Achievements and perspectives of top-down proteomics

Proteomics

Volumn 10, Issue 20, 2010, Pages 3566-3576

  Armirotti, Andrea ^a   Damonte, Gianluca ^b,c  

^a ADVANCED BIOTECHNOLOGY CENTER   (Italy)

^b UNIVERSITY OF GENOA   (Italy)

^c Center of Excellence for Biomedical Research   (Italy)

Author keywords

ESI; LC MS; MALDI; Phosphorylation; Technology; Top down

Indexed keywords

PROTEIN; SUPEROXIDE DISMUTASE;

AMINO ACID SEQUENCE; COLLISIONALLY ACTIVATED DISSOCIATION; ELECTRON; ELECTRON CAPTURE DETECTION; ELECTRON TRANSPORT; ELECTROSPRAY MASS SPECTROMETRY; ION CYCLOTRON RESONANCE MASS SPECTROMETRY; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN PHOSPHORYLATION; PROTEIN POLYMORPHISM; PROTEOMICS; PROTON TRANSPORT; REVERSED PHASE HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; REVIEW;

AMINO ACID SEQUENCE; HISTORY, 21ST CENTURY; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; PROTEINS; PROTEOMICS;

EID: 78649406605     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201000245     Document Type: Review

References (77)

1. 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.
2. Loo, J. A., Edmonds, C. G., Smith, R. D., Tandem mass spectrometry of very large molecules: serum albumin sequence information from multiply charged ions formed by electrospray ionization. Anal. Chem. 1991, 63, 2488-2499.
3. Mortz, E., O'Connor, P. B., Roepstorff, P., Kelleher, N. L. et al., Sequence tag identification of intact proteins by matching tanden mass spectral data against sequence data bases. Proc. Natl. Acad. Sci. USA 1996, 93, 8264-8267.
4. Sze, S. K., Ge, Y., Oh, H., 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.
5. Zubarev, R. A., Horn, D. M., Fridriksson, E. K., Kelleher, N. L. et al., Electron capture dissociation for structural characterization of multiply charged protein cations. Anal. Chem. 2000, 72, 563-573.
6. Armirotti, A., Bottom-Up Proteomics. Curr. Anal. Chem. 2009, 5, 116-130.
7. Blackburn, K., Goshe, M. B., Mass spectrometry bioinformatics: tools for navigating the proteomics landscape. Curr. Anal. Chem. 2009, 5, 131-143.
8. Delahunty, C. M., Yates 3rd, J. R., MudPIT: multidimensional protein identification technology. Biotechniques 2007, 43, 563, 565, 567 passim.
9. Kislinger, T., Gramolini, A. O., MacLennan, D. H., Emili, A., Multidimensional protein identification technology (MudPIT): technical overview of a profiling method optimized for the comprehensive proteomic investigation of normal and diseased heart tissue. J. Am. Soc. Mass Spectrom. 2005, 16, 1207-1220.
10. Perkel, J. M., iTRAQ gets put to the test. J. Proteome Res. 2009, 8, 4885.
11. Barnidge, D. R., Hall, G. D., Stocker, J. L., Muddiman, D. C., Evaluation of a cleavable stable isotope labeled synthetic peptide for absolute protein quantification using LC-MS/MS. J. Proteome Res. 2004, 3, 658-661
12. Gruhler, S., Kratchmarova, I., Stable isotope labeling by amino acids in cell culture (SILAC). Methods Mol. Biol. 2008, 424, 101-111.
13. Ramus, C., Gonzalez de Peredo, A., Dahout, C., Gallagher, M. et al., An optimized strategy for ICAT quantification of membrane proteins. Mol. Cell. Proteomics 2006, 5, 68-78.
14. Wang, C. I., Lewis, R. J., Emerging structure-function relationships defining monoamine NSS transporter substrate and ligand affinity. Biochem. Pharmacol. 2010, 79, 1083-1091.
15. Servent, D., Fruchart-Gaillard, C., Muscarinic toxins: tools for the study of the pharmacological and functional properties of muscarinic receptors. J. Neurochem. 2009, 109, 1193-1202.
16. Park, Y., Lee, I. S., Joo, E. J., Hahn, B. S. et al., A novel and one-step purification of human ceruloplasmin by acharan sulfate affinity chromatography. Arch. Pharmacal. Res. 2009, 32, 693-698.
17. Zvonok, N., Williams, J., Johnston, M., Pandarinathan, L. et al., Full mass spectrometric characterization of human monoacylglycerol lipase generated by large-scale expression and single-step purification. J. Proteome Res. 2008, 7, 2158-2164.
18. Echan, L. A., Tang, H. Y., Ali-Khan, N., Lee, K. et al., Depletion of multiple high-abundance proteins improves protein profiling capacities of human serum and plasma. Proteomics 2005, 5, 3292-3303.
19. Cohen, S. L., Chait, B. T., Mass spectrometry of whole proteins eluted from sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels. Anal. Biochem. 1997, 247, 257-267.
20. Morris, D. L., Sutton, J. N., Harper, R. G., Timperman, A. T., Reversed-phase HPLC separation of human serum employing a novel saw-tooth gradient: toward multidimensional proteome analysis. J. Proteome Res. 2004, 3, 1149-1154.
21. Tran, J. C., Doucette, A. A., Gel-eluted liquid fraction entrapment electrophoresis: an electrophoretic method for broad molecular weight range proteome separation. Anal. Chem. 2008, 80, 1568-1573.
22. Tran, J. C., Doucette, A. A., Multiplexed size separation of intact proteins in solution phase for mass spectrometry. Anal. Chem. 2009, 81, 6201-6209.
23. Meng, F. Y., Cargile, B. J., Patrie, S. M., Johnson, J. R. et al., Processing complex mixtures of intact proteins for direct analysis by mass spectrometry. Anal. Chem. 2002, 74, 2923-2929.
24. Zhang, Z. Q., Shah, B., Characterization of variable regions of monoclonal antibodies by top-down mass spectrometry. Anal. Chem. 2007, 79, 5723-5729.
25. Du, Y., Meng, F. Y., Patrie, S. M., Miller, L. M. et al., Improved molecular weight-based processing of intact proteins for interrogation by quadrupole-enhanced FT MS/MS. J. Proteome Res. 2004, 3, 801-806.
26. Millea, K. M., Krull, I. S., Cohen, S. A., Gebler, J. C. et al., Integration of multidimensional chromatographic protein separations with a combined "top-down" and "bottom-up" proteomic strategy. J. Proteome Res. 2006, 5, 135-146.
27. Simpson, D. C., Ahn, S., Pasa-Tolic, L., Bogdanov, B. et al., Using size exclusion chromatography-RPLC and RPLC-CIEF as two-dimensional separation strategies for protein profiling. Electrophoresis 2006, 27, 2722-2733.
28. Geng, X. D., Ke, C. Y., Chen, G., Liu, P. et al., On-line separation of native proteins by two-dimensional liquid chromatography using a single column. J. Chromatogr. A 2009, 1216, 3553-3562.
29. Patrie, S. M., Ferguson, J. T., Robinson, D. E., Whipple, D. et al., Top down mass spectrometry of o60-kDa proteins from Methanosarcina acetivorans using quadrupole FRMS with automated octopole collisionally activated dissociation. Mol. Cell. Proteomics 2006, 5, 14-25.
30. Whitelegge, J., Tandem mass spectrometry of integral membrane proteins for top-down proteomics. Trac-Trends Anal. Chem. 2005, 24, 576-582.
31. Lee, J. E., Kellie, J. F., Tran, J. C., Tipton, J. D. et al., A robust two-dimensional separation for top-down tandem mass spectrometry of the low-mass proteome. J. Am. Soc. Mass Spectrometry 2009, 20, 2183-2191.
32. Sheng, S., Chen, D., Van Eyk, J. E., Multidimensional liquid chromatography separation of intact proteins by chromatographic focusing and reversed phase of the human serum proteome - optimization and protein database. Mol. Cell. Proteomics 2006, 5, 26-34.
33. Zabrouskov, V., Han, X. M., Welker, E., Zhai, H. L. et al., Stepwise deamidation of ribonuclease A at five sites determined by top down mass spectrometry. Biochemistry 2006, 45, 987-992.
34. Bogdanov, B., Smith, R. D., Proteomics by FTICR mass spectrometry: top down and bottom up. Mass Spectrom. Rev. 2005, 24, 168-200.
35. Perry, R. H., Cooks, R. G., Noll, R. J., Orbitrap mass spectrometry: instrumentation, ion motion and applications. Mass Spectrom. Rev. 2008, 27, 661-699.
36. Suckau, D., Resemann, A., MALDI Top-Down sequencing: calling N- and C-terminal protein sequences with high confidence and speed. J. Biomol. Tech. 2009, 20, 258-262.
37. Demeure, K., Quinton, L., Gabelica, V., De Pauw, E., Rational selection of the optimum MALDI matrix for top-down proteomics by in-source decay. Anal. Chem. 2007, 79, 8678-8685.
38. Wang, J., Yang, S. C., Wu, S. M., Wang, H. X. et al., Application of PSD-MALDI-TOF-MS to protein identification. Yao Xue Xue Bao 2004, 39, 627-630.
39. Yoo, C., Suckau, D., Sauerland, V., Ronk, M. et al., Toward top-down determination of PEGylation site using MALDI insource decay MS analysis. J. Am. Soc. Mass Spectrom. 2009, 20, 326-333.
40. Suckau, D., Resemann, A., Schuerenberg, M., Hufnagel, P. et al., A novel MALDI LIFT-TOF/TOF mass spectrometer for proteomics. Anal. Bioanal. Chem. 2003, 376, 952-965.
41. Armirotti, A., Millo, E., Damonte, G., How to discriminate between leucine and isoleucine by low energy ESI-TRAP MSn. J. Am. Soc. Mass Spectrom. 2007, 18, 57-63
42. Zubarev, R. A., Electron-capture dissociation tandem mass spectrometry. Curr. Opin. Biotechnol. 2004, 15, 12-16.
43. Coon, J. J., Collisions or electrons? Protein sequence analysis in the 21st century. Anal. Chem. 2009, 81, 3208-3215.
44. Kelleher, N. L., Zubarev, R. A., Bush, K., Furie, B. et al., Localization of labile posttranslational modifications by electron capture dissociation: the case of gamma-carboxyglutamic acid. Anal. Chem. 1999, 71, 4250-4253.
45. Mirgorodskaya, E., Roepstorff, P., Zubarev, R. A., Localization of O-glycosylation sites in peptides by electron capture dissociation in a Fourier transform mass spectrometer. Anal. Chem. 1999, 71, 4431-4436.
46. McLafferty, F. W., Horn, D. M., Breuker, K., Ge, Y. et al., Electron capture dissociation of gaseous multiply charged ions by Fourier-transform ion cyclotron resonance. J. Am. Soc. Mass Spectrom. 2001, 12, 245-249.
47. Mikesh, L. M., Ueberheide, B., Chi, A., Coon, J. J. et al., The utility of ETD mass spectrometry in proteomic analysis. Biochim. Biophys. Acta-Proteins Proteomics 2006, 1764, 1811-1822.
48. Riter, L. S., Gooding, K. M., Hodge, B. D., Julian Jr, R. K., Comparison of the Paul ion trap to the linear ion trap for use in global proteomics. Proteomics 2006, 6, 1735-1740.
49. McLafferty, F. W., Breuker, K., Jin, M., Han, X. et al., Topdown MS, a powerful complement to the high capabilities of proteolysis proteomics. FEBS J. 2007, 274, 6256-6268.
50. Armirotti, A., Benatti, U., Damonte, G., Top-down proteomics with a quadrupole time-of-flight mass spectrometer and collision-induced dissociation. Rapid Commun. Mass Spectrom. 2009, 23, 661-666.
51. Crowe, M. C., Brodbelt, J. S., Infrared multiphoton dissociation (IRMPD) and collisionally activated dissociation of peptides in a quadrupole ion trap with selective IRMPD of phosphopeptides. J. Am. Soc. Mass Spectrom. 2004, 15, 1581-1592.
52. Hasegawa, T., Enomoto, A., Kato, T., Kawai, K. et al., Roles of induced expression of MAPK phosphatase-2 in tumor development in RET-MEN2A transgenic mice. Oncogene 2008, 27, 5684-5695.
53. Ralph, J. A., Morand, E. F., MAPK phosphatases as novel targets for rheumatoid arthritis. Expert Opin. Ther. Targets 2008, 12, 795-808.
54. Dunn, J. D., Reid, G. E., Bruening, M. L., Techniques for phosphopeptide enrichment prior to analysis by mass spectrometry. Mass Spectrom. Rev. 2010, 29, 29-54.
55. Han, G., Ye, M., Zou, H., Development of phosphopeptide enrichment techniques for phosphoproteome analysis. Analyst 2008, 133, 1128-1138.
56. Zhang, J., Dong, X., Hacker, T. A., Ge, Y., Deciphering modifications in swine cardiac troponin I by top-down highresolution tandem mass spectrometry. J. Am. Soc. Mass Spectrometry 2010, 21, 940-948.
57. Strader, M. B., Verberkmoes, N. C., Tabb, D. L., Connelly, H. M. et al., Characterization of the 70S ribosome from Rhodopseudomonas palustris using an integrated "topdown" and "bottom-up" mass spectrometric approach. J. Proteome Res. 2004, 3, 965-978.
58. Parks, B. A., Jiang, L., Thomas, P. M., Wenger, C. D. et al., Top-down proteomics on a chromatographic time scale using linear ion trap fourier transform hybrid mass spectrometers. Anal. Chem. 2007, 79, 7984-7991.
59. Sharma, S., Simpson, D. C., Tolic, N., Jaitly, N. et al., Proteomic profiling of intact proteins using WAX-RPLC 2-D separations and FTICR mass spectrometry. J. Proteome Res. 2007, 6, 602-610.
60. Chi, A., Bai, D. L., Geer, L. Y., Shabanowitz, J. et al., Analysis of intact proteins on a chromatographic time scale by electron transfer dissociation tandem mass spectrometry. Int. J. Mass Spectrometry 2007, 259, 197-203.
61. Siuti, N., Kelleher, N. L., Decoding protein modifications using top-down mass spectrometry. Nature Methods 2007, 4, 817-821.
62. Fagerquist, C. K., Garbus, B. R., Williams, K. E., Bates, A. H. et al., Web-based software for rapid top-down proteomic identification of protein biomarkers, with implications for bacterial identification. Appl. Environ. Microbiol. 2009, 75, 4341-4353.
63. Leduc, R. D., Kelleher, N. L., Using ProSight PTM and related tools for targeted protein identification and characterization with high mass accuracy tandem MS data. Curr. Protoc. Bioinformatics 2007. Chapter 13: p. Unit 13 6.
64. LeDuc, R. D., Taylor, G. K., Kim, Y. B., Januszyk, T. E. et al., ProSight PTM: an integrated environment for protein identification and characterization by top-down mass spectrometry. Nucl. Acids Res. 2004, 32, W340-W345.
65. Zamdborg, L., LeDuc, R. D., Glowacz, K. J., Kim, Y. B. et al., ProSight PTM 2.0: improved protein identification and characterization for top down mass spectrometry. Nucl. Acids Res. 2007, 35, W701-W706.
66. Tsai, Y. S., Scherl, A., Shaw, J. L.,MacKay, C. L. et al., Precursor ion independent algorithm for top-down shotgun proteomics. J. Am. Soc. Mass Spectrometry 2009, 20, 2154-2166.
67. Iavarone, A. T., Jurchen, J. C., Williams, E. R., Effects of solvent on the maximum charge state and charge state distribution of protein ions produced by electrospray ionization. J. Am. Soc. Mass Spectrometry 2000, 11, 976-985.
68. Lomeli, S. H., Yin, S., Ogorzalek Loo, R. R., Loo, J. A., Increasing charge while preserving noncovalent protein complexes for ESI-MS. J. Am. Soc. Mass Spectrometry 2009, 20, 593-596.
69. Pflieger, D., Przybylski, C., Gonnet, F., Le Caer, J.-P., et al., Analysis of human C1q by combined bottom-up and topdown mass spectrometry: detailed mapping of post-translational modifications and insights into the C1r/C1s binding sites. Mol. Cell Proteomics 2010, 9, 593-610.
70. Borchers, C. H., Thapar, R., Petrotchenko, E. V., Torres, M. P. et al., Combined top-down and bottom-up proteomics identifies a phosphorylation site in stem-loop-binding proteins that contributes to high-affinity RNA binding. Proc. Natl. Acad. Sci. USA 2006, 103, 3094-3099.
71. Garcia, B. A., Siuti, N., Thomas, C. E., Mizzen, C. A. et al., Characterization of neurohistone variants and post-translational modifications by electron capture dissociation mass spectrometry. Int. J. Mass Spectrometry 2007, 259, 184-196.
72. Matz, L. M., Asbury, G. R., Hill Jr, H. H., Two-dimensional separations with electrospray ionization ambient pressure high-resolution ion mobility spectrometry/quadrupole mass spectrometry. Rapid Commun. Mass Spectrom 2002, 16, 670-675.
73. Valentine, S. J., Plasencia, M. D., Liu, X., Krishnan, M. et al., Toward plasma proteome profiling with ion mobility-mass spectrometry. J. Proteome Res. 2006, 5, 2977-2984.
74. Breuker, K., Oh, H., Horn, D. M., Cerda, B. A. et al., Detailed unfolding and folding of gaseous ubiquitin ions characterized by electron capture dissociation. J. Am. Chem. Soc. 2002, 124, 6407-6420.
75. Han, X., 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.
76. Waanders, L. F., Hanke, S., Mann, M., Top-down quantitation and characterization of SILAC-labeled proteins. J. Am. Soc. Mass Spectrometry 2007, 18, 2058-2064.
77. Collier, T. S., Hawkridge, A. M., Georgianna, D. R., Payne, G. A. et al., Top-down identification and quantification of stable isotope labeled proteins from Aspergillus flavus using online nano-flow reversed-phase liquid chromatography coupled to a LTQ-FTICR mass spectrometer. Anal. Chem. 2008, 80, 4994-5001.