Summary
Proteomics may be defined as the systematic analysis of proteins expressed in a given organism (Elec-trophoresis 16:1090–1094, 1995). Important technical innovations in mass spectrometry (MS), protein identification methods, and database annotation, over the past decade, now make it possible to routinely identify thousands of proteins in complex biological samples (Nature 422:198–207, 2003). However, to gain new insights regarding fundamental biological questions, accurate protein quantification is also required. In this chapter, we present methods for the biochemical separation of different cellular compartments, two-dimensional chromatographic separation of the constituent peptide populations, and the recently published Spectral Counting Strategy, a label-free MS-based protein quantification technology (Cell 125:173–186, 2006; Anal Chem 76:4193–4201, 2004; Mol Cell Proteomics 4:1487–1502, 2005; Cell 125:1003–1013, 2006; Methods 40:135–142, 2006; Anal Chem 77:6218–6224, 2005; J Pro-teome Res 5:2339–2347, 2006). Additionally, highly accurate protein quantification based on isotope dilution, describing the isotope coded protein label (ICPL) – method shall be explained in detail (Mol Cell Proteomics 5:1543–1558, 2006; Proteomics 5:4–15, 2005).
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References
Wasinger, V. C., Cordwell, S. J., Cerpa-Poljak, A., Yan, J. X., Gooley, A. A., Wilkins, M. R., Duncan, M. W., Harris, R., Williams, K. L., and Humphery-Smith, I. (1995) Progress with gene-product mapping of the Mollicutes: Myco-plasma genitalium. Electrophoresis 16, 1090–4.
Steen, H., and Mann, M. (2004) The ABC's (and XYZ's) of peptide sequencing. Nat Rev Mol Cell Biol 5, 699–711.
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, 676–82.
Washburn, M. P., Wolters, D., and Yates, J. R., III (2001) Large-scale analysis of the yeast pro-teome by multidimensional protein identification technology. Nat Biotechnol 19, 242–7.
Ong, S. E., and Mann, M. (2005) Mass spec-trometry-based proteomics turns quantitative. Nat Chem Biol 1, 252–62.
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, 994–9.
Schmidt, A., Kellermann, J., and Lottspeich, F. (2005) A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 5, 4–15.
Munchbach, M., Quadroni, M., Miotto, G., and James, P. (2000) Quantitation and facilitated de novo sequencing of proteins by isotopic N-terminal labeling of peptides with a fragmentation-directing moiety. Anal Chem 72, 4047–57.
Regnier, F. E., and Julka, S. (2006) Primary amine coding as a path to comparative pro-teomics. Proteomics 6, 3968–79.
Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B., Parker, K., Hattan, S., Khainovski, N., Pillai, S., Dey, S., Daniels, S., Purkayastha, S., Juhasz, P., Martin, S., Bartlet-Jones, M., He, F., Jacobson, A., and Pappin, D. J. (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3, 1154–69.
Olsen, J. V., Blagoev, B., Gnad, F., Macek, B., Kumar, C., Mortensen, P., and Mann, M. (2006) Global, in vivo, and site-specific phos-phorylation dynamics in signaling networks. Cell 127, 635–48.
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 pro-teomics. Mol Cell Proteomics 1, 376–86.
Staes, A., Demol, H., Van Damme, J., Martens, L., Vandekerckhove, J., and Gevaert, K. (2004) Global differential non-gel proteomics by quantitative and stable labeling of tryptic peptides with oxygen-18. J Proteome Res 3, 786–91.
Kislinger, T., Rahman, K., Radulovic, D., Cox, B., Rossant, J., and Emili, A. (2003) PRISM, a generic large scale proteomic investigation strategy for mammals. Mol Cell Proteomics 2, 96–106.
Kislinger, T., Cox, B., Kannan, A., Chung, C., Hu, P., Ignatchenko, A., Scott, M. S., Gramolini, A. O., Morris, Q., Hallett, M. T., Rossant, J., Hughes, T. R., Frey, B., and Emili, A. (2006) Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell 125, 173–86.
Bisle, B., Schmidt, A., Scheibe, B., Klein, C., Tebbe, A., Kellermann, J., Siedler, F., Pfeiffer, F., Lottspeich, F., and Oesterhelt, D. (2006) Quantitative profiling of the membrane pro-teome in a halophilic archaeon. Mol Cell Pro-teomics 5, 1543–58.
Peng, J., Elias, J. E., Thoreen, C. C., Lick-lider, L. J., and Gygi, S. P. (2003) Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/ LC-MS/MS) for large-scale protein analysis: the yeast proteome. J Proteome Res 2, 43–50.
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, 5383–92.
Perkins, D. N., Pappin, D. J., Creasy, D. M., and Cottrell, J. S. (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Elec-trophoresis 20, 3551–67.
Oesterhelt, D., and Stoeckenius, W. (1974) Isolation of the cell membrane of Halobacterium halobium and its fractionation into red and purple membrane. Methods Enzymol 31, 667–78.
Oesterhelt, D., and Krippahl, G. (1983) Pho-totrophic growth of halobacteria and its use for isolation of photosynthetically-deficient mutants. Ann Microbiol (Paris) 134B, 137–50.
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, 141–3.
Rappsilber et al. (2003) Anal Chem 75 (3), 663–70.
Tebbe, A., Klein, C., Bisle, B., Siedler, F., Scheffer, B., Garcia-Rizo, C., Wolfertz, J., Hickmann, V., Pfeiffer, F., and Oesterhelt, D. (2005) Analysis of the cytosolic proteome of Halobacterium salinarum and its implication for genome annotation. Proteomics5, 168–79.
Moore, R. E., Young, M. K., and Lee, T. D. (2002) Qscore: an algorithm for evaluating SEQUEST database search results. J Am Soc Mass Spectrom 13, 378–86.
Andersen, J. S., and Mann, M. (2006) Organellar proteomics: turning inventories into insights. EMBO Rep 7, 874–9.
Chen, E. I., Hewel, J., Felding-Habermann, B., and Yates, J. R., III (2006) Large scale protein profiling by combination of protein fractionation and multidimensional protein identification technology (MudPIT). Mol Cell Proteomics 5, 53–6.
Simpson, D. C., Ahn, S., Pasa-Tolic, L., Bogdanov, B., Mottaz, H. M., Vilkov, A. N., Anderson, G. A., Lipton, M. S., and Smith, R. D. (2006) Using size exclusion chroma-tography-RPLC and RPLC-CIEF as two-dimensional separation strategies for protein profiling. Electrophoresis 27, 2722–33.
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, 4193–201.
Old, W. M., Meyer-Arendt, K., Aveline-Wolf, L., Pierce, K. G., Mendoza, A., Sevinsky, J. R., Resing, K. A., and Ahn, N. G. (2005) Comparison of label-free methods for quantifying human proteins by shotgun proteom-ics. Mol Cell Proteomics 4, 1487–502.
Roth, A. F., Wan, J., Bailey, A. O., Sun, B., Kuchar, J. A., Green, W. N., Phinney, B. S., Yates, J. R., III, and Davis, N. G. (2006) Global analysis of protein palmitoylation in yeast. Cell 125, 1003–13.
Roth, A. F., Wan, J., Green, W. N., Yates, J. R., and Davis, N. G. (2006) Proteomic identification of palmitoylated proteins. Methods 40, 135–42.
Zybailov, B., Coleman, M. K., Florens, L., and Washburn, M. P. (2005) Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling. Anal Chem 77, 6218–24.
Zybailov, B., Mosley, A. L., Sardiu, M. E., Coleman, M. K., Florens, L., and Washburn, M. P. (2006) Statistical analysis of membrane proteome expression changes in Saccharomy-ces cerevisiae. J Proteome Res 5, 2339–47.
Nesvizhskii, A. I., Keller, A., Kolker, E., and Aebersold, R. (2003) A statistical model for identifying proteins by tandem mass spec-trometry. Anal Chem 75, 4646–58.
Kokubu, M., Ishihama, Y., Sato, T., Nagasu, T., and Oda, Y. (2005) SpecifiCity of immobilized metal affinity-based IMAC/C18 tip enrichment of phosphopeptides for protein phosphorylation analysis. Anal Chem 77, 5144–54.
Aebersold, R., and Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198–207.
Gramolini A.O. et al. 2008 Comparative proteomics profiling of a phospholamban mutant mouse model of dilated cardiomy-opathy reveals progressive intracellular stress responses. Mol Cell Proteomics. 7(3):519–533.
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The author would like to thank Brian Raught for critical reading of the manuscript.
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Schmidt, A., Bisle, B., Kislinger, T. (2009). Quantitative Peptide and Protein Profiling by Mass Spectrometry. In: Lipton, M.S., Paša-Tolic, L. (eds) Mass Spectrometry of Proteins and Peptides. Methods In Molecular Biology, vol 492. Humana Press. https://doi.org/10.1007/978-1-59745-493-3_2
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DOI: https://doi.org/10.1007/978-1-59745-493-3_2
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