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Fast Atom Bombardment Mass Spectrometric Characterization of Peptides

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Peptide Analysis Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 36))

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Abstract

The structural characterization of peptides and proteins is an integral part of biotechnology/pharmaceutical industry research in order to develop novel therapeutic agents through the production of these compounds by synthesis and/or recombinant DNA techniques. The most commonly used methods are the indirect approach through the translation of the DNA sequence of the gene coding for the protein and the automated stepwise Edman degradation. Nevertheless, the former can introduce inaccuracies either from mistakes in reading DNA sequencing gels or from posttranslational modifications, and the latter cannot be used for N-terminally blocked proteins/peptides and certain modified amino acids. Recent developments in desorption ionization techniques and instrumentation have made mass spectrometry a complementary alternative, and in several cases, an effective method of choice over conventional analytical methods employed in the evaluation of a solid-phase synthetic peptide or a recombinant product.

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References

  1. Morris, H. R, Williams, D. H, and Ambler, R P. (1971) Determination of the sequences of protein-derived peptides and peptide mixtures by mass spectrometry Biochem. J. 125, 189–201.

    PubMed  CAS  Google Scholar 

  2. Rose, K., Priddle, J. D., Offord, R. E., and Esnouf, M. P. (1980) A mass-spectro-metric method for the estimation of the ratio of g-carboxyglutamic acid to glutamrc acid at specific sites in proteins. Biochem. J. 187, 239–243.

    PubMed  CAS  Google Scholar 

  3. Rose, K., Simona, M., and Offord, R. (1983) Amino acid sequence determination by g.l.c.-mass spectrometry of permethylated peptides. Biochem J. 215, 261–272.

    PubMed  CAS  Google Scholar 

  4. Biemann, K., Gapp, F., and Seibl, J. (1959) Apphcation of mass spectrometry to structure problems. J. Am. Chem. Sot. 81, 2274,2275.

    Google Scholar 

  5. Carr, S. A., Herlihy, W. C., and Biemann, K. (1981) Advances m gas chromatographrc mass spectrometric protein sequencing. Biomed. Mass Spectrom. 8, 5l–61.

    Article  Google Scholar 

  6. Khorana, H. G., Gerber, G. E., Herlihy, W. C., Gray, P., Anderegg, R. J., Nihei, K., and Bremann, K. (1979) Amino acid sequence of bacteriorhodopsin. Proc. Natl. Acad. Sci. USA 76, 5046–5050.

    Article  PubMed  CAS  Google Scholar 

  7. Barber, M., Bordoli, R. S., Sedgewrck, R. D., and Tyler, A. N. (1981) Fast atom bombardment of solids (F.A.B.): a new ion source for mass spectrometry. .I. Chem. Sot. Chem. Comm 7, 325–327

    Article  Google Scholar 

  8. McFarlane, R. D. and Torgerson, T. F. (1976) Californium-252 plasma desorption mass spectroscopy. Science 191, 920–925.

    Article  Google Scholar 

  9. Sundqvist, B and McFarlane, R. D (1985) 252Cf-plasma desorption mass spectrometry. Mass Spectrom. Rev. 4, 421–460.

    Article  CAS  Google Scholar 

  10. Whitehouse, C. M., Dreyer, R. N., Yamashtta, M., and Fenn, J. B. (1985) Electrospray interface for liquid chromatography and mass spectrometers. Anal. Chem. 57, 675–679.

    Article  PubMed  CAS  Google Scholar 

  11. Loo, J. A., Udseth, H. R., and Smrth, R. D. (1988) Collisional effects on the charge distribution of ions from large molecules, formed by electrospray-ionization mass spectrometry Rapid Comm Mass Spectrom. 2, 207–210.

    Article  CAS  Google Scholar 

  12. Bruins, A. P., Covey, T. R., and Henion, J. D (1987) Ion spray interface for combined liquid chromatography/atmospheric pressure ionization mass spectrometry Anal. Chem. 59, 2642–2646.

    Article  CAS  Google Scholar 

  13. von Wyssenhoff, H., Selzle, H. L., and Schlag, E. W. (1985) Laser-desorbed large molecules in a supersonic jet. Z. Natueorsch. 40a, 674–676.

    Google Scholar 

  14. Li, L. and Lubman, D. (1989) Resonant two-photon ionization for the identification of thermal decomposition products in the laser desorption of small peptides. Rapid Comm. Mass Spectrom. 3, 12–16.

    Article  CAS  Google Scholar 

  15. Karas, M. and Hillenkamp, F. (1988) Laser desorption ionization of proteins with molecular masses exceeding 10000 Daltons. Anal. Chem. 60, 2299–2301.

    Article  PubMed  CAS  Google Scholar 

  16. Car-r, S. A., Helmling, M. E., Bean, M. F., and Roberts, G.D. (1991) Integretation of mass spectrometry in analytical biotechnology Anal. Chem. 63, 2802–2824.

    Article  CAS  Google Scholar 

  17. Chowdhury, S. K. and Chait, B.T. (1989) Recent developments in the mass spectrometry of peptides and proteins, in Annual Reports in Medicinal Chemistry—24, Ch. 27, Academic, San Diego, CA, pp. 253–263.

    Google Scholar 

  18. Barber, M. and Green, B. N. (1987) The analysis of small proteins in the molecular weight range 10–24 kDa by magnetic sector mass spectrometry. Rapid Comm. Mass Spectrom. 1, 80–83.

    Article  CAS  Google Scholar 

  19. Pramanik, B., Tsarbopoulos, A., Siegel, M., Tsao, R., Reichert, P., Bartner, P., Das, P., Her, G., Doelling, V., Nagabhushan, T. L., and Trotta, P. P. (1989) Cahfornium-252 plasma desorption and cesium ion liquid secondary ton mass spectrometry studies of some natural and recombinant proteins, in Proceedings of the 37th ASMS Conference on Mass Spectrometry and Allied Topics, Miami Beach, FL, pp. 893,894.

    Google Scholar 

  20. Tsarbopoulos, A., Pramatuk, B. N., Reichert, P., Siegel, M. M., Nagabhushan, T L., and Trotta, P. P. (1991) 252 Cf-Plasma desorption and cesium-ion liquid secondary-ion mass spectrometric analysis of recombinant proteins. Rapid Comm. Mass Spectrom. 5(2), 8l–85.

    Article  Google Scholar 

  21. Friedman, M., Krull, L. H., and Cavins, J. F. (1970) The chromatographic determination of cystine and cysteine residues m proteins as S-P-(4-pyridylethyl) cysteine. J. Biol. Chem. 245, 3868–3871.

    PubMed  CAS  Google Scholar 

  22. Andrews, P. C. and Dixon, J. E. (1987) A procedure for in situ alkylation of cystine residues on glass fiber prior to protein microsequence analysis. Anal. Biochem. 161, 524–528.

    Article  PubMed  CAS  Google Scholar 

  23. Pramanik, B. N., Das, P. R., and Bose, A. K. (1989) Molecular ion enhancement using salts in FAB matrices for studies on complex natural products. J. Natl. Prod. 52(3), 534–546.

    Article  CAS  Google Scholar 

  24. Chait, B.T. (1988) The use of 252Cf plasma desorption mass spectrometry for the analysis of synthetic peptides and proteins, in The Analysis of Peptides and Proteins by Mass Spectrometry (McNeal, J., ed.), John Wiley, New York, p. 21.

    Google Scholar 

  25. Biemann, K. and Scoble, H. A. (1987) Characterization by tandem mass spectrometry of structural modifications in proteins. Science 237, 992–998.

    Article  PubMed  CAS  Google Scholar 

  26. Williams, D. H., Bojesen, G., Auffret, A. D., and Taylor, L. (1981) Study of difficult peptides from paracoccus cytochrome c-550 and a dolphin cytochrome FEBS Lett. 128, 37–39

    Article  PubMed  CAS  Google Scholar 

  27. Williams, D. H., Bradley, C V., Santikarn, S., and Bojesen, G. (1982) Fast-atom-bombardment mass spectrometry. Biochem. J. 201, 105–117.

    PubMed  CAS  Google Scholar 

  28. Pramanik, B. N., Schering-Plough Internal Memo, Dec. 21, 1984.

    Google Scholar 

  29. Roepstorff, P. and Fohlman, J. (1984) Biomedical mass spectrometry, in Proposal for a Common Nomenclature for Sequence Ions in Mass Spectra ofPeptides. 11, 601.

    CAS  Google Scholar 

  30. Nagabhushan, T. L., Kosecki, R., Pramanik, B., Labdon, J., and Trotta, P. P. (1989) Purification and sequencing of interferons and other biologically active proteins and polypeptides, in Frontiers in Bioprocessing (Sikdar, S. K., Bier, M., and Todd, P., eds.), CRC, Boca Raton, FL, Chapter 5, pp. 51–62.

    Google Scholar 

  31. McLafferty, F. W. (ed.) (1983) Tandem Mass Spectrometty. John Wiley, New York.

    Google Scholar 

  32. Hunt, D. F., Yates, J. R., Shabanowitz, J., Winston, S., and Hauer, C. (1986) Protein sequencing by tandem mass spectrometry. Proc. Natl. Acad. Sci. USA 83, 6233–6237.

    Article  PubMed  CAS  Google Scholar 

  33. Biemann, K. and Martin, S. (1987) Mass spectrometric determination of the amino acid sequence of peptides and proteins. Mass Spectrom Rev. 6, 1–76.

    Article  CAS  Google Scholar 

  34. Gibson, B. W. and Biemann, K. (1984) Strategy for the mass spectrometric verification and correction of the primary structures of proteins deduced from their DNA sequences. Proc. Natl. Acad. Sci. USA 81, 1956–1960.

    Article  PubMed  CAS  Google Scholar 

  35. Morris, H. R., Panico, M, and Taylor, G W. (1983) FAB-mapping of recombi-nant-DNA protein products. Biochem. Biophys. Res. Commun. 117, 299–305.

    Article  PubMed  CAS  Google Scholar 

  36. Tsarbopoulos, A., Becker, G. W., Occolowitz, J. L., and Jardine, I. (1988) Peptide and protein mapping by 252Cf-plasma desorption mass spectrometry. Anal Biochem. 171, 113–123

    Article  PubMed  CAS  Google Scholar 

  37. Lee, T. D. and Vemuri, S. (1990) MacPro mass: a computer program to correlate mass spectral data to peptide and protein structures. Biomed. Environ. Mass Spectrom. 19, 639–645.

    Article  PubMed  CAS  Google Scholar 

  38. Pramanik, B. N., Tsarbopoulos, A., Labdon, J. E., Trotta, P. P., and Nagabhushan, T. L. (1991) Structural analysis of biologically active peptides and recombinant proteins and their modified counterparts by mass spectrometry. J. Chromatogr. 562, 377–389.

    Article  PubMed  CAS  Google Scholar 

  39. Dixon, J. E., Yazdanparast, R., Smith, D., and Andrews, P. C. (1987) Identification of posttranslational modifications in neuropeptides, in Methods in Protein Sequence Analysis, 1986 (Walsh, K. A., ed.), Humana, Clifton, NJ, p. 493

    Google Scholar 

  40. Tsunasawa, S. and Sakiyama, F. (1984) Amino-terminal acetylation of protems: An overview. Methods Enzymol. 106, 165–170

    Article  PubMed  CAS  Google Scholar 

  41. Carr, S. A. and Biemann, K. (1984) Identification of posttranslationally modified amino acids in proteins by mass spectrometry. Methods Enzymol. 106, 29–58.

    Article  PubMed  CAS  Google Scholar 

  42. Carr, S. A., Bean, M. F., Helmhng, M. E., and Roberts, G. D. (1990) Integration of mass spectrometry in biopharmaceutical research, in Biological Mass Spectrometry (Burlingame, A. L. and McCloskey, J. A., eds.), Elsevier, Amsterdam, p. 621.

    Google Scholar 

  43. Geiger, T. and Clarke, S. (1987) Deamidation, isomerization and racemlzation at asparaginyl and aspartyl residues in peptides. J. Biol. Chem. 262, 785–794.

    PubMed  CAS  Google Scholar 

  44. Gibson, B. W. (1990) The identification and sequence analysis of phosphorylated and sulfated peptides by liquid secondary ion mass spectrometry, in Biological Mass Spectrometry (ai]Burlingame, A. L. and McCloskey, J. A., eds.), Elsevier, Amsterdam, p. 315.

    Google Scholar 

  45. Bateman, A, Solomon, S., and Bennett, H. P. J. (1990) Post-translational modification of bovine pro-opiomelanocortin. J. Biol. Chem. 265, 22,130–22,136

    PubMed  CAS  Google Scholar 

  46. Morris, H R and Pucci, P (1985) A new method for rapid assignment of S-S bridges in proteins Biochem. Biophys. Res. Commun. 126, 1122–1128.

    Article  PubMed  CAS  Google Scholar 

  47. Lydon, N., Favre, C, Bove, S., Neyret, O, Benureau, S, Levine, A. M., Seelig, G. F., Nagabhushan, T. L., and Trotta, P. P. (1985) Immunochemical mapping of a-2 interferon Biochemistry 24, 4131–4141.

    Article  PubMed  CAS  Google Scholar 

  48. Her, G. R., Pramanik, B. N., Kumarasamy, R., Bartner, P., Das, P., Tindall, S. H., Nagabhushan, T. L., Trotta, P. P., and Tsarbopoulos, A. (1990) Structural characterization of the recombinant human interleukin-4 N-linked carbohydrate chains by mass spectrometry, in Proceedings of the 38th ASMS Conference on Mass Spec-trometry and Allied Topics, Tucson, AZ., pp 1341,1342.

    Google Scholar 

  49. Carr, S. A. and Roberts, G. D. (1986) Carbohydrate mapping by mass spectrometry a novel method for identifying attachment sites of Asn-linked sugars in gly-coproteins. Anal. Biochem. 157, 396–406.

    Article  PubMed  CAS  Google Scholar 

  50. Ganem, B., Li, Y. T., and Henion, J. D. (1991) Detection of non-covalent receptor-hgand complexes by mass spectrometry. J. Am. Chem. Sot. 113, 6294–6296.

    Article  CAS  Google Scholar 

  51. Ganem, B., Li, Y. T., and Hemon, J. D. (1991) Observatton of non-covalent enzyme-substrate and enzyme-product complexes by ion-spray mass spectrometry J. Am. Chem. Sot. 113, 7818,7819

    Google Scholar 

  52. Baca, M. and Kent, S. B. H (1992) Direct observation of a ternary complex between the dimeric enzyme HIV-l protease and a substrate-based inhibitor. J Am. Chem. Sot 114, 3992,3993.

    Google Scholar 

  53. Ganguly, A. K., Pramanik, B. N., Tsarbopoulos, A, Covey, T. R., Huang, E. C., and Fuhrman, S. A. (1992) Mass-spectrometrrc detection of the noncovalent GDP-bound conformational state of the human H-ras protein. J. Am. Chem. Sot 114, 6559–6560.

    Article  CAS  Google Scholar 

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Das, P.R., Pramanik, B.N. (1994). Fast Atom Bombardment Mass Spectrometric Characterization of Peptides. In: Dunn, B.M., Pennington, M.W. (eds) Peptide Analysis Protocols. Methods in Molecular Biology, vol 36. Humana Press. https://doi.org/10.1385/0-89603-274-4:85

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  • DOI: https://doi.org/10.1385/0-89603-274-4:85

  • Publisher Name: Humana Press

  • Print ISBN: 978-0-89603-274-3

  • Online ISBN: 978-1-59259-523-5

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