Application of FT-ICR MS for the study of protein complexes

Applied Spectroscopy Reviews

Volumn 44, Issue 3, 2009, Pages 231-244

  Liu, Yaqin ^a,b   Pan, Yuanjiang ^a  

^a ZHEJIANG UNIVERSITY   (China)

^b ZHEJIANG UNIVERSITY   (China)

Author keywords

Electron capture dissociation; Electrospray ionization; Fourier transform ion cyclotron resonance mass spectrometry; Protein complexes

Indexed keywords

AMINES; BINDING ENERGY; BINDING SITES; CYCLOTRONS; DISSOCIATION; ELECTRON CYCLOTRON RESONANCE; ELECTROSPRAY IONIZATION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; IONIZATION; IONS; MASS SPECTROMETERS; MASS SPECTROMETRY; NUCLEIC ACIDS; PLASMAS; RESONANCE; SPECTRUM ANALYSIS; STOICHIOMETRY;

BIOLOGICAL SAMPLES; ELECTRON CAPTURE DISSOCIATION; FOURIER TRANSFORM ION CYCLOTRON RESONANCE MASS SPECTROMETRY; FT-ICR MS; ION MANIPULATIONS; MASS ACCURACIES; PEPTIDE COMPLEXES; PROTEIN COMPLEXES; PROTEIN-NUCLEIC ACIDS; PROTEIN-PROTEIN COMPLEXES; RESOLVING POWER; TANDEM MASS SPECTROMETRIES;

FOURIER TRANSFORMS;

EID: 62349126177     PISSN: 05704928     EISSN: 1520569X     Source Type: Journal    
DOI: 10.1080/05704920902717880     Document Type: Review

References (66)

1. Comisarow, M. B. and Marshall, A. G. (1974) Fourier transform ion cyclotron resonance. Chem. Phys. Lett., 25, pp. 282-283.
2. Comisarow, M. B. and Marshall, A. G. (1974) Frequency-sweep Fourier transform ion cyclotron resonance spectroscopy. Chem. Phys. Lett., 26, pp. 489-490.
3. Cottingham, K. (2006) FTMS: Overcoming challenges. Anal. Chem., 78, pp. 655-657.
4. Marshall, A. G. and Hendrickson, C. L. (1998) Fourier transform ion cyclotron resonance mass spectrometry: A primer. Spectrom. Rev., 17, pp. 1-35.
5. Jensen, P. K. (1998) Probing proteomes using capillary isoelectric focusing-electrospray ionization Fourier fransform ion cyclotron resonance mass spectrometry. Anal. Chem., 71, pp. 2076-2084.
6. Loo, J. A. (1997) Studying noncovalent protein complexes by electrospray ionization mass spectrometry. Mass Spectrom. Rev., 16, pp. 1-23.
7. Loo, J. A. (2000) Electrospray ionization mass spectrometry: A technology for studying noncovalent macromolecular complexes. Int. J. Mass Spectrom., 200, pp. 175-186.
8. Heck, A. J. and Van Den Heuvel, R.H. (2004) Investigation of intact protein complexes by mass spectrometry. Mass Spectrom. Rev., 23, pp. 368-389.
9. Sihlbom, C. (2006) Mass Spectrometry for Comparative Proteomics of Degenerative and Regenerative Processes in the Brain, Vasastadens Bokbinderi AB Press, Goteborg, Sweden
10. Yamashita, M. and Fenn, J. B. (1984) Electrospray ion source. Another variation on the free-jet theme. J. Phys. Chem., 88, pp. 4451-4459.
11. Yamashita, M. and Fenn, J. B. (1984) Negative ion production with the electrospray ion source. J. Phys. Chem., 88, pp. 4671-4675.
12. 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, pp. 64-71.
13. Karas, M. and Hillenkamp, F. (1988) Laser desorption ionization of proteins with molecular masses exceeding 10,000 Daltons. Anal. Chem., 60, pp. 2299-2301.
14. Tanaka, K., Waki, H., Ido, Y., Akita, S., Yoshida, Y. and Yohida, T. (1988) Protein and polymer analyses up to m/z 100,000 by laser ionization time-of-flight mass spectrometry. Rapid Comm. Mass Spectrom., 2, pp. 151-153.
15. Oda, Y., Nagasu, T. and Chait, B. T. (2001) Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome. Nat. Biotechnol., 19, pp. 379-382.
16. Deng, Y. and Smith, D. L. (1999) Hydrogen exchange demonstrates three domains in aldolase unfold sequentially. J. Mol. Biol., 294, pp. 247-258.
17. Gygi, S. P., Rist, B. and Aebersold, R. (2000) Measuring gene expression by quantitative proteome analysis. Curr. Opin. Biotechnol., 11, pp. 396-401.
18. Aquilina, J. A., Benesch, J. L. P., Bateman, O. A., Slingsby, C. and Robinson, C. V. (2003) Polydispersity of a mammalian chaperone: Mass spectrometry reveals the population of oligomers in α B-crystallin. Proc. Natl. Acad. Sci., 100, pp. 10611-10616.
19. Sobott, F. and Robinson, C. V. (2002) Protein complexes gain momentum. Curr. Opin. Struct. Biol., 12, pp. 729-734.
20. Turner, K. B. and Hagan, N. A. (2006) Mapping noncovalent ligand binding to stemloop domains of the HIV-1 packaging signal by tandem mass spectrometry. J. Am. Soc. Mass Spectrom., 17, pp. 1401-1411.
21. Yu, Y. H. and Sweeney, M. D. (2006) Potential inhibitors of chemokine function: Analysis of noncovalent complexes of chemokine and small polyanionic molecules by ESI FT-ICR mass spectrometry. J. Am. Soc. Mass Spectrom., 17, pp. 524-535.
22. Yamada, N. and Suzuki, E. (2002) Identification of the interface of a large protein-protein complex using H/D exchange and Fourier transform ion cyclotron resonance mass spectrometry. Rapid Comm. Mass Spectrom., 16, pp. 293-299.
23. Ganem, B., Li, Y. T. and Henion, J. D. (1991) Detection of noncovalent receptor-ligand complexes by mass spectrometry. J. Am. Chem. Soc., 113, pp. 6294-6296.
24. Hofstadler, S. A., Sannes-Lowery, K. A. and Hannis, J. C. (2005) Analysis of nucleic acids by FTICR MS. Mass Spectrom. Rev., 24, pp. 265-285.
25. Smith, R. D., Bruce, J. E., Wu, Q. and Lei, Q. P. (1997) New mass spectrometric methods for the study of noncovalent associations of biopolymers. Chem. Soc. Rev., 26, pp. 191-202.
26. Pramanik, B. N., Bartner, P. L., Mirza, U. A., Liu, Y. H. and Ganguly, A. K. (1998) Electrospray ionization mass spectrometry for the study of non-covalent complexes: An emerging technology. J. Mass Spectrom., 33, pp. 911-920.
27. Miranker, A. D. (2000) Protein complexes and analysis of their assembly by mass spectrometry. Curr. Opin. Struct. Biol., 10, pp. 601-606.
28. Hofstadler, S. A. and Griffey, R. H. (2001) Analysis of noncovalent complexes of DNA and RNA by mass spectrometry. Chem. Rev., 101, pp. 377-390.
29. Beck, J. L., Colgrave, M. L., Ralph, S. F. and Sheil, M. M. (2001) Electrospray ionization mass spectrometry of oligonucleotide complexes with drugs, metals, and proteins. Mass Spectrom. Rev., 20, pp. 61-87.
30. Akashi, S. (2006) Investigation of molecular interaction within biological macromolecular complexes by mass spectrometry. Med. Res. Rev., 26, pp. 339-368.
31. Zubarev, R. A., Kelleher, N. L. and McLafferty, F. W. (1998) Electron capture dissociation of multiply charged protein cations. A nonergodic process. J. Am. Chem. Soc., 120, pp. 3265-3266.
32. Horn, D. M., Zubarev, R. A. and McLafferty, F. W. (2000) Automated de novo sequencing of proteins by tandem high-resolution mass spectrometry. Proc. Natl. Acad. Sci., 97, pp. 10313-10317.
33. Ge, Y., Lawhorn, B. G., ElNaggar, M., Strauss, E., Park, J. H., Begley, T. P. and McLafferty, F. W. (2002) Top down characterization of larger proteins (45 kDa) by electron capture dissociation mass spectrometry. J. Am. Chem. Soc., 124, pp. 672-678.
34. 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, pp. 126-134.
35. Shi, S. D., Hemling, M. E., Carr, S. A., Horn, D. M., Lindh, I. and McLafferty, F. W. (2001) Phosphopeptide/phosphoprotein mapping by electron capture dissociation mass spectrometry. Anal. Chem., 73, pp. 19-22.
36. Xie, Y., Zhang, J., Yin, S. and Loo, J. A. (2006) Top-down ESI-ECD-FT-ICR mass spectrometry localizes noncovalent protein-ligand binding sites. J. Am. Chem. Soc., 128, pp. 14432-14433.
37. Zubarev, R. A. (2004) Electron-capture dissociation tandem mass spectrometry. Curr. Opin. Biotechnol., 15, pp. 12-16.
38. Cooper, H. J., Hakansson, K. and Marshall, A. G. (2005) The role of electron capture dissociation in biomolecular analysis. Mass Spectrom. Rev., 24, pp. 201-222.
39. Marshall, A. G., Wang, T. C. L. and Ricca, T. L. (1985) Tailored excitation for Fourier-transform ion-cyclotron resonance mass spectrometry. J. Am. Chem. Soc., 107, p. 7893.
40. Guan, S. H. and Marshall, A. G. (1996) Stored waveform inverse Fourier transform (SWIFT) ion excitation in trapped-ion mass spectrometry: Theory and applications. Int. J. Mass Spectrom., 158, pp. 5-37.
41. Wigger, M. and Eyler, J. R. (2002) Fourier transform-ion cyclotron resonance mass spectrometric resolution, identification, and screening of non-covalent complexes of Hck Src homology 2 domain receptor and ligands from a 324-member peptide combinatorial library. J. Am. Soc. Mass Spectrom., 13, pp. 1162-1169.
42. Rappsilber, J., Siniossoglou, S., Hurt, E. C. and Mann, M. A. (2000) Generic strategy to analyze the spatial organization of multi-protein complexes by cross-linking and mass spectrometry. Anal. Chem., 72, pp. 267-275.
43. Kalkhof, S., Ihling, C., Mechtler, K. and Sinz, A. (2005) Chemical cross-linking and high-performance Fourier transform ion cyclotron resonance mass spectrometry for protein interaction analysis: Application to a calmodulin/target peptide complex. Anal. Chem., 77, pp. 495-503.
44. Schulz, D. M., Ihling, C., Clore, G. M. and Sinz, A. (2004) Mapping the topology and determination of a low-resolution three-dimensional structure of the calmodulin-melittin complex by chemical cross-linking and high-resolution FTICRMS: Direct demonstration of multiple binding modes. Biochemistry, 43, pp. 4703-4715.
45. Schmidt, A., Kalkhof, S., Ihling, C., Cooper, D. M. and Sinz, A. (2005) Mapping protein interfaces by chemical cross-linking and FTICR mass spectrometry: Application to a calmodulin/adenylyl cyclase 8 peptide complex. Eur. J. Mass Spectrom., 11, pp. 524-534.
46. Ihling, C., Schmidt, A., Kalkhof, S., Stingl, C., Mechtler, K., Haack, M., Schulz, D. M., Cooper, D. M., Beck-Sickinger, A. G. and Sinz, A. (2006) Isotope-labeled cross-linkers and Fourier transform ion cyclotron resonance mass spectrometry for structural analysis of a protein/peptide complex. J. Am. Soc. Mass Spectrom., 17, pp. 1100-1113.
47. Hofstadler, S. A. (1999) Multiplexed screening of neutral mass-tagged RNA targets against ligand libraries with electrospray ionization FTICR MS: A paradigm for high-throughput affinity screening. Anal. Chem., 71, pp. 3436-3440.
48. Sannes-Lowery, K. A., Drader, J. J., Griffey, R. H. and Hofstadler, S. A. (2000) Fourier transform ion cyclotron resonance mass spectrometry as a high throughput affinity screen to identify RNA binding ligands. Trends Anal. Chem., 19, pp. 481-491.
49. Hofstadler, S. A. and Griffey, R. H. (2000) Mass spectrometry as a drug discovery platform against RNA targets. Curr. Opin. Drug Discov. Dev., 3, pp. 423-431.
50. Bearss, D. J., Hurley, L. H. and Von Hoff, D. D. (2000) Telomere maintenance mechanisms as a target for drug development. Oncogene, 19, pp. 6632-6641.
51. Sannes-Lowery, K. A. (2004) High throughput drug discovery with ESI-FTICR. Int. J. Mass Spectrom., 238, pp. 197-206.
52. Hanson, C. L. and Robinson, C. V. (2004) Protein-nucleic acid interactions and the expanding role of mass spectrometry. J. Biol. Chem., 279, pp. 24907-24910.
53. Mazzitelli, C. L. and Brodbelt, J. S. (2006) Evaluation of binding of perylene diimide and benzannulated perylene diimide ligands to DNA by electrospray ionization mass spectrometry. J. Am. Soc. Mass Spectrom., 17, pp. 593-604.
54. Cheng, X., Harms, A. C., Goudreau, P. N., Terwilliger, T. C. and Smith, R. D. (1996) Direct measurement of oligonucleotide binding stoichiometry of gene V protein by mass spectrometry. Proc. Natl. Acad. Sci., 93, pp. 7022-7027.
55. Yu, E. and Fabris, D. (2003) Direct probing of RNA structures and RNA-protein interactions in the HIV-1 packaging signal by chemical modification and electrospray ionization Fourier transform mass spectrometry. J. Mol. Biol., 330, pp. 211-223.
56. Yu, E. and Fabris, D. (2004) Toward multiplexing the application of solvent accessibility probes for the investigation of RNA three-dimensional structures by electrospray ionization-Fourier transform mass spectrometry. Anal. Biochem., 334, pp. 356-366.
57. Fisher, R. J., Fivash, M. J., Stephen, A. G., Hagan, N. A., Shenoy, S. R., Medaglia, M. V., Smith, L. R., Worthy, K. M., Simpson, J. T., Shoemaker, R., McNitt, K. L., Johnson, D. G., Hixson, C. V., Gorelick, R. J., Fabris, D., Henderson, L. E. and Rein, A. (2006) Complex interactions of HIV-1 nucleocapsid protein with oligonucleotides. Nucleic Acids Res., 34, pp. 472-484.
58. Zhang, J. H., Schubothe, K., Li, B. S., Russell, S. and Lebrilla, C. B. (2005) Infrared multiphoton dissociation of O-linked mucin-type oligosaccharides. Anal. Chem., 77, pp. 208-214.
59. Yu, Y. H. and Sweeney, M. D. (2005) Chemokine-glycosaminoglycan binding: Specificity for CCR2 ligand binding to highly sulfated oligosaccharides using FTICR mass spectrometry. J. Biol. Chem., 280, pp. 32200-32208.
60. Sweeney, M. D., Yu, Y. H. and Leary, J. A. (2006) Effects of sulfate position on heparin octasaccharide binding to CCL2 examined by tandem mass spectrometry. J. Am. Soc. Mass Spectrom., 17, pp. 1114-1119.
61. Mormann, M. and Zamfir, A. D. (2007) Analysis of oversulfation in a chondroitin sulfate oligosaccharide fraction from bovine aorta by nanoelectrospray ionization quadrupole time-of-flight and FT-ICR mass spectrometry. J. Am. Soc. Mass Spectrom., 18, pp. 179-187.
62. Seipert, R. R., Barboza, M., LoCascio, R. G., Mills, D. A., Freeman, S. L., German, J. B. and Lebrilla, C. B. (2008) Analysis and quantitation of fructooligosaccharides using matrix-assisted laser desorption/ ionization Fourier transform ion cyclotron resonance mass spectrometry. Anal. Chem., 80, pp. 159-165.
63. Akashi, S. and Takio, K. (2000) Characterization of the interface structure of enzyme-inhibitor complex by using hydrogen-deuterium exchange and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. Protein Sci., 9, pp. 2497-2505.
64. Gao, H. and Leary, J. (2007) Noncovalent complexes of APS reductase from M. tuberculosis: Delineating a mechanistic model using ESI-FTICR MS. J. Am. Soc. Mass Spectrom., 18, pp. 167-178.
65. Cooper, H. J. and Case, M. A. (2003) Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometric analysis of metal-ion selected dynamic protein libraries. J. Am. Chem. Soc., 125, pp. 5331-5339.
66. Fagerquist, C. K. (2003) An Antibiotic linked to peptides and proteins is released by electron capture dissociation Fourier transform ion cyclotron resonance mass spectrometry. J. Am. Soc. Mass Spectrom., 14, pp. 302-310.