What does the future hold for top down mass spectrometry?

Critical Insight

Abstract

Mass spectrometry (MS) research has revolutionized modern biological and biomedical fields. At the heart of the majority of mass spectrometry experiments is the use of Bottom Up mass spectrometry methods where proteins are first proteolyzed into smaller fragments before MS interrogation. The advent of electron capture dissociation and, more recently, electron-transfer dissociation, however, has allowed Top Down (analysis of intact proteins) or middle down (analysis of large polypeptides) mass spectrometry to both experience large increases in development, growth, and overall usage. Nevertheless, for high-throughput large-scale proteomic studies, Bottom Up mass spectrometry has easily dominated the field. As Top Down mass spectrometry methodology and technology continue to develop, will it genuinely be able to compete with Bottom Up mass spectrometry for whole proteome analysis? Discussed here are the current approaches, applications, issues, and future view of high-throughput Top Down mass spectrometry.

References

  1. 1.
    Chu, D. S.; Liu, H.; Nix, P.; Wu, T. F.; Ralston, E. J.; Yates, J. R., 3rd; Meyer, B. J. Sperm Chromatin Proteomics Identifies Evolutionarily Conserved Fertility Factors. Nature 2006, 443(7107), 101–105.CrossRefGoogle Scholar
  2. 2.
    Koomen, J. M.; Haura, E. B.; Bepler, G.; Sutphen, R.; Remily-Wood, E. R.; Benson, K.; Hussein, M.; Hazlehurst, L. A.; Yeatman, T. J.; Hildreth, L. T.; Sellers, T. A.; Jacobsen, P. B.; Fenstermacher, D. A.; Dalton, W. S. Proteomic Contributions to Personalized Cancer Care. Mol. Cell. Proteom. 2008, 7(10), 1780–1794.CrossRefGoogle Scholar
  3. 3.
    de Godoy, L. M.; Olsen, J. V.; Cox, J.; Nielsen, M. L.; Hubner, N. C.; Frohlich, F.; Walther, T. C.; Mann, M. Comprehensive Mass-Spectrometry-Based Proteome Quantification of Haploid Versus Diploid Yeast. Nature 2008, 455(7217), 1251–1254.CrossRefGoogle Scholar
  4. 4.
    Nita-Lazar, A.; Saito-Benz, H.; White, F. M. Quantitative Phosphoproteomics by Mass Spectrometry: Past, Present, and Future. Proteomics 2008, 8(21), 4433–4443.CrossRefGoogle Scholar
  5. 5.
    Brill, L. M.; Motamedchaboki, K.; Wu, S.; Wolf, D. A. Comprehensive Proteomic Analysis of Schizosaccharomyces Pombe by Two-Dimensional HPLC-Tandem Mass Spectrometry. Methods 2009, 48(3), 311–319.CrossRefGoogle Scholar
  6. 6.
    Wisniewski, J. R.; Zougman, A.; Nagaraj, N.; Mann, M. Universal Sample Preparation Method for Proteome Analysis. Nat. Methods 2009, 6(5), 359–362.CrossRefGoogle Scholar
  7. 7.
    Zhai, B.; Villen, J.; Beausoleil, S. A.; Mintseris, J.; Gygi, S. P. PhosphoProteome Analysis of Drosophila Melanogaster Embryos. J. Proteome Res 2008, 7(4), 1675–1682.CrossRefGoogle Scholar
  8. 8.
    Swaney, D. L.; Wenger, C. D.; Thomson, J. A.; Coon, J. J. Human Embryonic Stem Cell Phosphoproteome Revealed by Electron Transfer Dissociation Tandem Mass Spectrometry. Proc. Natl. Acad. Sci. U.S.A. 2009, 106(4), 995–1000.CrossRefGoogle Scholar
  9. 9.
    Kelleher, N. L. Top-Down Proteomics. Anal Chem 2004, 76(11), 197A-203A.CrossRefGoogle Scholar
  10. 10.
    Kelleher, N. L.; Taylor, S. V.; Grannis, D.; Kinsland, C.; Chiu, H. J.; Begley, T. P.; McLafferty, F. W. Efficient Sequence Analysis of the Six Gene Products (7–74 kDa) from the Escherichia Coli Thiamin Biosynthetic Operon by Tandem High-Resolution Mass Spectrometry. Protein Sci. 1998, 7(8), 1796–1801.CrossRefGoogle Scholar
  11. 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(4952), 201–204.CrossRefGoogle Scholar
  12. 12.
    Miranker, A.; Robinson, C. V.; Radford, S. E.; Aplin, R. T.; Dobson, C. M. Detection of Transient Protein Folding Populations by Mass Spectrometry. Science 1993, 262(5135), 896–900.CrossRefGoogle Scholar
  13. 13.
    Senko, M. W.; Beu, S. C.; McLafferty, F. W. High-Resolution Tandem Mass Spectrometry of Carbonic Anhydrase. Anal. Chem. 1994, 66(3), 415–418.CrossRefGoogle Scholar
  14. 14.
    Yergey, J. A.; Cotter, R. J.; Heller, D.; Fenselau, C. Resolution Requirements for Middle Molecule Mass Spectrometry. Anal. Chem. 1984, 56(12), 2262–2263.CrossRefGoogle Scholar
  15. 15.
    Benesch, J. L.; Robinson, C. V. Mass Spectrometry of Macromolecular Assemblies: Preservation and Dissociation. Curr. Opin. Struct. Biol. 2006, 16(2), 245–251.CrossRefGoogle Scholar
  16. 16.
    McLafferty, F. W.; Breuker, K.; Jin, M.; Han, X.; Infusini, G.; Jiang, H.; Kong, X.; Begley, T. P. Top-Down MS, a Powerful Complement to the High Capabilities of Proteolysis Proteomics. FEBS J. 2007, 274(24), 6256–6268.CrossRefGoogle Scholar
  17. 17.
    Siuti, N.; Kelleher, N. L. Decoding Protein Modifications Using Top Down Mass Spectrometry. Nat. Methods 2007, 4(10), 817–821.CrossRefGoogle Scholar
  18. 18.
    Meng, F.; Cargile, B. J.; Patrie, S. M.; Johnson, J. R.; McLoughlin, S. M.; Kelleher, N. L. Processing Complex Mixtures of Intact Proteins for Direct Analysis by Mass Spectrometry. Anal. Chem. 2002, 74(13), 2923–2929.CrossRefGoogle Scholar
  19. 19.
    Roth, M. J.; Forbes, A. J.; Boyne, M. T., 2nd; Kim, Y. B.; Robinson, D. E.; Kelleher, N. L. Precise and Parallel Characterization of Coding Polymorphisms, Alternative Splicing, and Modifications in Human Proteins by Mass Spectrometry. Mol. Cell. Proteom. 2005, 4(7), 1002–1008.CrossRefGoogle Scholar
  20. 20.
    Sharma, S.; Simpson, D. C.; Tolic, N.; Jaitly, N.; Mayampurath, A. M.; Smith, R. D.; Pasa-Tolic, L. Proteomic Profiling of Intact Proteins Using WAX-RPLC 2-D Separations and FTICR Mass Spectrometry. J. Proteome Res. 2007, 6(2), 602–610.CrossRefGoogle Scholar
  21. 21.
    VerBerkmoes, N. C.; Bundy, J. L.; Hauser, L.; Asano, K. G.; Razumovskaya, J.; Larimer, F.; Hettich, R. L.; Stephenson, J. L. Jr. Integrating Top-Down and Bottom-Up Mass Spectrometric Approaches for Proteomic Analysis of Shewanella Oneidensis. J. Proteome Res. 2002, 1(3), 239–252.CrossRefGoogle Scholar
  22. 22.
    Zhou, F.; Johnston, M. V. Protein Characterization by On-Line Capillary Isoelectric Focusing, Reversed-Phase Liquid Chromatography, and Mass Spectrometry. Anal. Chem. 2004, 76(10), 2734–2740.CrossRefGoogle Scholar
  23. 23.
    Weber, G.; Bocek, P. Recent Developments in Preparative Free Flow Isoelectric Focusing. Electrophoresis 1998, 19(10), 1649–1653.CrossRefGoogle Scholar
  24. 24.
    Malmstrom, J.; Lee, H.; Nesvizhskii, A. I.; Shteynberg, D.; Mohanty, S.; Brunner, E.; Ye, M.; Weber, G.; Eckerskorn, C.; Aebersold, R. Optimized Peptide Separation and Identification for Mass Spectrometry-Based Proteomics via Free-Flow Electrophoresis. J. Proteome Res. 2006, 5(9), 2241–2249.CrossRefGoogle Scholar
  25. 25.
    Wang, Y.; Hancock, W. S.; Weber, G.; Eckerskorn, C.; Palmer-Toy, D. Free Flow Electrophoresis Coupled with Liquid Chromatography-Mass Spectrometry for a Proteomic Study of the Human Cell Line (K562/CR3). J. Chromatogr. A 2004, 1053(1/2), 269–278.CrossRefGoogle Scholar
  26. 26.
    Ouvry-Patat, S. A.; Torres, M. P.; Quek, H. H.; Gelfand, C. A.; O’Mullan, P.; Nissum, M.; Schroeder, G. K.; Han, J.; Elliott, M.; Dryhurst, D.; Ausio, J.; Wolfenden, R.; Borchers, C. H. Free-Flow Electrophoresis for Top-Down Proteomics by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Proteomics 2008, 8(14), 2798–2808.CrossRefGoogle Scholar
  27. 27.
    Boersema, P. J.; Mohammed, S.; Heck, A. J. Hydrophilic Interaction Liquid Chromatography (HILIC) in Proteomics. Anal. Bioanal. Chem. 2008, 391(1), 151–159.CrossRefGoogle Scholar
  28. 28.
    Gilar, M.; Olivova, P.; Daly, A. E.; Gebler, J. C. Orthogonality of Separation in Two-Dimensional Liquid Chromatography. Anal. Chem. 2005, 77(19), 6426–6434.CrossRefGoogle Scholar
  29. 29.
    Boersema, P. J.; Divecha, N.; Heck, A. J.; Mohammed, S. Evaluation and Optimization of ZIC-HILIC-RP as an Alternative MudPIT Strategy. J. Proteome Res. 2007, 6(3), 937–946.CrossRefGoogle Scholar
  30. 30.
    McNulty, D. E.; Annan, R. S. Hydrophilic Interaction Chromatography Reduces the Complexity of the Phosphoproteome and Improves Global Phosphopeptide Isolation and Detection. Mol. Cell. Proteom. 2008, 7(5), 971–980.CrossRefGoogle Scholar
  31. 31.
    Hagglund, P.; Bunkenborg, J.; Elortza, F.; Jensen, O. N.; Roepstorff, P. A New Strategy for Identification of N-Glycosylated Proteins and Unambiguous Assignment of Their Glycosylation Sites Using HILIC Enrichment and Partial Deglycosylation. J. Proteome Res. 2004, 3(3), 556–566.CrossRefGoogle Scholar
  32. 32.
    Lindner, H.; Sarg, B.; Meraner, C.; Helliger, W. Separation of Acetylated Core Histones by Hydrophilic-Interaction Liquid Chromatography. J. Chromatogr. A 1996, 743(1), 137–144.CrossRefGoogle Scholar
  33. 33.
    Mizzen, C. A.; Alpert, A. J.; Levesque, L.; Kruck, T. P.; McLachlan, D. R. Resolution of Allelic and Nonallelic Variants of Histone H1 by Cation-Exchange-Hydrophilic-Interaction Chromatography. J. Chromatogr. B Biomed. Sci. Appl. 2000, 44(1), 33–46.CrossRefGoogle Scholar
  34. 34.
    Lindner, H. H. Analysis of Histones, Histone Variants, and Their Post-Translationally Modified Forms. Electrophoresis 2008, 29(12), 2516–2532.CrossRefGoogle Scholar
  35. 35.
    Jenuwein, T.; Allis, C. D. Translating the Histone Code. Science 2001, 293(5532), 1074–1080.CrossRefGoogle Scholar
  36. 36.
    Garcia, B. A. Mass Spectrometric Analysis of Histone Variants and Post-translational Modifications. Front Biosci. Schol. Ed. 2009, 1, 142–153.CrossRefGoogle Scholar
  37. 37.
    Pesavento, J. J.; Bullock, C. R.; LeDuc, R. D.; Mizzen, C. A.; Kelleher, N. L. Combinatorial Modification of Human Histone H4 Quantitated by Two-Dimensional Liquid Chromatography Coupled with Top Down Mass Spectrometry. J. Biol. Chem. 2008, 283(22), 14927–14937.CrossRefGoogle Scholar
  38. 38.
    Garcia, B. A.; Pesavento, J. J.; Mizzen, C. A.; Kelleher, N. L. Pervasive Combinatorial Modification of Histone H3 in Human Cells. Nat. Methods 2007, 4(6), 487–489.CrossRefGoogle Scholar
  39. 39.
    Taverna, S. D.; Ueberheide, B. M.; Liu, Y.; Tackett, A. J.; Diaz, R. L.; Shabanowitz, J.; Chait, B. T.; Hunt, D. F.; Allis, C. D. Long-Distance Combinatorial Linkage Between Methylation and Acetylation on Histone H3 N Termini. Proc. Natl. Acad. Sci. U.S.A. 2007, 104(7), 2086–2091.CrossRefGoogle Scholar
  40. 40.
    Reid, G. E.; McLuckey, S. A. ‘Top Down’ Protein Characterization via Tandem Mass Spectrometry. J. Mass Spectrom. 2002, 37(7), 663–675.CrossRefGoogle Scholar
  41. 41.
    Stephenson, J. L.; McLuckey, S. A.; Reid, G. E.; Wells, J. M.; Bundy, J. L. Ion/Ion Chemistry as a Top-Down Approach for Protein Analysis. Curr. Opin. Biotechnol. 2002, 13(1), 57–64.CrossRefGoogle Scholar
  42. 42.
    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(5), 495–505.CrossRefGoogle Scholar
  43. 43.
    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. Mass Spectrom. 2004, 15(10), 1478–1486.CrossRefGoogle Scholar
  44. 44.
    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(5), 661–666.CrossRefGoogle Scholar
  45. 45.
    Pitteri, S. J.; McLuckey, S. A. Recent Developments in the Ion/Ion Chemistry of High-Mass Multiply Charged Ions. Mass Spectrom. Rev. 2005, 24(6), 931–958.CrossRefGoogle Scholar
  46. 46.
    Xia, Y.; McLuckey, S. A. Evolution of Instrumentation for the Study of Gas-Phase Ion/Ion Chemistry via Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2008, 19(2), 173–189.CrossRefGoogle Scholar
  47. 47.
    Hu, Q.; Noll, R. J.; Li, H.; Makarov, A.; Hardman, M.; Cooks, R. G. The Orbitrap: A New Mass Spectrometer. J. Mass Spectrom. 2005, 40(4), 430–443.CrossRefGoogle Scholar
  48. 48.
    Scigelova, M.; Makarov, A. Orbitrap Mass Analyzer—Overview and Applications in Proteomics. Proteomics 2006, 6(Suppl 2), 16–21.CrossRefGoogle Scholar
  49. 49.
    Macek, B.; Waanders, L. F.; Olsen, J. V.; Mann, M. Top-Down Protein Sequencing and MS3 on a Hybrid Linear Quadrupole Ion Trap-Orbitrap Mass Spectrometer. Mol. Cell. Proteom. 2006, 5(5), 949–958.CrossRefGoogle Scholar
  50. 50.
    Olsen, J. V.; de Godoy, L. M.; Li, G.; Macek, B.; Mortensen, P.; Pesch, R.; Makarov, A.; Lange, O.; Horning, S.; Mann, M. Parts Per Million Mass Accuracy on an Orbitrap Mass Spectrometer via Lock Mass Injection into a C-Trap. Mol. Cell. Proteom. 2005, 4(12), 2010–2021.CrossRefGoogle Scholar
  51. 51.
    Waanders, L. F.; Hanke, S.; Mann, M. Top-Down Quantitation and Characterization of SILAC-Labeled Proteins. J. Am. Soc. Mass Spectrom. 2007, 18(11), 2058–2064.CrossRefGoogle Scholar
  52. 52.
    Bondarenko, P. V.; Second, T. P.; Zabrouskov, V.; Makarov, A. A.; Zhang, Z. Mass Measurement and Top-Down HPLC/MS Analysis of Intact Monoclonal Antibodies on a Hybrid Linear Quadrupole Ion Trap-Orbitrap Mass Spectrometer. J. Am. Soc. Mass Spectrom. 2009, 20(8), 1415–1424.CrossRefGoogle Scholar
  53. 53.
    Zubarev, R. A.; Kelleher, N. L.; McLafferty, F. W. Electron Capture Dissociation of Multiply Charged Protein Cations: A Nonergodic Process. J. Am. Chem. Soc. 1998, 120, 3265–3266.CrossRefGoogle Scholar
  54. 54.
    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(5796), 109–112.CrossRefGoogle Scholar
  55. 55.
    Cooper, H. J.; Akbarzadeh, S.; Heath, J. K.; Zeller, M. Data-Dependent Electron Capture Dissociation FT-ICR Mass Spectrometry for Proteomic Analyses. J. Proteome Res. 2005, 4(5), 1538–1544.CrossRefGoogle Scholar
  56. 56.
    Syka, J. E.; Coon, J. J.; Schroeder, M. J.; Shabanowitz, J.; Hunt, D. F. Peptide and Protein Sequence Analysis by Electron Transfer Dissociation Mass Spectrometry. Proc. Natl. Acad. Sci. U.S.A. 2004, 101(26), 9528–9533.CrossRefGoogle Scholar
  57. 57.
    Coon, J. J.; Ueberheide, B.; Syka, J. E.; Dryhurst, D. D.; Ausio, J.; Shabanowitz, J.; Hunt, D. F. Protein Identification Using Sequential Ion/Ion Reactions and Tandem Mass Spectrometry. Proc. Natl. Acad. Sci. U.S.A. 2005, 102(27), 9463–9468.CrossRefGoogle Scholar
  58. 58.
    McAlister, G. C.; Phanstiel, D.; Good, D. M.; Berggren, W. T.; Coon, J. J. Implementation of Electron-Transfer Dissociation on a Hybrid Linear Ion Trap-Orbitrap Mass Spectrometer. Anal. Chem. 2007, 79(10), 3525–3534.CrossRefGoogle Scholar
  59. 59.
    Williams, D. K., Jr.; McAlister, G. C.; Good, D. M.; Coon, J. J.; Muddiman, D. C. Dual Electrospray Ion Source for Electron-Transfer Dissociation on a Hybrid Linear Ion Trap-Orbitrap Mass Spectrometer. Anal. Chem. 2007, 79(20), 7916–7919.CrossRefGoogle Scholar
  60. 60.
    McAlister, G. C.; Berggren, W. T.; Griep-Raming, J.; Horning, S.; Makarov, A.; Phanstiel, D.; Stafford, G.; Swaney, D. L.; Syka, J. E.; Zabrouskov, V.; Coon, J. J. A Proteomics Grade Electron Transfer Dissociation-Enabled Hybrid Linear Ion Trap-Orbitrap Mass Spectrometer. J. Proteome Res. 2008, 7(8), 3127–3136.CrossRefGoogle Scholar
  61. 61.
    Stephenson, J. L., Jr.; McLuckey, S. A. Charge Manipulation for Improved Mass Determination of High-Mass Species and Mixture Components by Electrospray Mass Spectrometry. J. Mass Spectrom. 1998, 33(7), 664–672.CrossRefGoogle Scholar
  62. 62.
    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 Spectrom. 2000, 11(11), 976–985.CrossRefGoogle Scholar
  63. 63.
    Iavarone, A. T.; Williams, E. R. Mechanism of Charging and SuperCharging Molecules in Electrospray Ionization. J. Am. Chem. Soc. 2003, 125(8), 2319–2327.CrossRefGoogle Scholar
  64. 64.
    Krusemark, C. J.; Ferguson, J. T.; Wenger, C. D.; Kelleher, N. L.; Belshaw, P. J. Global Amine and Acid Functional Group Modification of Proteins. Anal. Chem. 2008, 80(3), 713–720.CrossRefGoogle Scholar
  65. 65.
    Kjeldsen, F.; Giessing, A. M.; Ingrell, C. R.; Jensen, O. N. Peptide Sequencing and Characterization of Post-Translational Modifications by Enhanced Ion-Charging and Liquid Chromatography Electron-Transfer Dissociation Tandem Mass Spectrometry. Anal. Chem. 2007, 79(24), 9243–9252.CrossRefGoogle Scholar
  66. 66.
    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 Spectrom. 2009, 20(4), 593–596.CrossRefGoogle Scholar
  67. 67.
    Taylor, G. K.; Kim, Y. B.; Forbes, A. J.; Meng, F.; McCarthy, R.; Kelleher, N. L. Web and Database Software for Identification of Intact Proteins Using “Top Down” Mass Spectrometry. Anal. Chem. 2003, 75(16), 4081–4086.CrossRefGoogle Scholar
  68. 68.
    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, Unit 13 6.Google Scholar
  69. 69.
    Pesavento, J. J.; Kim, Y. B.; Taylor, G. K.; Kelleher, N. L. Shotgun Annotation of Histone Modifications: A New Approach for Streamlined Characterization of Proteins by Top Down Mass Spectrometry. J. Am. Chem. Soc. 2004, 26(11), 3386–3387.CrossRefGoogle Scholar
  70. 70.
    Frank, A. M.; Pesavento, J. J.; Mizzen, C. A.; Kelleher, N. L.; Pevzner, P. A. Interpreting Top-Down Mass Spectra Using Spectral Alignment. Anal. Chem. 2008, 80(7), 2499–2505.CrossRefGoogle Scholar
  71. 71.
    Karabacak, N. M.; Li, L.; Tiwari, A.; Hayward, L. J.; Hong, P.; Easterling, M. L.; Agar, J. N. Sensitive and Specific Identification of Wild Type and Variant Proteins from 8 to 669 kDa Using Top Down Mass Spectrometry. Mol. Cell. Proteom. 2009, 8(4), 846–856.CrossRefGoogle Scholar
  72. 72.
    Geer, L. Y.; Markey, S. P.; Kowalak, J. A.; Wagner, L.; Xu, M.; Maynard, D. M.; Yang, X.; Shi, W.; Bryant, S. H. Open Mass Spectrometry Search Algorithm. J. Proteome Res. 2004, 3(5), 958–964.CrossRefGoogle Scholar
  73. 73.
    Bailey, C. M.; Sweet, S. M.; Cunningham, D. L.; Zeller, M.; Heath, J. K.; Cooper, H. J. SLoMo: Automated Site Localization of Modifications from ETD/ECD Mass Spectra. J. Proteome Res. 2009, 8(4), 1965–1971.CrossRefGoogle Scholar
  74. 74.
    Fagerquist, C. K.; Garbus, B. R.; Williams, K. E.; Bates, A. H.; Boyle, S.; Harden, L. A. Web-Based Software for Rapid Top-Down Proteomic Identification of Protein Biomarkers, with Implications for Bacterial Identification. Appl. Environ. Microbiol. 2009, 75(13), 4341–4353.CrossRefGoogle Scholar
  75. 75.
    Sadygov, R. G.; Good, D. M.; Swaney, D. L.; Coon, J. J. A New Probabilistic Database Search Algorithm for ETD Spectra. J. Proteome Res. 2009, 8(6), 3198–3205.CrossRefGoogle Scholar
  76. 76.
    Roth, M. J.; Parks, B. A.; Ferguson, J. T.; Boyne, M. T. 2nd; Kelleher, N. L. “Proteotyping”: Population Proteomics of Human Leukocytes Using Top Down Mass Spectrometry. Anal. Chem. 2008, 80(8), 2857–2866.CrossRefGoogle Scholar
  77. 77.
    Parks, B. A.; Jiang, L.; Thomas, P. M.; Wenger, C. D.; Roth, M. J.; Boyne, M. T. 2nd; Burke, P. V.; Kwast, K. E.; Kelleher, N. L. Top-Down Proteomics on a Chromatographic Time Scale Using Linear Ion Trap Fourier Transform Hybrid Mass Spectrometers. Anal. Chem. 2007, 79(21), 7984–7991.CrossRefGoogle Scholar
  78. 78.
    Collier, T. S.; Hawkridge, A. M.; Georgianna, D. R.; Payne, G. A.; Muddiman, D. C. Top-Down Identification and Quantification of Stable Isotope Labeled Proteins from Aspergillus flavus Using On-Line Nano-Flow Reversed-Phase Liquid Chromatography Coupled to a LTQ-FTICR Mass Spectrometer. Anal. Chem. 2008, 80(13), 4994–5001.CrossRefGoogle Scholar
  79. 79.
    Bunger, M. K.; Cargile, B. J.; Ngunjiri, A.; Bundy, J. L.; Stephenson, J. L., Jr. Automated Proteomics of E. Coli via Top-Down Electron-Transfer Dissociation Mass Spectrometry. Anal. Chem. 2008, 80(5), 1459–1467.CrossRefGoogle Scholar
  80. 80.
    Chi, A.; Bai, D. L.; Geer, L. Y.; Shabanowitz, J.; Hunt, D. F. Analysis of Intact Proteins on a Chromatographic Time Scale by Electron Transfer Dissociation Tandem Mass Spectrometry. Int. J. Mass Spectrom. 2007, 259(1/3), 197–203.CrossRefGoogle Scholar
  81. 81.
    Wu, S. L.; Kim, J.; Hancock, W. S.; Karger, B. Extended Range Proteomic Analysis (ERPA): A New and Sensitive LC-MS Platform for High Sequence Coverage of Complex Proteins with Extensive Post-Translational Modifications-Comprehensive Analysis of β-Casein and Epidermal Growth Factor Receptor (EGFR). J. Proteome Res. 2005, 4(4), 1155–1170.CrossRefGoogle Scholar
  82. 82.
    Zhang, J.; Wu, S. L.; Kim, J.; Karger, B. L. Ultratrace Liquid Chromatography/Mass Spectrometry Analysis of Large Peptides with Post-Translational Modifications Using Narrow-Bore Poly(Styrene-Divinylbenzene) Monolithic Columns and Extended Range Proteomic Analysis. J. Chromatogr. A 2007, 1154(1/2), 295–307.CrossRefGoogle Scholar
  83. 83.
    Good, D. M.; Wirtala, M.; McAlister, G. C.; Coon, J. J. Performance Characteristics of Electron Transfer Dissociation Mass Spectrometry. Mol. Cell. Proteom. 2007, 6(11), 1942–1951.CrossRefGoogle Scholar
  84. 84.
    Molina, H.; Horn, D. M.; Tang, N.; Mathivanan, S.; Pandey, A. Global Proteomic Profiling of Phosphopeptides Using Electron Transfer Dissociation Tandem Mass Spectrometry. Proc. Natl. Acad. Sci. U.S.A. 2007, 104(7), 2199–2204.CrossRefGoogle Scholar
  85. 85.
    Boyne, M. T.; Garcia, B. A.; Li, M.; Zamdborg, L.; Wenger, C. D.; Babai, S.; Kelleher, N. L. Tandem Mass Spectrometry with Ultrahigh Mass Accuracy Clarifies Peptide Identification by Database Retrieval. J. Proteome Res. 2009, 8(1), 374–379.CrossRefGoogle Scholar

Copyright information

© American Society for Mass Spectrometry 2010

Authors and Affiliations

  1. 1.Department of Molecular Biology and Department of ChemistryPrinceton UniversityPrincetonUSA
  2. 2.Department of ChemistryPrinceton UniversityPrincetonUSA

Personalised recommendations