Database searching with mass-spectrometric information

Trends in Biotechnology

Volumn 18, Issue SUPPL.1, 2000, Pages 22-27

  Beavis, Ronald C ^a   Fenyö, David ^a  

^a ProteoMetrics LLC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 10644233222     PISSN: 01677799     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0167-7799(00)00009-3     Document Type: Review

References (28)

1. Mortz, E. et al. (1994) Identification of proteins in polyacrylamide gels by mass spectrometric peptide mapping combined with database search. Biol. Mass Spectrom. 23, 249-261
2. Clauser, K.R. et al. (1995) Rapid mass spectrometric peptide sequencing and mass matching for characterization of human melanoma proteins isolated by two-dimensional PAGE. Proc. Natl. Acad. Sci. U. S. A. 92, 5072-5076
3. Fey, S.J. et al. (1997) Proteome analysis of Saccharomyces cerevisiae: a methodological outline. Electrophoresis 18, 1361-1372
4. Patterson, S.D. (1997) Identification of low to subpicomolar quantities of electrophoretically separated proteins: towards protein chemistry in the post-genome era. Biochem. Soc. Trans. 25, 255-262
5. Link, A.J. et al. (1997) Identifying the major proteome components of Haemophilus influenzae type-strain NCTC 8143. Electrophoresis 18, 1314-1334
6. Wigge, P.A. et al. (1998) Analysis of the Saccharomyces spindle pole by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry J. Cell Biol. 141, 967-977
7. Rout, M.P et al. (2000) The yeast nuclear pore complex: composition, architecture, and transport mechanism. J. Cell Biol. 148, 635-652
8. Yates, J.R., III et al. (1997) Direct analysis of protein mixtures by tandem mass spectrometry. J. Protein Chem. 16, 495-197
9. Courchesne, P.L. et al. (1998) Optimization of capillary chromatography ion trap-mass spectrometry for identification of gel-separated proteins. Electrophoresis 19, 956-967
10. Figeys, D et al. (1999) Data-dependent modulation of solid-phase extraction capillary electrophoresis for the analysis of complex peptide and phosphopeptide mixtures by tandem mass spectrometry: application to endothelial nitric oxide synthase. Anal. Chem. 71, 2279-2287
11. Henzel, W.J. et al. (1993) Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc. Natl. Acad. Sci. U. S. A. 90, 5011-5015
12. Mann, M. et al. (1993) Use of mass spectrometric molecular weight information to identify proteins in sequence databases. Biol. Mass Spectrom. 22, 338-345
13. Pappin, D.D.J. et al. (1993) Rapid identification of proteins by peptide-mass fingerprinting. Curr. Biol. 3, 327-332
14. Yates, J.R., III et al. (1993) Peptide mass maps: a highly informative approach to protein identification. Anal. Biochem. 214, 397-408
15. James, P. et al. (1993) Protein identification by mass profile fingerprinting. Biochem. Biophys. Res. Commun. 195, 58-64
16. Zhang, W. and Chait, B.T. (2000) ProFound - an expert system for protein identification using mass spectrometric peptide mapping information. Anal. Chem. 72, 2482-2489
17. Perkins, D.N. et al. (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551-3567
18. Berndt, R et al. (1999) Reliable automatic protein identification from matrix-assisted laser desorption/ionization mass spectrometric peptide fingerprints. Electrophoresis 20, 3521-3526
19. Gras, R. et al. (1999) Improving protein identification from peptide mass fingerprinting through a parameterized multi-level scoring algorithm and an optimized peak detection. Electrophoresis 20, 3535-3550
20. Eng, J.K. et al. (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5, 976
21. Mann, M. and Wilm, M. (1994) Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal. Chem. 66, 4390-1399
22. Washburn, M.P. and Yates, J.R., III (2000) New methods of proteome analysis: multidimensional chromatography and mass spectrometry. In Proteomics: A Trends Guide (Blackstock, W and Mann, M., eds), pp. 27-30, Elsevier
23. Clauser, K.R. et al. (1999) Role of accurate mass measurement (± 10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal. Chem. 71, 2871-2882
24. Fenyö, D. et al. (1998) Protein identification using mass spectrometric information. Electrophoresis 19, 998-1005
25. Wilkins, M.R. et al. (1998) Multiple parameter cross-species protein identification using Multildent - a world-wide web accessible tool. Electrophoresis 19, 3199-3206
26. Service, R.F. (2000) Proteomics: can Celera do it again? Science 287, 2136-2138
27. Eriksson, J. et al. (2000) A statistical basis for testing the significance of mass spectrometric protein identification results. Anal. Chem. 72, 999-1005
28. Küster, B. et al. (1999) Identifying proteins in genome databases using mass spectrometry. In Proceedings of the 47th ASMS Conference on Mass Spectrometry and Allied Topics, pp. 1897-1898, American Society for Mass Spectrometry