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Fast atom bombardment mass spectrometric characterization of peptides

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Abstract

Structural characterization of peptides in the range of 500–5000 Da, using fast atom bombardment (FAB) and Cs+ ion liquid secondary ion mass spectrometry (SIMS), is reviewed. These include syntheitc peptides Kemptamide (mol wt 1516); GIF-C15 (mol wt 1875), an isolated natural product as an acylated pentapeptide; and polypeptides generated from enzymatic digests of proteins. MS data is shown to reveal molecular weight and sequence information as well as determine disulfide bonds between cysteine residues and glycosylation sites in the case of a glycopeptide. The complementarity of MS technique to classical biochemical methods for peptide characterization is highlighted. The reader is briefly acquainted with two newer ionization techniques namely, electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI). Synthetic chemists and biochemists can refer to the in-depth review articles that are cited throughout this article.

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References

  1. Morris, H. R., Williams, D. H., and Ambler, R. P. (1971) Determination of the sequences of proteinderived 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-spectrometric method for the estimation of the ratio of g-carboxyglutamic acid to glutamic 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) Application of mass spectrometry to structure problems.J. Am. Chem. Soc. 81, 2274,2275.

    Article  CAS  Google Scholar 

  5. Carr, S. A., Herlihy, W. C., and Biemann, K. (1981) Advances in gas chromatographic mass spectrometric protein sequencing.Biomed. Mass Spectrom. 8, 51–61.

    Article  CAS  Google Scholar 

  6. Khorana, H. G., Gerber, G. E., Herlihy, W. C., Gray, C. P., Anderegg, R. J., Nihei, K., and Biemann, 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., Sedgewick, R. D., and Tyler, A. N. (1981) Fast atom bombardment of solids (F.A.B.): a new ion source for mass spectrometry.J. Chem. Soc. 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., Yamashita, 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 Smith, 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 Wyssnhoff, H., Selzle, H. L., and Schlag, E. W. (1985) Laser-desorbed large molecules in a supersonic jet.Z. Naturforsch. 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. Carr, 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  PubMed  CAS  Google Scholar 

  17. Chowdhury, S. K. and Chait, B. T. (1989) Recent developments in the mass spectrometry of peptides and proteins, inAnnual Reports in Medicinal Chemistry vol 24, 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) Californium-252 plasma desorption and cesium ion liquid secondary ion mass spectrometry studies of some natural and recombinant proteins, inProceedings of the 37th ASMS Conference on Mass Spectrometry and Allied Topics, Miami Beach, FL, pp. 893,894.

  20. Tsarbopoulos, A., Pramanik, 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), 81–85.

    Article  CAS  Google Scholar 

  21. Friedman, M., Krull, L. H., and Cavins, J. F. (1970) The chromatographic determination of cystine and cysteine residues in proteins as S-β-(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 of252Cf plasma desorption mass spectrometry for the analysis of synthetic peptides and proteins, inThe Analysis of Peptides and Proteins by Mass Spectrometry (McNeal, C. J., ed.), 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 c.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.

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

  30. Nagabhushan, T. L., Kosecki, R., Pramanik, B., Labdon, J., and Trotta, P. P. (1989) Purification and sequecing of interferons and other biologically active proteins and polypeptides, inFrontiers 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 Spectrometry, 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 proteis.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 Taulor, G. W. (1983) FAB-mapping of recombinant-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, inMethods 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 proteins: An overview.Methods Enzymol. 106, 165–170.

    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., Helmling, M. E., and Roberts, G. D. (1990) Integration of mass spectrometry in biopharmaceutical research, inBiological 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 racemization 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 sequece analysis of phosphorylated and sulfated peptides by liquid secondary ion mass spectrometry, inBiological Mass Spectrometry (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, 130–136.

    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. B., 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 α-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, inProceedings of the 38th ASMS Conference on Mass Spectrometry and Allied Topics, Tucson, AZ., pp. 1341,1342.

  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 glycoproteins.Anal. Biochem. 157, 396–406.

    Article  PubMed  CAS  Google Scholar 

  50. Tsarbopoulolus, A., Pramanik, B. N., Nagabhushan, T. L., and Covey, T. R. (1995) Structural analysis of the CHO-derived Interleukin-4 by liquid chromatography/electrospray ionization mass spectometry.J. Mass Spectometry 30, 1752–1763.

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  52. Ganem, B., Li, Y. T., and Henion, J. D. (1991) Observation of non-covalent enzyme-substrate and enzyme-product complexes by ion-spray mass spectrometry.J. Am. Chem. Soc. 113, 7818–7819.

    Article  CAS  Google Scholar 

  53. Baca, M. and Kent, S. B. H. (1992) Direct observation of a ternary complex between the dimeric enzyme HIV-1 protease and a substrate-based inhibitor.J. Am. Chem. Soc. 114, 3992–3993.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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Das, P.R., Pramanik, B.N. Fast atom bombardment mass spectrometric characterization of peptides. Mol Biotechnol 9, 141–154 (1998). https://doi.org/10.1007/BF02760815

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