REFERENCES
- [1] Biemann, K., and Papayannopoulos, I. A. 1994. Sequencing of Proteins. Accounts of Chemical Research, 27: 370-378.
- [2] Biemann K. 1995. Coming of Age of MS in Peptide/Protein Chemistry. Protein Science, 4: 1920-1927.
- [3] Johnson, R. S., Martin, S. A., Biemann, K., Stults, J. T., and Watson, J. T. 1987. Novel fragmentation process of peptides by CAD-MS/MS: differentiation of leucine and isoleucine. Analytical Chemistry, 59: 2621-5.
- [4] Stults, J. T., and Watson, J. T. 1987. Identification of a new type of fragment ion in the CAD spectra of peptides allows leucine/isoleucine differentiation. Biomed. Environ. Mass Spectrom, 14: 583-6.
- [5] Sadagopan, N., and Watson, J. T. 2001. Mass spectrometric evidence for mechanisms of fragmentation of chargederivatized peptides. Journal of the American Society for Mass Spectrometry, 12(4): 399-409.
- [6] Stults, J. T. 1990. Peptide sequencing by mass spectrometry. Methods Biochem Anal, 34: 145-201.
- [7] Hanash S. 2003.Disease proteomics. Nature, 422(6928): 226-32.
- [8] Zhang, G., Fan, H., Xu, C., Bao, H., and Yang, P. 2003. On-line preconcentration of in-gel digest by ion-exchange chromatography for protein ID using HPLC-ESI-MS/MS. Analytical Biochemistry, 313: 327-330.
- [9] Le Bihan T., Duewel, H. S., and Figeys, D. 2003. On-line strong cation exchange m-HPLC-ESI-MS/MS for protein identification and process optimization. Journal of the American Society for Mass Spectrometry, 14: 719-727.
- [10] Kislinger, T., and Emili, A. 2005. Multidimensional protein identification technology: current status and future prospects. Expert Review of Proteomics, 2: 27-39.
- [11] Kelleher, N. L. 2004. Top-down proteomics. Analytical Chemistry, 76, (11): 196A-203A.
- [12] 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 Spectrometry Reviews, 24, (2): 126-134.
- [13] Bogdanov, B., and Smith, R. D. 2005. Proteomics by FTICR mass spectrometry: Top down and bottom up. Mass Spectrometry Reviews, 24, (2): 168-200.
- [14] Deterding, L. J., Bhattacharjee, S., Ramirez, D. C., Mason, R.P., and Tomer, K. B. 2007. Top-Down and Bottom-Up Mass Spectrometric Characterization of Human Myoglobin-Centered Free Radicals Induced by Oxidative Damage. Analytical Chemistry, 79, (16): 6236-6248.
- [15] Elias, J. E., Haas, W., Faherty, B. K., and Gygi, S. P. 2005. Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nature Methods, 2, (9): 667-675.
- [16] Hu, Q., Noll, R. J., Li, H., Makarov, A., Hardman, M., and Cooks, R. G. 2005. The Orbitrap: A new mass spectrometer. Journal of Mass Spectrometry, 40, (4): 430-443.
- [17] Hu, Q., Cooks, R. G., and Noll, R. J. 2007. Phase-Enhanced Selective Ion Ejection in an Orbitrap MS. Journal of the American Society for Mass Spectrometry, 18: 980-983.
- [18] Makarov, A. 2000. Electrostatic axially harmonic orbital trapping: a highpe -rformance technique of mass analysis. Analyticay Chemistry. 72(6): 1156-62.
- [19] Makarov, A. 2006. "Theory and Practice of the Orbitrap Mass Analyzer". In: 54th Annual Conf American Social Mass Spectrometry, Seattle, MOF 3:40.
- [20] Makarov, A., Denisov, E., Kholomeev, A., Balschun, W., Lange, O., Strupat, K. and Horning, S. 2006. Performance Evaluation of a Hybrid Linear Ion Trap/Orbitrap Mass Spectrometer. Analyticay Chemistry, 78: 2113-2120.
- [21] Makarov, A., Denisov, E., Lange, O., and Horning, S. 2006. Dynamic Range of Mass Accuracy in LTQ Orbitrap Hybrid MS. Journal of the American Society for Mass Spectrometry, 17: 977-982.
- [22] Scherperel, G., Yan, H., Wang, Y., and Reid, G. E. 2006. 'Top-down' characterization of site-directed mutagenesis products of Staphylococcus aureus dihydroneopterin aldolase by multistage tandem mass spectrometry in a linear quadrupole ion trap. Analyst (Cambridge, United Kingdom) 131(2): 291-302.
- [23] Sze, S. K., Ge, Y., Oh, H., and McLafferty, F. W. 2002. Top-down mass spectrometry of a 29-kDa protein for characterization of any posttranslational modification to within one residue. Process National Academy Science. U S A 99, (4): 1774-9.
- [24] Stephenson, J. L., McLuckey, S. A., Reid, G. E., Wells, J. M., and Bundy, J. L. 2002. Ion/ion chemistry as a top-down approach for protein analysis. Current Opinion in Biotechnology, 13, (1): 57-64.
- [25] McLafferty, F. W., Horn, D. M., Breuker, K., Ge, Y., Lewis, M. A., Cerda, B., Zubarev, R. A., and Carpenter, B. K. 2001. ECD of gaseous multiply charged ions by FT-ICR. Journal of the American Society for Mass Spectrometry, 12: 245-9.
- [26] Shi, S. D, Hemling, M. E, Carr, S. A, Horn, D. M., Lindh, I., and McLafferty, F. W. 2001. Phosphopeptide/phosphopr otein mapping by ECD-MS. Analytical Chemistry, 73: 19-22.
- [27] Cooper, H. J., Håkansson, K., and Marshall, A. G., 2005. The role of electron capture dissociation in biomolecular analysis. Mass Spectrometry Reviews, 24: 201-222
- [28] Davidson, W., and Frego, L. 2002. Micro-HPLC/FTMS with ECD of protein enzymatic digests. Rapid Commun Mass Spectrom, 16: 993-8.
- [29] Haselmann, K. F., Budnik, B. A., Olsen, J. V., Nielsen, M. L., Reis, C. A., Clausen, H., Johnsen, A. H., and Zubarev, R. A. 2001. Advantages of external accumulation for ECD in FTMS. Analytical Chemistry, 73: 2998-3005.
- [30] Palmblad, M., Tsybin, Y. O., Ramstrom, M., Bergquist, J., and Hakansson, P. 2002. Liquid chromatography and ECDin FT-ICR-MS. Rapid Commun Mass Spectrom, 16: 988-92.
- [31] Polfer, N. C., Haselmann, K. F., Zubarev, R. A., and Langridge-Smith, P. R. 2002. Electron capture dissociation of polypeptides using a 3 Tesla FT-ICR-MS. Rapid Commun Mass Spectrom, 16: 936-43.
- [32] McFarland, M. A., Chalmers, M. J., Quinn, J. P., Hendrickson, C. L., and Marshall, A. G. 2005. Evaluation and Optimization of ECD Efficiency in FT-ICR MS. Journal of the American Society for Mass Spectrometry, 16: 1060-1066.
- [33] Cooper, H. J., Hudgins, R. R., Hakansson, K., and Marshall, A. G. 2002. Characterization of amino acid side chain losses in electron capture dissociation. Journal of the American Society for Mass Spectrometry, 13(3): 241-9.
- [34] Haselmann, K. F., Budnik, B. A., and Zubarev, R. A. 2000. ECD of b (2+) peptide fragments reveals the presence of the acylium ion structure. Rapid Communications in Mass Spectrometry, 14: 2242-6.
- [35] Adams, C. M., Kjeldsen, F., Zubarev, R. A., Budnik, B. A., and Haselmann, K. F. 2004. ECD distinguishes a single-amino acid and probes the tertiary structure. Journal of the American Society for Mass Spectrometry, 15: 1087-1098.
- [36] Chamot-Rooke, J., van der Rest, G., Dalleu, A., Bay, S., and Lemoine, J. 2007. The Combination of Electron Capture Dissociation and Fixed Charge Derivatization Increases Sequence Coverage for O-Glycosylated and O-Phosphorylated Peptides. Journal of the American Society for Mass Spectrometry. FIELD Full Journal Title: Journal of the American Society for Mass Spectrometry, 18, (8): 1405-1413.
- [37] Liu, H., and Hkansson, K. 2006. Electron Capture Dissociation of Tyrosine O-Sulfated Peptides Complexed with Divalent Metal Cations. Analytical Chemistry, 78, (21): 7570-7576.
- [38] Parks, B. A., Jiang, L., Thomas, P. M., Wenger, C.D., Roth, M. J., Boyne, M. T., II, Burke, P. V., Kwast, K. E., and Kelleher, N. L. 2007. Top-Down Proteomics on a Chromatographic Time Scale Using Linear Ion Trap FT Hybrid MS. Analytical Chemistry, 79, (21): 7984-7991.
- [39] Turecek, F. 2003. N-C(alpha) Bond Dissociation Energies and Kinetics in Amide and Peptide Radicals. Is the Dissociation a Non-ergodic Process? Journal of the American Society, 125, (19): 5954-63.
- [40] Turecek, F., and Syrstad, E. A. 2003. Mechanism and energetics of intramolecular hydrogen transfer in amide and Peptide radicals and cation-radicals. Journal of the American Chemamic Society, 125, (11): 3353-69.
- [41] O'Connor, P. B., Lin, C., Cournoyer, J. J., Pittman, J. L., Belyayev, M., and Budnik, B. A. 2006. Long-Lived Electron Capture Dissociation Product Ions Experience Radical Migration via Hydrogen Abstraction. Journal of the American Society for Mass Spectrometry, 17, (4): 576-585.
- [42] Silivra, O. A., Kjeldsen, F., Ivonin, I. A., and Zubarev, R. A. 2005. Electron capture dissociation of polypeptides in a 3D quadrupole ion trap: Implementation and first results. Journal of the American Society for Mass Spectrometry, 16: 22-27.
- [43] Syka, J. E. P., Coon, J. J., Schroeder, M. J., Shabanowitz, J., and Hunt, D. F. 2004. Peptide and protein sequence analysis by ETD-MS. Process National Academy Scencei. USA 101: 9528-9533.
- [44] Coon, J. J., Syka, J. E. P., Shabanowitz, J., and Hunt, D. F. 2005. Tandem mass spectrometry for peptide and protein sequence analysis. BioTechniques, 38, (4): 519,521,523.
- [45] Coon, J. J., Shabanowitz, J., Hunt, D. F., and Syka, J. E. P. 2005. Electron Transfer Dissociation of Peptide Anions. Journal of the American Society for Mass Spectrometry, 16, (6): 880-882.
- [46] Chi, A., Bai, D. L., Geer, L. Y., Shabanowitz, J., and Hunt, D. F. 2007. Analysis of intact proteins on a chromatographic time scale by ETD-MS/MS. International Journal of Mass Spectrometry and Ion Processes, 259: 197-203
- [47] Mikesh, L. M., Ueberheide, B., Chi, A., Coon, J. J., Syka, J. E. P., Shabanowitz, J., and Hunt, D. F. 2006. The utility of ETD mass spectrometry in proteomic analysis. Biochimica et Biophysica Acta, Proteins and Proteomics, 1764, (12): 1811-1822.
- [48] Mikesh, L. M., Ueberheide, B., Chi, A., Coon, J. J., Syka, J. E. P., Shabanowitz, J., and Hunt, D. F. 2006. The utility of ETD mass spectrometry in proteomic analysis. Biochimica Biophysica Acta, Proteins Proteomics, 1764, (12): 1811-1822.
- [49] Huang, T. Y., Emory, J. F., O'Hair, R. A. J., and McLuckey, S. A. 2006. Electron-Transfer Reagent Anion Formation via ESI and CAD. Analytical Chemistry, 78: 7387-7391.
- [50] Swaney, D. L., McAlister, G. C., Wirtala, M., Schwartz, J. C., Syka, J. E. P., and Coon, J. J. 2007. Supplemental Activation Method for High-Efficiency ETD of Doubly Protonated Peptide Precursors. Analytical Chemistry, 79: 477-485.
- [51] Liang, X., Hager, J. W., and McLuckey, S. A. 2007. Transmission Mode Ion/Ion Electron-Transfer Dissociation in a Linear Ion Trap. Analytical Chemistry, 79: 1073-1081.
- [52] Liang, X., Han, H., Xia, Y., and McLuckey, S. A. 2007. A Pulsed Triple Ionization Source for Sequential Ion/Ion Reactions in an Electrodynamic Ion Trap. Journal of the American Society for Mass Spectrometry, 18: 369-376.
- [53] Liang, X., and McLuckey, S. A. 2007. Transmission Mode Ion/Ion Proton Transfer Reactions in a Linear Ion Trap. Journal of the American Society for Mass Spectrometry, 18: 882-890.
- [54] Zarling, A. L., Polefrone, J. M., Evans, A. M., Mikesh, L. M., Shabanowitz, J., Lewis, S., Engelhard, V. H., and Hunt, D. F. 2006. Identification of class I MHC-associated phosphopeptides as targets for cancer immunotherapy. Process National Academy Science. USA 103: 14889-14894.
- [55] Catalina, M. I., Koeleman, C. A. M., Deelder, A. M., and Wuhrer, M. 2007. ETD of N-glycopeptides: loss of the entire N-glycosylated asparagine side chain. Rapid Communications in Mass Spectrometry, 21: 1053-1061.
- [56] Sparkman, O. D. 2006. Mass Spectrometry PittCon 2006. Journal of the American Society for Mass Spectrometry, 17: 873-884.
- [57] Sparkman, O. D. 2007. Mass Spectrometry PittCon 2007. Journal of the American Society for Mass Spectrometry, 18.
- [58] Coon, J. J., Ueberheide, B., Syka, J. E. P., Dryhurst, D. D., Ausio, J., Shabanowitz, J., and Hunt, D. F. 2005. Protein identification using sequential ion/ion reactions and tandem mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America, 102, (27): 9463-9468.
- [59] O'Connor, P. B., Cournoyer, J. J., Pitteri, S. J., Chrisman, P. A., and McLuckey, S. A. 2006. Differentiation of Aspartic and Isoaspartic Acids Using ETD. Journal of the American Society for Mass Spectrometry, 17, (1): 15-19.