Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation

Molecular and Cellular Proteomics

Volumn 10, Issue 8, 2011, Pages

  Thakur, Suman S ^a   Geiger, Tamar ^a   Chatterjee, Bhaswati ^a   Bandilla, Peter ^a   Froḧlich, Florian ^a   Cox, Juergen ^a   Mann, Matthias ^a  

^a MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CELL PROTEIN; FUNGAL PROTEIN; PROTEOME; SACCHAROMYCES CEREVISIAE PROTEIN;

ACCURACY; ARTICLE; CONCENTRATION (PARAMETERS); FRACTIONATION; HUMAN; LIQUID CHROMATOGRAPHY; MAMMAL CELL; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DETERMINATION; PROTEOMICS; QUANTITATIVE ASSAY; REPRODUCIBILITY; SEQUENCE ANALYSIS; TANDEM MASS SPECTROMETRY; TECHNIQUE; YEAST; CELL FRACTIONATION; CELL STRAIN HEK293; CULTURE TECHNIQUE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; ISOLATION AND PURIFICATION; ISOTOPE LABELING; LIMIT OF DETECTION; METABOLISM; SACCHAROMYCES CEREVISIAE;

MAMMALIA;

CELL CULTURE TECHNIQUES; CELL FRACTIONATION; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; HEK293 CELLS; HUMANS; ISOTOPE LABELING; LIMIT OF DETECTION; METABOLIC NETWORKS AND PATHWAYS; PROTEOME; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TANDEM MASS SPECTROMETRY;

EID: 80051624900     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M110.003699     Document Type: Article

References (32)

1. Aebersold, R., and Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198-207 (Pubitemid 36362757)
2. Yates, J. R., 3rd, Gilchrist, A., Howell, K. E., and Bergeron, J. J. (2005) Proteomics of organelles and large cellular structures. Nat. Rev. Mol. Cell Biol. 6, 702-714 (Pubitemid 41742794)
3. Cravatt, B. F., Simon, G. M., and Yates, J. R., 3rd (2007) The biological impact of mass-spectrometry-based proteomics. Nature 450, 991-1000 (Pubitemid 350273629)
4. Bantscheff, M., Eberhard, D., Abraham, Y., Bastuck, S., Boesche, M., Hobson, S., Mathieson, T., Perrin, J., Raida, M., Rau, C., Reader, V., Sweetman, G., Bauer, A., Bouwmeester, T., Hopf, C., Kruse, U., Neubauer, G., Ramsden, N., Rick, J., Kuster, B., and Drewes, G. (2007) Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nat Biotechnol 25, 1035-1044 (Pubitemid 47517638)
5. Choudhary, C., and Mann, M. (2010) Decoding signalling networks by mass spectrometry-based proteomics. Nat. Rev. Mol. Cell Biol. 11, 427-439
6. de, Godoy, L. M., Olsen, J. V., Cox, J., Nielsen, M. L., Hubner, N. C., Fröhlich, F., Walther, T. C., and Mann, M. (2008) Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 455, 1251-1254
7. Ghaemmaghami, S., Huh, W. K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K., and Weissman, J. S. (2003) Global analysis of protein expression in yeast. Nature 425, 737-741 (Pubitemid 37314318)
8. Huh, W. K., Falvo, J. V., Gerke, L. C., Carroll, A. S., Howson, R. W., Weissman, J. S., and O'Shea, E. K. (2003) Global analysis of protein localization in budding yeast. Nature 425, 686-691 (Pubitemid 37314307)
9. Link, A. J., Eng, J., Schieltz, D. M., Carmack, E., Mize, G. J., Morris, D. R., Garvik, B. M., and Yates, J. R., 3rd (1999) Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol. 17, 676-682 (Pubitemid 29316146)
10. Washburn, M. P., Wolters, D., and Yates, J. R., 3rd (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242-247 (Pubitemid 32220565)
11. Guiochon, G. (2006) The limits of the separation power of unidimensional column liquid chromatography. J. Chromatogr. A 1126, 6-49
12. MacNair, J. E., Lewis, K. C., and Jorgenson, J. W. (1997) Ultrahigh-pressure reversed-phase liquid chromatography in packed capillary columns. Anal. Chem. 69, 983-989
13. Shen, Y., Zhao, R., Belov, M. E., Conrads, T. P., Anderson, G. A., Tang, K., Pasa-Tolić, L., Veenstra, T. D., Lipton, M. S., Udseth, H. R., and Smith, R. D. (2001) Packed capillary reversed-phase liquid chromatography with high-performance electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for proteomics. Anal. Chem. 73, 1766-1775 (Pubitemid 32862442)
14. Luo, Q., Shen, Y., Hixson, K. K., Zhao, R., Yang, F., Moore, R. J., Mottaz, H. M., and Smith, R. D. (2005) Preparation of 20-microm-i.d. silica-based monolithic columns and their performance for proteomics analyses. Anal. Chem. 77, 5028-5035 (Pubitemid 41076696)
15. Liu, H., Finch, J. W., Lavallee, M. J., Collamati, R. A., Benevides, C. C., and Gebler, J. C. (2007) Effects of column length, particle size, gradient length and flow rate on peak capacity of nano-scale liquid chromatography for peptide separations. J. Chromatogr. A 1147, 30-36 (Pubitemid 46428262)
16. Motoyama, A., Venable, J. D., Ruse, C. I., and Yates, J. R., 3rd (2006) Automated ultra-high-pressure multidimensional protein identification technology (UHP-MudPIT) for improved peptide identification of proteomic samples. Anal. Chem. 78, 5109-5118 (Pubitemid 44100648)
17. Iwasaki, M., Miwa, S., Ikegami, T., Tomita, M., Tanaka, N., and Ishihama, Y. (2010) One-dimensional capillary liquid chromatographic separation coupled with tandem mass spectrometry unveils the Escherichia coli proteome on a microarray scale. Anal. Chem. 82, 2616-2620
18. Domon, B., and Aebersold, R. (2006) Mass spectrometry and protein analysis. Science 312, 212-217
19. Mann, M., and Kelleher, N. L. (2008) Precision proteomics: the case for high resolution and high mass accuracy. Proc. Natl. Acad. Sci. U.S.A. 105, 18132-18138
20. Picotti, P., Bodenmiller, B., Mueller, L. N., Domon, B., and Aebersold, R. (2009) Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell 138, 795-806
21. 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 (Pubitemid 36176744)
22. Olsen, J. V., de Godoy, L. M., Li, G., Macek, B., Mortensen, P., Pesch, R., Makarov, A., Lange, O., Horning, S., and Mann, M. (2005) Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap. Mol. Cell Proteomics 4, 2010-2021 (Pubitemid 41830195)
23. Cox, J., Matic, I., Hilger, M., Nagaraj, N., Selbach, M., Olsen, J. V., and Mann, M. (2009) A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics. Nat. Protocols 4, 698-705
24. Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A., Olsen, J. V., and Mann, M. (2011) Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment. J. Proteome Res. 10, 1794-1805
25. Cox, J., and Mann, M. (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367-1372
26. Olsen, J. V., Schwartz, J. C., Griep-Raming, J., Nielsen, M. L., Damoc, E., Denisov, E., Lange, O., Remes, P., Taylor, D., Splendore, M., Wouters, E. R., Senko, M., Makarov, A., Mann, M., and Horning, S. (2009) A dual pressure linear ion trap orbitrap instrument with very high sequencing speed. Mol. Cell Proteomics 8, 2759-2769
27. Malmström, J., Beck, M., Schmidt, A., Lange, V., Deutsch, E. W., and Aebersold, R. (2009) Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. Nature 460, 762-765
28. Zubarev, R. A., Nielsen, M. L., Fung, E. M., Savitski, M. M., Kel-Margoulis, O., Wingender, E., and Kel, A. (2008) Identification of dominant signaling pathways from proteomics expression data. J. Proteomics 71, 89-96 (Pubitemid 351711646)
29. Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., and Hattori, M. (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res. 32, D277-280 (Pubitemid 38081656)
30. 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 (Pubitemid 47175624)
31. Waanders, L. F., Almeida, R., Prosser, S., Cox, J., Eikel, D., Allen, M. H., Schultz, G. A., and Mann, M. (2008) A novel chromatographic method allows on-line reanalysis of the proteome. Mol. Cell Proteomics 7, 1452-1459
32. Makarov, A., Denisov, E., and Lange, O. (2009) Performance evaluation of a high-field Orbitrap mass analyzer. J. Am. Soc. Mass Spectrom. 20, 1391-1396