Top-down protein characterization facilitated by ion/ion reactions on a quadrupole/time of flight platform

Proteomics

Volumn 10, Issue 20, 2010, Pages 3577-3588

  Huang, Teng Yi ^a   McLuckey, Scott A ^a  

^a PURDUE UNIVERSITY   (United States)

Author keywords

Electron transfer dissociation; Ion ion reaction; Proton transfer reaction; Quadrupole TOF; Technology; Top down

Indexed keywords

CARBONATE DEHYDRATASE; CYTOCHROME C; INSULIN; MYOGLOBIN; UBIQUITIN;

AMINO ACID SEQUENCE; ELECTRON TRANSPORT; ION CYCLOTRON RESONANCE MASS SPECTROMETRY; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTON TRANSPORT; QUADROPOLE TIME OF FLIGHT MASS SPECTROMETRY; REVIEW; STRUCTURAL PROTEOMICS; TANDEM MASS SPECTROMETRY;

AMINO ACID SEQUENCE; ANIMALS; IONS; MOLECULAR SEQUENCE DATA; PROTEINS; PROTEOMICS; TANDEM MASS SPECTROMETRY;

EID: 78649438767     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201000187     Document Type: Review

References (56)

1. Whitehouse, C. M., Dreyer, R. N., Yamashita, M., Fenn, J. B., Electrospray interface for liquid chromatographs and mass spectrometers. Anal. Chem. 1985, 57, 675-679.
2. Fenn, J. B., Mann, M., Meng, C. K., Wong, S. F., Whitehouse, C. M., Electrospray ionization for mass spectrometry of large biomolecules. Science 1989, 246, 64-71.
3. Kelleher, N. L., Lin, H. Y., Valaskovic, G. A., Aaserud, D. J. et al., Top down versus bottom up protein characterization by tandem high-resolution mass spectrometry. J. Am. Chem. Soc. 1999, 121, 806-812.
4. Kelleher, N. L., Top-down proteomics. Anal. Chem. 2004, 76, 197A-203A.
5. Chait, B. T., Mass spectrometry: bottom-up or top-down? Science 2006, 314, 65-66.
6. McLafferty, F. W., Breuker, K., Jin, M., Han, X. et al., Top-down MS, a powerful complement to the high capabilities of proteolysis proteomics. FEBS J. 2007, 274, 6256-6268.
7. Han, X. M., Jin, M., Breuker, K., McLafferty, F. W., Extending top-down mass spectrometry to proteins with masses greater than 200 kilodaltons. Science 2006, 314, 109-112.
8. Horn, D. M., Zubarev, R. A., McLafferty, F. W., Automated de novo sequencing of proteins by tandem high-resolution mass spectrometry. Proc. Natl.Acad. Sci. USA2000, 97, 10313-10317.
9. Ge, Y., Lawhorn, B. G. E. I., Naggar, M., Strauss, E. et al., Top down characterization of larger proteins (45 kDa) by electron capture dissociation mass spectrometry. J. Am. Chem. Soc. 2000, 124, 672-678.
10. Sze, S. K., Ge, Y., Oh, H. B., McLafferty, F. W., Top down mass spectrometry of a 29 kDa protein for characterization of any posttranslational modification to within one residue. Proc. Natl. Acad. Sci. USA 2002, 99, 1774-1779.
11. Loo, J. A., Edmonds, C. G., Smith, R. D., Primary sequence information from intact proteins by electrospray ionization tandem mass spectrometry. Science 1990, 248, 201-204
12. Carroll, J., Altman, M. C., Fearnley, I. M., Walker, J. E., Identification of membrane proteins by tandem mass spectrometry of protein ions. Proc. Natl. Acad. Sci. USA 2007, 102, 9463-9468.
13. Nemeth-Cawley, J. F., Tangarone, B. S., Rouse, J. C., "Top Down" characterization is a complementary technique to peptide sequencing for identifying protein species in complex mixtures. J. Proteome Res. 2003, 2, 495-505.
14. Ginter, J. M., Zhou, F., Johnston, M. V., Generating protein sequence tags by combining cone and conventional collision induced dissociation in a quadrupole time-of-flight mass spectrometer. J.Am. Soc. MassSpectrom. 2004, 15, 1478-1486.
15. Macek, B., Waanders, L. F., Olsen, J. V., Mann, M., Topdown protein sequencing and MS3 on a hybrid linear quadrupole ion trap-orbitrap mass spectrometer. Mol. Cell. Proteomics 2006, 5, 949-958.
16. Pitteri, S. J., McLuckey, S. A., Recent developments in the ion/ion chemistry of high-mass multiply charged ions. Mass Spectrom. Rev. 2005, 26, 931-958.
17. McLuckey, S. A., Huang, T. Y., Ion/ion reactions: new chemistry for analytical MS. Anal. Chem. 2009, 81, 8669-8676.
18. Stephenson Jr, J. L., McLuckey, S. A., Ion/ion reactions for oligopeptide mixture analysis: Application to mixtures comprised of 0.5-100 kDa components. J. Am. Soc. Mass Spectrom 1998, 9, 585-596.
19. Stephenson Jr, J. L., McLuckey, S. A., Ion/ion proton transfer reactions for protein mixture analysis. Anal. Chem. 1996, 68, 4026-4032.
20. Hogan, J. M., McLuckey, S. A., Charge state dependent collision-induced dissociation of native and reduced porcine elastase. J. Mass Spectrom. 2003, 38, 245-256.
21. Stephenson Jr, J. L., McLuckey, S. A., Simplification of product ion spectra derived from multiply-charged parent ions via ion/ion chemistry. Anal. Chem. 1998, 70, 3533-3544.
22. He, M., Reid, G. E., Shang, H., Lee, G. U., McLuckey, S. A., Dissociation of multiple protein ion charge states following a single gas-phase purification and concentration procedure. Anal. Chem. 2002, 74, 4653-4661.
23. Amunugama, R., Hogan, J. M., Newton, K. A., McLuckey, S. A., Whole protein dissociation in a quadrupole ion trap: Identification of an a priori unknown modified protein. Anal. Chem. 2004, 76, 720-727.
24. Coon, J. J., Ueberheide, B., Syka, J. E. P., Dryhurst, D. D. et al., Protein identification using sequential ion/ion reactions and tandem mass spectrometry. Proc. Natl. Acad. Sci. USA 2005, 102, 9463-9468.
25. Liu, J., Huang, T. Y., McLuckey, S. A., Top-down protein identification/characterization of a priori unknown proteins via ion trap collision-induced dissociation and ion/ion reactions in a quadrupole/time-of-flight tandem mass spectrometer. Anal. Chem. 2009, 81, 1433-1441.
26. McLuckey, S. A., Reid, G. E., Wells, J. M., Ion parking during ion/ion reactions in electrodynamic ion traps. Anal. Chem. 2002, 74, 336-346.
27. Reid, G. E., Shang, H., Hogan, J. M., Lee, G. U., McLuckey, S. A., Gas-phase concentration, purification, and identification of whole proteins from complex mixtures. J. Am. Chem. Soc. 2002, 124, 7353-7362.
28. Reid, G. E., Wells, J. M., Badman, E. R., McLuckey, S. A., Performance of a quadrupole ion trap mass spectrometer adapted for ion/ion reaction studies. Int. J. Mass Spectrom. 2003, 222, 243-258.
29. Chrisman, P. A., Pitteri, S. J., McLuckey, S. A., Parallel ion parking: Improving conversion of parents to first-generation products in electron transfer dissociation. Anal. Chem. 2005, 77, 3411-3414.
30. He, M., McLuckey, S. A., Two ion/ion charge inversion steps to form a doubly protonated peptide from a singly protonated peptide in the gas phase. J. Am. Chem. Soc. 2003, 125, 7756-7757.
31. He, M., McLuckey, S. A., Increasing the negative charge of a macroanion in the gas phase via sequential charge inversion reactions. Anal. Chem. 2004, 76, 4189-4192.
32. He, M., Emory, J. F., McLuckey, S. A., Reagent anions for charge inversion of polypeptide/protein cations in the gas phase. Anal. Chem. 2005, 77, 3173-3182.
33. Gunawardena, H. P., Emory, J. F., McLuckey, S. A., Phosphopeptide anion characterization via sequential charge inversion and electron-transfer dissociation. Anal. Chem. 2006, 78, 3788-3793.
34. Payne, A. H., Glish, G. L., Gas-phase ion/ion interactions between peptides or proteins and iron ions in a quadrupole ion trap. Int. J. Mass Spectrom. 2001, 204, 47-54.
35. Newton, K. A., McLuckey, S. A., Gas-phase peptide/protein cationizing agent switching via ion/ion reactions. J. Am. Chem. Soc. 2003, 125, 12404-12405.
36. Newton, K. A., McLuckey, S. A., Generation and manipulation of sodium cationized peptides in the gas phase. J. Am. Soc. Mass Spectrom. 2004, 15, 607-615.
37. Newton, K. A., He, M., Amunugama, R., McLuckey, S. A., Selective cation removal from gaseous polypeptide ions: proton vs. sodium ion abstraction via ion/ion reactions. Phys. Chem. Chem. Phys. 2004, 6, 2710-2717.
38. Gunawardena, H. P., O'Hair, R. A. J., McLuckey, S. A., Selective disulfide bond cleavage in gold(I) cationized polypeptide ions formed via gas-phase ion/ion cation switching. J. Proteome. Res. 2006, 5, 2087-2092.
39. Syka, J. E. P., Coon, J. J., Schroeder, M. J., Shabanowitz, J. et al., Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. USA 2004, 101, 9528-9533.
40. Coon, J. J., Collisions or Electrons? Protein Sequence Analysis in the 21st Century. Anal. Chem. 2009, 81, 3208-3215.
41. Han, H., Xia, Y., Yang, M., McLuckey, S. A., Rapidly alternating transmission mode electron-transfer dissociation and collisional activation for the characterization of polypeptide ions. Anal. Chem. 2008, 80, 3492-3497.
42. Reid, G. E., McLuckey, S. A., 'Top down' protein characterization via tandem mass spectrometry. J. Mass Spectrom. 2002, 37, 663-675.
43. Stephenson, J. L., McLuckey, S. A., Reid, G. E., Wells, J. M. et al., Ion/ion chemistry as a top-down approach for protein analysis. Curr. Opin. Biotechnol. 2002, 13, 57-64.
44. Bowers, J. J., Liu, J., Gunawardena, H. P., McLuckey, S. A., Protein identification via ion-trap collision-induced dissociation and examination of low-mass product ions. J. Mass Spectrom. 2008, 43, 23-34.
45. Bunger, M. K., Cargile, B. J., Ngunjiri, A., Bundy, J. L., Stephenson, J. L., Automated proteomics of E. coli via topdown electron-transfer dissociation mass spectrometry. Anal. Chem. 2008, 80, 1459-1467.
46. Liu, J., Chrisman, P. A., Erickson, D. E., McLuckey, S. A., Relative information content and top-down proteomics by mass spectrometry: utility of ion/ion proton-transfer reactions in electrospray-based approaches. Anal. Chem. 2007, 79, 1073-1081.
47. Xia, Y., Chrisman, P. A., Erickson, D. E., Liu, J. et al., Implementation of ion/ion reactions in a quadrupole/time-of-flight tandem mass spectrometer. Anal. Chem. 2006, 78, 4146-4154.
48. Xia, Y., X. Liang, X., McLuckey, S. A., Pulsed dual electrospray ionization for ion/ion reactions. J. Am. Soc. Mass Spectrom. 2005, 16, 1750-1756.
49. Liang, X., Xia, Y., McLuckey, S. A., Alternately pulsed nanoelectrospray ionization/atmospheric pressure chemical ionization for ion/ion reactions in an electrodynamic ion trap. Anal. Chem. 2006, 78, 3208-3212.
50. Chanthamontri, C., Liu, J., McLuckey, S. A., Charge state dependent fragmentation of gaseous alpha-synuclein cations via ion trap and beam-type collisional activation. Int. J. Mass Spectrom. 2009, 283, 9-16.
51. Xia, Y., Han, H., McLuckey, S. A., Activation of intact electron-transfer products of polypeptides and proteins in cation transmission mode ion/ion reactions. Anal. Chem. 2008, 80, 1111-1117.
52. Han, H., Londry, F. A., Erickson, D. E., McLuckey, S. A., Tailored-waveform collisional activation of peptide ion electron transfer survivor ions in cation transmission mode ion/ion reaction experiments. Analyst 2009, 134, 681-689.
53. Xia, Y., Thomson, B. A., McLuckey, S. A., Bidirectional ion transfer between quadrupole arrays: MSn ion/ion reaction experiments on a quadrupole/time-of-flight tandem mass spectrometer. Anal. Chem. 2007, 79, 8199-8206.
54. Liang, X., Hager, J. W., McLuckey, S. A., Transmission mode ion/ion electron-transfer dissociation in a linear ion trap. Anal. Chem. 2007, 79, 3363-3370.
55. Emory, J. F., Hassell, K. H., Londry, F. A., McLuckey, S. A., Transmission mode ion/ion reactions in the radiofrequencyonly ion guide of hybrid tandem mass spectrometers. Rapid Commun. Mass Spectrom. 2009, 23, 409-418.
56. Liu, J., Huang, T. Y., McLuckey, S. A., Simultaneous transmission mode collision-induced dissociation and ion/ion reactions for top-down protein identification/characterization using a quadrupole/time-of-flight tandem mass spectrometer. Anal. Chem. 2009, 81, 2159-2167.