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Approaches and Applications of Quantitative LC-MS for Proteomics and Activitomics

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LC-MS/MS in Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 658))

Abstract

LC-MS is a powerful technique in biomolecular research. In addition to its uses as a tool for protein and peptide quantization, LC-MS can also be used to quantify the activity of signalling and metabolic pathways in a multiplex and comprehensive manner, i.e. as an ‘activitomic’ tool. Taking cancer research as an illustrative example of application, this review discusses the concepts of biochemical pathway analysis using LC-MS-based proteomic and activitomic techniques.

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References

  1. Greis, K. D. (2007) Mass spectrometry for enzyme assays and inhibitor screening: an emerging application in pharmaceutical research. Mass Spectrom. Rev. 26, 324–339.

    Article  PubMed  CAS  Google Scholar 

  2. Cutillas, P. R., Khwaja, A., Graupera, M., Pearce, W., Gharbi, S., Waterfield, M., and Vanhaesebroeck, B. (2006) Ultrasensitive and absolute quantification of the phosphoinositide 3-kinase/Akt signal transduction pathway by mass spectrometry. Proc. Natl. Acad. Sci. USA 103, 8959–8964.

    Article  PubMed  CAS  Google Scholar 

  3. Cascante, M., Boros, L. G., Comin-Anduix, B., de Atauri, P., Centelles, J. J., and Lee, P. W. (2002) Metabolic control analysis in drug discovery and disease. Nat. Biotechnol. 20, 243–249.

    Article  PubMed  CAS  Google Scholar 

  4. Comin-Anduix, B., Boren, J., Martinez, S., Moro, C., Centelles, J. J., Trebukhina, R., Petushok, N., Lee, W. N., Boros, L. G., and Cascante, M. (2001) The effect of thiamine supplementation on tumour proliferation. A metabolic control analysis study. Eur. J. Biochem. 268, 4177–4182.

    Article  PubMed  CAS  Google Scholar 

  5. Guha, U., Chaerkady, R., Marimuthu, A., Patterson, A. S., Kashyap, M. K., Harsha, H. C., Sato, M., Bader, J. S., Lash, A. E., Minna, J. D., Pandey, A., and Varmus, H. E. (2008) Comparisons of tyrosine phosphorylated proteins in cells expressing lung cancer-specific alleles of EGFR and KRAS. Proc. Natl. Acad. Sci. USA 105, 14112–14117.

    Article  PubMed  CAS  Google Scholar 

  6. Kim, J. E., and White, F. M. (2006) Quantitative analysis of phosphotyrosine signaling networks triggered by CD3 and CD28 costimulation in Jurkat cells. J. Immunol. 176, 2833–2843.

    PubMed  CAS  Google Scholar 

  7. Kruger, M., Kratchmarova, I., Blagoev, B., Tseng, Y. H., Kahn, C. R., and Mann, M. (2008) Dissection of the insulin signaling pathway via quantitative phosphoproteomics. Proc. Natl. Acad. Sci. USA 105, 2451–2456.

    Article  PubMed  Google Scholar 

  8. Larive, R. M., Urbach, S., Poncet, J., Jouin, P., Mascre, G., Sahuquet, A., Mangeat, P. H., Coopman, P. J., and Bettache, N. (2009) Phosphoproteomic analysis of Syk kinase signaling in human cancer cells reveals its role in cell–cell adhesion. Oncogene 28(24), 2337–2347.

    Google Scholar 

  9. Olsen, J. V., Blagoev, B., Gnad, F., Macek, B., Kumar, C., Mortensen, P., and Mann, M. (2006) Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127, 635–648.

    Article  PubMed  CAS  Google Scholar 

  10. Rikova, K., Guo, A., Zeng, Q., Possemato, A., Yu, J., Haack, H., Nardone, J., Lee, K., Reeves, C., Li, Y., Hu, Y., Tan, Z., Stokes, M., Sullivan, L., Mitchell, J., Wetzel, R., Macneill, J., Ren, J. M., Yuan, J., Bakalarski, C. E., Villen, J., Kornhauser, J. M., Smith, B., Li, D., Zhou, X., Gygi, S. P., Gu, T. L., Polakiewicz, R. D., Rush, J., and Comb, M. J. (2007) Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell 131, 1190–1203.

    Article  PubMed  CAS  Google Scholar 

  11. Rush, J., Moritz, A., Lee, K. A., Guo, A., Goss, V. L., Spek, E. J., Zhang, H., Zha, X. M., Polakiewicz, R. D., and Comb, M. J. (2005) Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Nat. Biotechnol. 23, 94–101.

    Article  PubMed  CAS  Google Scholar 

  12. Trinidad, J. C., Specht, C. G., Thalhammer, A., Schoepfer, R., and Burlingame, A. L. (2006) Comprehensive identification of phosphorylation sites in postsynaptic density preparations. Mol. Cell. Proteomics 5, 914–922.

    Article  PubMed  CAS  Google Scholar 

  13. Villen, J., and Gygi, S. P. (2008) The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry. Nat. Protoc. 3, 1630–1638.

    Article  PubMed  Google Scholar 

  14. Lienhard, G. E. (2008) Non-functional phosphorylations? Trends Biochem. Sci. 33, 351–352.

    Article  PubMed  CAS  Google Scholar 

  15. Greenman, C., Stephens, P., Smith, R., Dalgliesh, G. L., Hunter, C., Bignell, G., Davies, H., Teague, J., Butler, A., Stevens, C., Edkins, S., O'Meara, S., Vastrik, I., Schmidt, E. E., Avis, T., Barthorpe, S., Bhamra, G., Buck, G., Choudhury, B., Clements, J., Cole, J., Dicks, E., Forbes, S., Gray, K., Halliday, K., Harrison, R., Hills, K., Hinton, J., Jenkinson, A., Jones, D., Menzies, A., Mironenko, T., Perry, J., Raine, K., Richardson, D., Shepherd, R., Small, A., Tofts, C., Varian, J., Webb, T., West, S., Widaa, S., Yates, A., Cahill, D. P., Louis, D. N., Goldstraw, P., Nicholson, A. G., Brasseur, F., Looijenga, L., Weber, B. L., Chiew, Y. E., DeFazio, A., Greaves, M. F., Green, A. R., Campbell, P., Birney, E., Easton, D. F., Chenevix-Trench, G., Tan, M. H., Khoo, S. K., Teh, B. T., Yuen, S. T., Leung, S. Y., Wooster, R., Futreal, P. A., and Stratton, M. R. (2007) Patterns of somatic mutation in human cancer genomes. Nature 446, 153–158.

    Article  PubMed  CAS  Google Scholar 

  16. Sawyers, C. L. (2008) The cancer biomarker problem. Nature 452, 548–552.

    Article  PubMed  CAS  Google Scholar 

  17. Miller, M. L., Jensen, L. J., Diella, F., Jorgensen, C., Tinti, M., Li, L., Hsiung, M., Parker, S. A., Bordeaux, J., Sicheritz-Ponten, T., Olhovsky, M., Pasculescu, A., Alexander, J., Knapp, S., Blom, N., Bork, P., Li, S., Cesareni, G., Pawson, T., Turk, B. E., Yaffe, M. B., Brunak, S., and Linding, R. (2008) Linear motif atlas for phosphorylation-dependent signaling. Sci. Signal. 1, ra2.

    Article  PubMed  Google Scholar 

  18. Linding, R., Jensen, L. J., Pasculescu, A., Olhovsky, M., Colwill, K., Bork, P., Yaffe, M. B., and Pawson, T. (2008) NetworKIN: a resource for exploring cellular phosphorylation networks. Nucleic Acids Res. 36, D695–D699.

    Article  PubMed  CAS  Google Scholar 

  19. Linding, R., Jensen, L. J., Ostheimer, G. J., van Vugt, M. A., Jorgensen, C., Miron, I. M., Diella, F., Colwill, K., Taylor, L., Elder, K., Metalnikov, P., Nguyen, V., Pasculescu, A., Jin, J., Park, J. G., Samson, L. D., Woodgett, J. R., Russell, R. B., Bork, P., Yaffe, M. B., and Pawson, T. (2007) Systematic discovery of in vivo phosphorylation networks. Cell 129, 1415–1426.

    Article  PubMed  CAS  Google Scholar 

  20. Metz, T. O., Page, J. S., Baker, E. S., Tang, K., Ding, J., Shen, Y., and Smith, R. D. (2008) High resolution separations and improved ion production and transmission in metabolomics. Trends Anal. Chem. 27, 205–214.

    Article  CAS  Google Scholar 

  21. Metz, T. O., Zhang, Q., Page, J. S., Shen, Y., Callister, S. J., Jacobs, J. M., and Smith, R. D. (2007) The future of liquid chromatography–mass spectrometry (LC-MS) in metabolic profiling and metabolomic studies for biomarker discovery. Biomark. Med. 1, 159–185.

    Article  PubMed  CAS  Google Scholar 

  22. Elstrom, R. L., Bauer, D. E., Buzzai, M., Karnauskas, R., Harris, M. H., Plas, D. R., Zhuang, H., Cinalli, R. M., Alavi, A., Rudin, C. M., and Thompson, C. B. (2004) Akt stimulates aerobic glycolysis in cancer cells. Cancer Res. 64, 3892–3899.

    Article  PubMed  CAS  Google Scholar 

  23. Vizan, P., Boros, L. G., Figueras, A., Capella, G., Mangues, R., Bassilian, S., Lim, S., Lee, W. N., and Cascante, M. (2005) K-ras codon-specific mutations produce distinctive metabolic phenotypes in NIH3T3 mice [corrected] fibroblasts. Cancer Res. 65, 5512–5515.

    Article  PubMed  CAS  Google Scholar 

  24. Wise, D. R., DeBerardinis, R. J., Mancuso, A., Sayed, N., Zhang, X. Y., Pfeiffer, H. K., Nissim, I., Daikhin, E., Yudkoff, M., McMahon, S. B., and Thompson, C. B. (2008) Myc regulates a transcriptional program that stimulates mitochondrial glutaminolysis and leads to glutamine addiction. Proc. Natl. Acad. Sci. USA 105, 18782–18787.

    Article  PubMed  CAS  Google Scholar 

  25. Sreekumar, A., Poisson, L. M., Rajendiran, T. M., Khan, A. P., Cao, Q., Yu, J., Laxman, B., Mehra, R., Lonigro, R. J., Li, Y., Nyati, M. K., Ahsan, A., Kalyana-Sundaram, S., Han, B., Cao, X., Byun, J., Omenn, G. S., Ghosh, D., Pennathur, S., Alexander, D. C., Berger, A., Shuster, J. R., Wei, J. T., Varambally, S., Beecher, C., and Chinnaiyan, A. M. (2009) Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature 457, 910–914.

    Article  PubMed  CAS  Google Scholar 

  26. Bi, X., Lin, Q., Foo, T. W., Joshi, S., You, T., Shen, H. M., Ong, C. N., Cheah, P. Y., Eu, K. W., and Hew, C. L. (2006) Proteomic analysis of colorectal cancer reveals alterations in metabolic pathways: mechanism of tumorigenesis. Mol. Cell. Proteomics 5, 1119–1130.

    Article  PubMed  CAS  Google Scholar 

  27. Chan, E. C., Koh, P. K., Mal, M., Cheah, P. Y., Eu, K. W., Backshall, A., Cavill, R., Nicholson, J. K., and Keun, H. C. (2009) Metabolic profiling of human colorectal cancer using high-resolution magic angle spinning nuclear magnetic resonance (HR-MAS NMR) spectroscopy and gas chromatography mass spectrometry (GC/MS). J. Proteome Res. 8, 352–361.

    Article  PubMed  CAS  Google Scholar 

  28. Parsons, D. W., Wang, T. L., Samuels, Y., Bardelli, A., Cummins, J. M., DeLong, L., Silliman, N., Ptak, J., Szabo, S., Willson, J. K., Markowitz, S., Kinzler, K. W., Vogelstein, B., Lengauer, C., and Velculescu, V. E. (2005) Colorectal cancer: mutations in a signalling pathway. Nature 436, 792.

    Article  PubMed  CAS  Google Scholar 

  29. Wakelam, M. J., Pettitt, T. R., and Postle, A. D. (2007) Lipidomic analysis of signaling pathways. Methods Enzymol. 432, 233–246.

    Article  PubMed  CAS  Google Scholar 

  30. Engelman, J. A., Luo, J., and Cantley, L. C. (2006) The evolution of phosphatidylinositol 3-kinases as regulators of growth and metabolism. Nat. Rev. Genet. 7, 606–619.

    Article  PubMed  CAS  Google Scholar 

  31. Yuan, T. L., and Cantley, L. C. (2008) PI3K pathway alterations in cancer: variations on a theme. Oncogene 27, 5497–5510.

    Article  PubMed  CAS  Google Scholar 

  32. Carpenter, C. L., and Cantley, L. C. (1990) Phosphoinositide kinases. Biochemistry 29, 11147–11156.

    Article  PubMed  CAS  Google Scholar 

  33. Fruman, D. A., Meyers, R. E., and Cantley, L. C. (1998) Phosphoinositide kinases. Annu. Rev. Biochem. 67, 481–507.

    Article  PubMed  CAS  Google Scholar 

  34. Niggli, V. (2005) Regulation of protein activities by phosphoinositide phosphates. Annu. Rev. Cell. Dev. Biol. 21, 57–79.

    Article  PubMed  CAS  Google Scholar 

  35. Pettitt, T. R., Dove, S. K., Lubben, A., Calaminus, S. D., and Wakelam, M. J. (2006) Analysis of intact phosphoinositides in biological samples. J. Lipid Res. 47, 1588–1596.

    Article  PubMed  CAS  Google Scholar 

  36. Milne, S. B., Ivanova, P. T., DeCamp, D., Hsueh, R. C., and Brown, H. A. (2005) A targeted mass spectrometric analysis of phosphatidylinositol phosphate species. J. Lipid Res. 46, 1796–1802.

    Article  PubMed  CAS  Google Scholar 

  37. Mann, M., Hendrickson, R. C., and Pandey, A. (2001) Analysis of proteins and proteomes by mass spectrometry. Annu. Rev. Biochem. 70, 437–473.

    Article  PubMed  CAS  Google Scholar 

  38. 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.

    PubMed  CAS  Google Scholar 

  39. Cox, J., and Mann, M. (2007) Is proteomics the new genomics? Cell 130, 395–398.

    Article  PubMed  CAS  Google Scholar 

  40. Brunet, S., Thibault, P., Gagnon, E., Kearney, P., Bergeron, J. J., and Desjardins, M. (2003) Organelle proteomics: looking at less to see more. Trends Cell. Biol. 13, 629–638.

    Article  PubMed  CAS  Google Scholar 

  41. Dreger, M. (2003) Subcellular proteomics. Mass Spectrom. Rev. 22, 27–56.

    Article  PubMed  CAS  Google Scholar 

  42. Robinson, C. V., Sali, A., and Baumeister, W. (2007) The molecular sociology of the cell. Nature 450, 973–982.

    Article  PubMed  CAS  Google Scholar 

  43. Taylor, S. W., Fahy, E., and Ghosh, S. S. (2003) Global organellar proteomics. Trends Biotechnol. 21, 82–88.

    Article  PubMed  CAS  Google Scholar 

  44. 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.

    Article  PubMed  CAS  Google Scholar 

  45. Andersen, J. S., Wilkinson, C. J., Mayor, T., Mortensen, P., Nigg, E. A., and Mann, M. (2003) Proteomic characterization of the human centrosome by protein correlation profiling. Nature 426, 570–574.

    Article  PubMed  CAS  Google Scholar 

  46. Fabbro, M., Zhou, B. B., Takahashi, M., Sarcevic, B., Lal, P., Graham, M. E., Gabrielli, B. G., Robinson, P. J., Nigg, E. A., Ono, Y., and Khanna, K. K. (2005) Cdk1/Erk2- and Plk1-dependent phosphorylation of a centrosome protein, Cep55, is required for its recruitment to midbody and cytokinesis. Dev. Cell 9, 477–488.

    Article  PubMed  CAS  Google Scholar 

  47. Guarguaglini, G., Duncan, P. I., Stierhof, Y. D., Holmstrom, T., Duensing, S., and Nigg, E. A. (2005) The forkhead-associated domain protein Cep170 interacts with Polo-like kinase 1 and serves as a marker for mature centrioles. Mol. Biol. Cell 16, 1095–1107.

    Article  PubMed  CAS  Google Scholar 

  48. Graser, S., Stierhof, Y. D., and Nigg, E. A. (2007) Cep68 and Cep215 (Cdk5rap2) are required for centrosome cohesion. J. Cell Sci. 120, 4321–4331.

    Article  PubMed  CAS  Google Scholar 

  49. Yan, X., Habedanck, R., and Nigg, E. A. (2006) A complex of two centrosomal proteins, CAP350 and FOP, cooperates with EB1 in microtubule anchoring. Mol. Biol. Cell 17, 634–644.

    Article  PubMed  CAS  Google Scholar 

  50. Dunkley, T. P., Watson, R., Griffin, J. L., Dupree, P., and Lilley, K. S. (2004) Localization of organelle proteins by isotope tagging (LOPIT). Mol. Cell. Proteomics 3, 1128–1134.

    Article  PubMed  CAS  Google Scholar 

  51. Foster, L. J., de Hoog, C. L., Zhang, Y., Xie, X., Mootha, V. K., and Mann, M. (2006) A mammalian organelle map by protein correlation profiling. Cell 125, 187–199.

    Article  PubMed  CAS  Google Scholar 

  52. Sadowski, P. G., Dunkley, T. P., Shadforth, I. P., Dupree, P., Bessant, C., Griffin, J. L., and Lilley, K. S. (2006) Quantitative proteomic approach to study subcellular localization of membrane proteins. Nat. Protoc. 1, 1778–1789.

    Article  PubMed  CAS  Google Scholar 

  53. Tan, D. J., Dvinge, H., Christoforou, A., Bertone, P., Martinez Arias, A., and Lilley, K. S. (2009) Mapping organelle proteins and protein complexes in Drosophila melanogaster. J Proteome Res. 8(6), 2667–2678.

    Google Scholar 

  54. Cutillas, P. R., Biber, J., Marks, J., Jacob, R., Stieger, B., Cramer, R., Waterfield, M., Burlingame, A. L., and Unwin, R. J. (2005) Proteomic analysis of plasma membrane vesicles isolated from the rat renal cortex. Proteomics 5, 101–112.

    Article  PubMed  CAS  Google Scholar 

  55. Abu-Farha, M., Elisma, F., and Figeys, D. (2008) Identification of protein–protein interactions by mass spectrometry coupled techniques. Adv. Biochem. Eng. Biotechnol. 110, 67–80.

    PubMed  CAS  Google Scholar 

  56. Kocher, T., and Superti-Furga, G. (2007) Mass spectrometry-based functional proteomics: from molecular machines to protein networks. Nat. Methods 4, 807–815.

    Article  PubMed  Google Scholar 

  57. Lee, W. C., and Lee, K. H. (2004) Applications of affinity chromatography in proteomics. Anal. Biochem. 324, 1–10.

    Article  PubMed  CAS  Google Scholar 

  58. Simpson, R. J., and Dorow, D. S. (2001) Cancer proteomics: from signaling networks to tumor markers. Trends Biotechnol. 19, S40–S48.

    Article  PubMed  CAS  Google Scholar 

  59. Yarmush, M. L., and Jayaraman, A. (2002) Advances in proteomic technologies. Annu. Rev. Biomed. Eng. 4, 349–373.

    Article  PubMed  CAS  Google Scholar 

  60. Christofk, H. R., Vander Heiden, M. G., Wu, N., Asara, J. M., and Cantley, L. C. (2008) Pyruvate kinase M2 is a phosphotyrosine-binding protein. Nature 452, 181–186.

    Article  PubMed  CAS  Google Scholar 

  61. Christofk, H. R., Vander Heiden, M. G., Harris, M. H., Ramanathan, A., Gerszten, R. E., Wei, R., Fleming, M. D., Schreiber, S. L., and Cantley, L. C. (2008) The M2 splice isoform of pyruvate kinase is important for cancer metabolism and tumour growth. Nature 452, 230–233.

    Article  PubMed  CAS  Google Scholar 

  62. Rigaut, G., Shevchenko, A., Rutz, B., Wilm, M., Mann, M., and Seraphin, B. (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 17, 1030–1032.

    Article  PubMed  CAS  Google Scholar 

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Cutillas, P.R., Timms, J.F. (2010). Approaches and Applications of Quantitative LC-MS for Proteomics and Activitomics. In: Cutillas, P., Timms, J. (eds) LC-MS/MS in Proteomics. Methods in Molecular Biology, vol 658. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-780-8_1

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  • DOI: https://doi.org/10.1007/978-1-60761-780-8_1

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