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Instrumentation for LC-MS/MS in Proteomics

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LC-MS/MS in Proteomics

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

Abstract

Mass spectrometers now have sufficient sensitivity and acquisition rates to allow analysis of complex proteomic samples on a chromatographic timescale. In this chapter the different instrument options for protein and peptide analysis will be presented, along with their relative strengths and weaknesses for producing different types of information, such as protein identification, modification characterization, or reporting quantitative measurements.

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References

  1. Fenn, J. B, Mann, M., Meng, C. K., Wong, S. F., and Whitehouse, C. M. (1989) Electrospray ionization for mass spectrometry of large biomolecules. Science 246, 64–71.

    Article  PubMed  CAS  Google Scholar 

  2. Hillenkamp. F., and Karas, M. (1990) Mass spectrometry of peptides and proteins by matrix-assisted ultraviolet laser desorption/ionization. Methods Enzymol. 193, 280–295.

    Article  PubMed  CAS  Google Scholar 

  3. Iribarne, J. V., and Thomson, B. A. (1976) On the evaporation of small ions from charged droplets. J. Chem. Phys. 64, 2287–2294.

    Article  Google Scholar 

  4. Nguyen, S., and Fenn, J. B. (2007) Gas-phase ions of solute species from charged droplets of solutions. Proc. Natl. Acad. Sci. USA 104. 1111–1117.

    Article  PubMed  CAS  Google Scholar 

  5. Wilm, M., Shevchenko, A., Houthaeve, T. et al. (1996) Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry. Nature 379, 466–469.

    Article  PubMed  CAS  Google Scholar 

  6. MacNair, J. E., Patel, K. D., and Jorgenson, J. W. (1999) Ultrahigh-pressure reversed-phase capillary liquid chromatography: isocratic and gradient elution using columns packed with 1.0-micron particles. Anal. Chem. 71, 700–708.

    Article  PubMed  CAS  Google Scholar 

  7. Plumb, R., Castro-Perez, J., Granger, J., Beattie, I., Joncour, K., and Wright, A. (2004) Ultra-performance liquid chromatography coupled to quadrupole-orthogonal time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 18, 2331–2337.

    Article  PubMed  CAS  Google Scholar 

  8. 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.

    Article  PubMed  CAS  Google Scholar 

  9. Strittmatter, E. F., Ferguson, P. L., Tang, K., and Smith, R. D. (2003) Proteome analyses using accurate mass and elution time peptide tags with capillary LC time-of-flight mass spectrometry. J. Am. Soc. Mass Spectrom. 14, 980–991.

    Article  PubMed  CAS  Google Scholar 

  10. Douglas, D. J., Frank, A. J., and Mao, D. (2005) Linear ion traps in mass spectrometry. Mass Spectrom. Rev. 24, 1–29.

    Article  PubMed  CAS  Google Scholar 

  11. 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.

    Article  PubMed  CAS  Google Scholar 

  12. Stafford, G. C., Kelley, P. E., Syka, J. E. P., Reynolds, W. E., and Todd, J. F. J. (1984) Recent improvements in and analytical applications of advanced ion trap technology. Int. J. Mass Spectrom. Ion Process. 60, 85–98.

    Article  CAS  Google Scholar 

  13. Schwartz, J. C., Zhou, X., Bier, M. E., inventors (1996) Method and apparatus of increasing dynamic range and sensitivity of a mass spectrometer, U.S. Patent 5572022.

    Google Scholar 

  14. Coon, J. J., Shabanowitz, J., Hunt, D. F., and Syka, J. E. (2005) Electron transfer dissociation of peptide anions. J. Am. Soc. Mass Spectrom. 16, 880–882.

    Article  PubMed  CAS  Google Scholar 

  15. Pitteri, S. J., and McLuckey, S. A. (2005) Recent developments in the ion/ion chemistry of high-mass multiply charged ions. Mass Spectrom. Rev. 24, 931–958.

    Article  PubMed  CAS  Google Scholar 

  16. Comisarow, M. B., and Marshall, A. G. (1974) Fourier transform ion cyclotron resonance spectroscopy. Chem. Phys. Lett. 25, 282–283.

    Article  CAS  Google Scholar 

  17. Cody, R. B., Burnier, R. C., and Freiser, B. S. (1982) Collision-induced dissociation with Fourier transform mass spectrometry. Anal. Chem. 54, 96–101.

    Article  CAS  Google Scholar 

  18. Gauthier, J. W., Trautman, T. R., and Jacobsen, D. B. (1991) Sustained off-resonance irradiation for CAD involving FTMS. CAD technique that emulates infrared multiphoton dissociation. Anal. Chim. Acta 246, 211–225.

    Article  CAS  Google Scholar 

  19. Little, D. P., Speir, J. P., Senko, M. W, O'Connor, P. B., and McLafferty, F. W. (1994) Infrared multiphoton dissociation of large multiply charged ions for biomolecule sequencing. Anal. Chem. 66, 2809–2815.

    Article  PubMed  CAS  Google Scholar 

  20. Zubarev, R. A. (2004) Electron-capture dissociation tandem mass spectrometry. Curr. Opin. Biotechnol. 15, 12–16.

    Article  PubMed  CAS  Google Scholar 

  21. Marshall, A. G., Hendrickson, C. L., and Jackson, G. S. (1998) Fourier transform ion cyclotron resonance mass spectrometry: a primer. Mass Spectrom. Rev. 17, 1–35.

    Article  PubMed  CAS  Google Scholar 

  22. Meng, F., Forbes, A. J., Miller, L. M., and Kelleher, N. L. (2005) Detection and localization of protein modifications by high resolution tandem mass spectrometry. Mass Spectrom. Rev. 24, 126–134.

    Article  PubMed  CAS  Google Scholar 

  23. Hu, Q., Noll, R. J., Li, H., Makarov, A., Hardman, M., and Graham Cooks, R. (2005) The Orbitrap: a new mass spectrometer. J. Mass Spectrom. 40, 430–443.

    Article  PubMed  CAS  Google Scholar 

  24. Makarov, A., Denisov, E., Kholomeev, A. et al. (2006) Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer. Anal. Chem. 78, 2113–2120.

    Article  PubMed  CAS  Google Scholar 

  25. Lange, V., Picotti, P., Domon, B., and Aebersold, R. (2008) Selected reaction monitoring for quantitative proteomics: a tutorial. Mol. Syst. Biol. 4, 222.

    Article  PubMed  Google Scholar 

  26. Stahl-Zeng, J., Lange, V., Ossola, R. et al. (2007) High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol. Cell. Proteomics 6, 1809–1817.

    Article  PubMed  CAS  Google Scholar 

  27. Le Blanc, J. C., Hager, J. W., Ilisiu, A. M., Hunter, C., Zhong, F., and Chu, I. (2003) Unique scanning capabilities of a new hybrid linear ion trap mass spectrometer (Q TRAP) used for high sensitivity proteomics applications. Proteomics 3, 859–869.

    Article  PubMed  Google Scholar 

  28. Mamyrin, B. A., Karataev, V. I., Shmikk, D. V., and Zagulin, V. A. (1973) Sov. Phys. JETP 37, 45.

    Google Scholar 

  29. Chernushevich, I. V., Loboda, A. V., and Thomson, B. A. (2001) An introduction to quadrupole-time-of-flight mass spectrometry. J. Mass Spectrom. 36, 849–865.

    Article  PubMed  CAS  Google Scholar 

  30. Olsen, J. V., Macek, B., Lange, O., Makarov, A., Horning, S., and Mann, M. (2007) Higher-energy C-trap dissociation for peptide modification analysis. Nat. Methods 4, 709–712.

    Article  PubMed  CAS  Google Scholar 

  31. McAlister, G. C., Phanstiel, D., Good, D. M., Berggren, W. T., and Coon, J. J. Implementation of electron-transfer dissociation on a hybrid linear ion trap–orbitrap mass spectrometer. Anal. Chem. 79, 3525–3534.

    Google Scholar 

  32. Syka, J. E., Marto, J. A., Bai, D. L. et al. (2004) Novel linear quadrupole ion trap/FT mass spectrometer: performance characterization and use in the comparative analysis of histone H3 post-translational modifications. J. Proteome Res. 3, 621–626.

    Article  PubMed  CAS  Google Scholar 

  33. Biemann, K. (1990) Appendix 5. Nomenclature for peptide fragment ions (positive ions). Methods Enzymol. 193, 886–888.

    Article  PubMed  CAS  Google Scholar 

  34. McLachlin, D. T., and Chait, B. T. (2001) Analysis of phosphorylated proteins and peptides by mass spectrometry. Curr. Opin. Chem. Biol. 5, 591–602.

    Article  PubMed  CAS  Google Scholar 

  35. Paizs, B., and Suhai, S. (2005) Fragmentation pathways of protonated peptides. Mass Spectrom. Rev. 24, 508–548.

    Article  PubMed  CAS  Google Scholar 

  36. Ross, P. L., Huang, Y. N., Marchese, J. N. et al. (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 3, 1154–1169.

    Article  PubMed  CAS  Google Scholar 

  37. Bateman, R. H., Carruthers, R., Hoyes, J. B. et al. (2002) A novel precursor ion discovery method on a hybrid quadrupole orthogonal acceleration time-of-flight (Q-TOF) mass spectrometer for studying protein phosphorylation. J. Am. Soc. Mass Spectrom. 13, 792–803.

    Article  PubMed  CAS  Google Scholar 

  38. Good, D. M., Wirtala, M., McAlister, G. C., and Coon, J. J. (2007) Performance characteristics of electron transfer dissociation mass spectrometry. Mol. Cell. Proteomics 6, 1942–1951.

    Article  PubMed  CAS  Google Scholar 

  39. Swaney, D. L., McAlister, G. C., Coon, J. J. (2008) Decision tree-driven tandem mass spectrometry for shotgun proteomics. Nat. Methods 5, 959–964.

    Article  PubMed  CAS  Google Scholar 

  40. Kelleher, N. L., Zubarev, R. A., Bush, K. et al. (1999) Localization of labile posttranslational modifications by electron capture dissociation: the case of gamma-carboxyglutamic acid. Anal. Chem. 71, 4250–4253.

    Article  PubMed  CAS  Google Scholar 

  41. Mirgorodskaya, E., Roepstorff, P., and Zubarev, R. A. (1999) Localization of O-glycosylation sites in peptides by electron capture dissociation in a Fourier transform mass spectrometer. Anal. Chem. 71, 4431–4436.

    Article  PubMed  CAS  Google Scholar 

  42. Vosseller, K., Trinidad, J. C., Chalkley, R. J. et al. (2006) O-Linked N-acetylglucosamine proteomics of postsynaptic density preparations using lectin weak affinity chromatography and mass spectrometry. Mol. Cell. Proteomics 5, 923–934.

    Article  PubMed  CAS  Google Scholar 

  43. Chi, A., Huttenhower, C., Geer, L. Y. et al. (2007) Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc. Natl. Acad. Sci. USA 104, 2193–2198.

    Article  PubMed  CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, USA

    Robert Chalkley

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  1. Robert Chalkley
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Editor information

Editors and Affiliations

  1. Bart’s and the London School of Medicine, Institute of Cancer, Queen Mary, Universtiy of London, Charterhouse Square, London, EC1M 6BQ, United Kingdom

    Pedro R. Cutillas

  2. , EGA Institute for Women's Health, University College London, Gower Street, London, WC1E 6BT, United Kingdom

    John F. Timms

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Chalkley, R. (2010). Instrumentation for LC-MS/MS in Proteomics. 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_3

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  • DOI: https://doi.org/10.1007/978-1-60761-780-8_3

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-60761-779-2

  • Online ISBN: 978-1-60761-780-8

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