., Foster, L. J., and Mann, M. (2003) A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat. Biotechnol. 21, 315-318
8. Ranish, J. A., Yi, E. C., Leslie, D. M., Purvine, S. O., Goodlett, D. R., Eng, J., and Aebersold, R. (2003) The study of macromolecular complexes by quantitative proteomics. Nat. Genet. 33, 349-355
9. Schulze, W. X., and Mann, M. (2004) A novel proteomic screen for peptide-protein interactions. J. Biol. Chem. 279, 10756-10764
10. Oda, Y., Owa, T., Sato, T., Boucher, B., Daniels, S., Yamanaka, H., Shinohara, Y., Yokoi, A., Kuromitsu, J., and Nagasu, T. (2003) Quantitative chemical proteomics for identifying candidate drug targets. Anal. Chem. 75, 2159-2165
11. Barr, J. R., Maggio, V. L., Patterson, D. G., Jr., Cooper, G. R., Henderson, L. O., Turner, W. E., Smith, S. J., Hannon, W. H., Needham, L. L., and Sampson, E. J. (1996) Isotope dilution-mass spectrometric quantification of specific proteins: model application with apolipoprotein A-1. Clin. Chem. 42, 1676-1682
12. 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
13. Havlis, J., and Shevchenko, A. (2004) Absolute quantification of proteins in solutions and in polyacrylamide gels by mass spectrometry. Anal. Chem. 76, 3029-3036
14. Corbin, R. W., Paliy, O., Yang, F., Shabanowitz, J., Platt, M., Lyons, C. E., Jr., Root, K., McAuliffe, J., Jordan, M. I., Kustu, S., Soupene, E., and Hunt, D. F. (2003) Toward a protein profile of Escherichia coli: comparison to its transcription profile. Proc. Natl. Acad. Sci. U. S. A. 100, 9232-9237
15. Lasonder, E., Ishihama, Y., Andersen, J. S., Vermunt, A. M., Pain, A., Sauerwein, R. W., Eling, W. M., Hall, N., Waters, A. P., Stunnenberg, H. G., and Mann, M. (2002) Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature 419, 537-542
16. Shen, Y., Zhao, R., Berger, S. J., Anderson, G. A., Rodriguez,'N., and Smith, R. D. (2002) High-efficiency nanoscale liquid chromatography coupled on-line with mass spectrometry using nanoelectrospray ionization for proteomics. Anal. Chem. 74, 4235-4249
17. Rappsilber, J., Ryder, U., Lamond, A. I., and Mann, M. (2002) Large-scale proteomic analysis of the human spliceosome. Genome. Res. 12, 1231-1245
18. Sanders, S. L., Jennings, J., Canutescu, A., Link, A. J., and Weil, P. A. (2002) Proteomics of the eukaryotic transcription machinery: identification of proteins associated with components of yeast TFIID by multidimensional mass spectrometry. Mol. Cell. Biol. 22, 4723-4738
19. Liu, H., Sadygov, R. G., and Yates, J. R., III (2004) A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 76, 4193-4201
20. Cox, B. J., Kislinger, T., Wigle, D. A., Brown, K., Manning, D., Jurisica, I., Emili, A., and Rossant, J. (2004) in Proceedings of the 52nd ASMS Conference on Mass Spectrometry and Allied Topics, May 23-27 2004, Nashville, Abstr. ThPS352, American Society for Mass Spectrometry, Santa Fe, NM
21. Allet, N., Barrillat, N., Baussant, T., Boiteau, C., Botti, P., Bougueleret, L., Budin, N., Canet, D., Carraud, S., Chiappe, D., Christmann, N., Colinge, J., Cusin, I., Dafflon, N., Depresle, B., Fasso, I., Frauchiger, P., Gaertner, H., Gleizes, A., Gonzalez-Couto, E., Jeandenans, C., Karmime, A., Kowall, T., Lagaché, S., Mahe, E., Masselot, A., Mattou, H., Moniatte, M., Niknejad, A., Paolini, M., Perret, F., Pinaud, N., Ranno, F., Raimondi, S., Reffas, S., Regamey, P. O., Rey, P. A., Rodriguez-Tome, P., Rose, K., Rossellat, G., Saudrais, C., Schmidt, C., Villain, M., and Zwahlen, C. (2004) In vitro and in silico processes to identify differentially expressed proteins. Proteomics 4, 2333-2351
22. Rappsilber, J., Ishihama, Y., and Mann, M. (2003) Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal. Chem. 75, 663-670
23. Ishihama, Y., Sato, T., Tabata, T., Miyamoto, N., Sagane, K., Nagasu, T., and Oda, Y. (2005) Quantitative mouse brain proteomics using culture-derived isotope tags as internal standards. Nat. Biotechnol. 23, 617-621
24. Ishihama, Y., Rappsilber, J., Andersen, J. S., and Mann, M. (2002) Microcolumns with self-assembled particle frits for proteomics. J. Chromatogr. A 979, 233-239
25. Meek, J. L. (1980) Prediction of peptide retention times in high-pressure liquid chromatography on the basis of amino acid composition. Proc. Natl. Acad. Sci. U. S. A. 77, 1632-1636
26. Sakamoto, Y., Kawakami, N., and Sasagawa, T. (1988) Prediction of peptide retention times. J. Chromatogr. 442, 69-79
27. Sweetman, G., Bantscheff, M., Schirle, M., Rick, J., and Kuster, B. (2004) in Proceedings of the 52nd ASMS Conference on Mass Spectrometry and Allied Topics, May 23-27, 2004, Nashville, Abstr. TPR361, American Society for Mass Spectrometry, Santa Fe, NM
28. Read, S. M., and Northcote, D. H. (1981) Minimization of variation in the response to different proteins of the Coomassie blue G dye-binding assay for protein. Anal. Biochem. 116, 53-64
29. Hager, J. W. (2002) A new linear ion trap mass spectrometer. Rapid Commun. Mass Spectrom. 16, 512-526
30. 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
31. 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
32. Gygi, S. P., Rochon, Y., Franza, B. R., and Aebersold, R. (1999) Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19, 1720-1730
33. Tsurugi, K. (1989) On the regulation of ribosome synthesis in eukaryotic cell. Seikagaku 61, 271-284
34. Mager, W. H. (1988) Control of ribosomal protein gene expression. Biochim. Biophys. Acta 949, 1-15