Abstract
Protein identification and analysis software performs a central role in the investigation of proteins from two-dimensional (2-D) gels. For protein identification, the user matches certain empirically gained information against a protein database to define a protein as already known or as novel. For protein analysis, information in protein databases can be used to predict certain properties about a protein, which can be useful for its empirical investigation. The two processes are thus complementary. Although there are numerable programs available for the above-mentioned applications, we have developed a set of original tools with a few main goals in mind. Specifically, these are:
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To utilize the extensive annotation available in the SWISS-PROT database (1) wherever possible.
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To have tools specifically, but not exclusively, applicable to proteins prepared by 2-D gel electrophoresis.
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To have all tools available on the World Wide Web and freely available to the scientific community.
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References
Bairoch, A. and Apweiler, R. (1997) The SWISS-PROT protein sequence data bank and its supplement TREMBL. Nucleic Acids Res. 24, 31–36.
Appel, R. D., Bairoch, A., and Hochstrasser, D. F. (1994) A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server. Trends Biochem. Sci. 19, 258–260.
Wilkins, M. R., Lindskog, I., Gasteiger, E., Bairoch, A., Sanchez, J.-C., Hochstrasser, D. F., et al. (1997) Detailed peptide characterisation using PeptideMass—a World-Wide Web accessible tool. Electrophoresis 18, 403–408.
Wilkins, M. R., Gasteiger, E., Tonella, L.., Ou, K., Sanchez, J.-C., Tyler, M., Gooely, A. A., Williams, K. L., Appel, R. D., and Hochstrasser, D. F. (1998) Protein identification with N-and C-terminal sequence tags in proteome projects. J. Mol. Biol. 278, 599–608.
Wilkins, M. R., Pasquali, C., Appel, R. D., Ou, K., Golaz, O., Sanchez, J.-C., et al. (1996) From Proteins to Proteomes: Large scale protein identification by two-dimensional electrophoresis and amino acid analysis. Bio/Technology 14, 61–65.
Wilkins, M. R., Ou, K., Appel, R. D., Sanchez, J.-C., Yan, J. X., Golaz, O., et al. (1996) Rapid protein identification using N-terminal “sequence tag” and amino acid analysis. Biochem. Biophys. Res. Commun. 221, 609–613.
Hobohm, U. and Sander, C. (1995) A sequence property approach to searching protein databases. J. Mol. Biol. 251, 390–399.
Cordwell, S. J., Wilkins, M. R., Cerpa-Poljak, A., Gooley, A. A., Duncan, M., Williams, K. L., et al (1995) Cross-species identification of proteins separated by two-dimensional gel electrophoresis using matrix-assisted laser desorption time of flight mass spectrometry and amino acid composition. Electrophoresis 16, 438–443.
Wheeler, C. H., Berry, S. L., Wilkins, M. R., Corbett, J. M., Ou, K., Gooley, A. A., et al. (1996) Characterisation of proteins from 2-D gels by matrix-assisted laser desorption mass spectrometry and amino acid compositional analysis. Electrophoresis 17, 580–587.
Bjellqvist, B., Hughes, G., Pasquali, C., Paquet, N., Ravier, F., Sanchez, J.-C., et al. (1993) The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis 14, 1023–1031.
Bjellqvist, B., Basse, B., Olsen, E., and Celis, J. E. (1994) Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions. Electrophoresis 15, 529–539.
Bairoch, A., Bucher, P., and Hofmann, K. (1995) The PROSITE database, its status in 1995. Nucleic Acids Res. 24, 189–196.
Pearson, W. R. (1991) Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics 11, 635–650.
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403–410.
Golaz, O., Wilkins, M. R., Sanchez, J.-C., Appel, R. D., Hochstrasser, D. F., and Williams, K. L. (1996) Identification of proteins by their amino acid composition: an evaluation of the method. Electrophoresis 17, 573–579.
Wilkins, M. R. and Williams, K. L. (1997) Cross-species protein identification using amino acid composition, peptide mass fingerprinting, isoelectric point and molecular mass: a theoretical evaluation. J. Theor. Biol. 186, 7–15.
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© 1999 Humana Press Inc., Totowa, NJ
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Wilkins, M.R. et al. (1999). Protein Identification and Analysis Tools in the ExPASy Server. In: Link, A.J. (eds) 2-D Proteome Analysis Protocols. Methods in Molecular Biology, vol 112. Humana Press. https://doi.org/10.1385/1-59259-584-7:531
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DOI: https://doi.org/10.1385/1-59259-584-7:531
Publisher Name: Humana Press
Print ISBN: 978-0-89603-524-9
Online ISBN: 978-1-59259-584-6
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