Abstract
We have broadened the utility of the SEQUEST computer algorithms to permit correlation of uninterpreted high-energy collision-induced dissociation spectra of peptides with all sequences in a database. SEQUEST now allows for the additional fragment ion types observed under high-energy conditions. We analyzed spectra from peptides isolated following trypsin digestion of 13 proteins. SEQUEST ranked the correct sequence first for 90% (18/20) of the spectra in searches of the OWL database, without constraint by enzyme cleavage specificity or species of origin. All false-positives were flagged by the scoring system. SEQUEST searches databases for sequences that correspond to the precursor ion mass ±0.5 u. Preliminary ranking of the top 500 candidates is done by calculation of fragment ion masses for each sequence, and comparison to the measured ion masses on the basis of ion series continuity, summed ion intensity, and immonium ion presence. Final ranking is done by construction of model spectra for the 500 candidates and constructing/performing of a cross-correlation analysis with the actual spectrum. Given the need to relate mounting genome sequence information with corresponding suites of proteins that comprise the cellular molecular machinery, tandem mass spectrometry appears destined to play the leading role in accelerating protein identification on the large scale required.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Olson, M. Proc. Nat. Acad. Sci. USA 1993, 90, 4338–4344.
Geneser, F. Textbook of Histology; Munksgaard, Copenhagen, 1986.
Patterson, S.D. Anal. Biochem. 1994, 221, 1–15.
Hunt, D.F.; Henderson, R.A.; Shabanowitz, J.; Sakaguchi, K.; Michel, H.; Sevilir, N.; Cox, A.L.; Apella, E.; Engelhard, V.N. Science 1992, 255, 1261–1263.
Clauser, K.R.; Hall, S.C.; Smith, D.M.; Webb, J.W.; Andrews, L.A.; Tran, H.U.; Epstein, L.B.; Burlingame, A.L. Nat. Acad. Sci. USA 1995, 92, 5072–5076.
Patterson, S.D.; Aebersold, R. Electrophoresis 1995, 16, 1791–1814.
Wilm, M.; Shevchenko, A.; Houthaeve, T.; Breit, S.; Schweigerer, L.; Fotsis, T.; Mann, M. Nature 1996, 379, 466–469.
Yates, J.R.; Speicher, S.; Griffin, P.R.; Hunkapiller, T. Anal. Biochem. 1993, 214, 397–408.
Henzel, W.J.; Billeci, T.M.; Stults, J.T.; Wong, S.C.; Grimley, C.; Watanabe, C. Proc. Nat. Acad. Sci. USA 1993, 90, 5011–5015.
James, P.; Quadroni, M.; Carfoli, E.; Gonnet, G. Biol. Mass Spectrom. 1993, 22, 338–345.
Mann, M.; Hojrup, P.; Roepstorff, P. Biol. Mass Spectrom. 1993, 22, 338–345.
Pappin, D.J.C.; Hojrup, P.; Bleasby, A.J. Curr. Biol. 1993, 3, 327–332.
Hunt, D.F.; Yates, J. R., III; Shabanowitz, J.; Winston, S.; Hauer, C.R. Proc. Nat. Acad. Sci. USA 1986, 84, 620–623.
Kaiser R.E. Jr.,; Cooks, R.G.; Syka, J.E.P.; Stafford, G.C. Rapid Commun. Mass Spectrom. 1990, 4, 30–33.
Medzihradszky, K.F.; Burlingame, A.L. Methods: A Companion to Methods Enzymol. 1994, 6, 284–303.
Medzihradszky, K.F.; Adams, G.A.; Burlingame, A.L.; Bateman, R.H.; Green, M.R. J. Am. Soc. Mass Spectrom. 1996, 7, 1–10.
Biemann, K. Ann. Rev. Biochem. 1992, 61, 977–1010.
Carr, S.A.; Roberts, G.; Annan, R.S.; Hemling, M.E.; Hoyes, J. Proceedings of the 43rd ASMS Conference on Mass Spectrometry and Allied Topics Atlanta, GA, 1995; p 620.
Kaufmann, R.; Kirsch, D.; Spengler, B. Int. J. Mass Spectrom. Ion Processes 1994, 131, 355–385.
Johnson, R.S.; Biemann, K. Biomed. Environ. Mass Spectrom. 1989, 18, 945–957.
Rouse, J.C.; Yu, W.; Martin, S.A. J. Am. Soc. Mass Spectrom. 1995, i6, 822–835.
Hines, W.M.; Falick, A.M.; Burlingame, A.L.; Gibson, B.W. J. Am. Soc. Mass Spectrom. 1992, 3, 326–336.
Papayannopoulos, I.A.; Biemann, K. J. Am. Soc. Mass Spectrom. 1991, 2, 174–177.
Scarberry, R.E.; Zhang, Z.; Knapp, D.R. J. Am. Soc. Mass Spectrom. 1995, 6, 947–961.
Eng, J.; McCormack, A.L.; Yates J.R. III, J. Am. Soc. Mass Spectrom. 1994, 5, 976–989.
Yates J.R. III,; Eng, J.; McCormack, A.L.; Schieitz, D. Anal. Chem. 1995, 67, 1426–1436.
Yates J.R. III,; Eng, J.; McCormack, A.L. Anal. Chem. 1995, 67, 3202–3210.
Mann, M.; Wilm, M. Anal. Chem. 1994, 66, 4390–4399.
Biemann, K. Methods Enzymol. 1990, 193, 886–888.
Mann, M. Proceedings of the 43rd ASMS Conference on Mass Spectrometry and Allied Topics; Atlanta, GA, 1995; p. 639.
Falick, A.M.; Hines, W.M.; Medzihradszky, K.F.; Baldwin, M.A.; Gibson, B.W. J. Am. Soc. Mass Spectrom. 1993, 4, 882–893.
Hall, S.C.; Smith, D.M.; Masiarz, F.R.; Soo, V.W.; Tran, H.U.; Epstein, L.B.; Burlingame, A.L. Proc. Nat. Acad. Sci. USA 1993, 90, 1927–1931.
Wen, D.X.; Livingston, B.D.; Medzihradszky, K.F.; Keim, S.; Burlingame, A.L.; Paulson, J.C. J. Biol. Chem. 1992, 267, 21011–21019.
Brown, J.D.; Hann, B.C.; Medzihradszky, K.F.; Niwa, M.; Burlingame, A.L.; Walter, P. EMBO J. 1994, 13, 4390–4400.
Walls, F.C.; Baldwin, M.A.; Falick, A.M.; Gibson, B.W.; Kaur, S.; Maltby, D.A.; Gillece-Castro, B.L.; Medzihradszky, K.F.; Evans, S.; Burlingame, A.L., In Biological Mass Spectrometry Burlingame, A.L.; McCloskey, T.A., Eds.; Elsevier: Amsterdam, 1990; pp 197–216.
Walls, F.C.; Hall, S.C.; Medzihradszky, K.F.; Yu, Z.; Burlingame, A.L.; Evans, S.; Hoffman, A.D.; Buchanan, R.; Glover, S. Proceedings of the 41st ASMS Conference on Mass Spectrometry and Allied Topics; San Francisco, CA., 1993; pp 937a–937b.
Burlingame, A.L., In Biological Mass Spectrometry Present and Future Matsuo T.; Caprioli, R. M.; Gross, M.L.; Seyama, Y., Eds.; Wiley: Chichester, 1994; 147–164.
Gibson, B.W.; Biemann, K. Proc. Nat. Acad. Sci. USA 1984, 81, 1956–1960
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Yates, J.R., Eng, J.K., Clauser, K.R. et al. Search of sequence databases with uninterpreted high-energy collision-induced dissociation spectra of peptides. J Am Soc Mass Spectrom 7, 1089–1098 (1996). https://doi.org/10.1016/S1044-0305(96)00079-7
Received:
Revised:
Accepted:
Issue Date:
DOI: https://doi.org/10.1016/S1044-0305(96)00079-7