Abstract
Protein identification and analysis software performs a central role in the investigation of proteins from two-dimensional (2-D) gels and mass spectrometry. For protein identification, the user matches certain empirically acquired 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 numerous programs available for those applications, we have developed a set of original tools with a few main goals in mind. Specifically, these are:
-
1.
To utilize the extensive annotation available in the Swiss-Prot database (1) wherever possible, in particular the position-specific annotation in the Swiss-Prot feature tables to take into account posttranslational modifications and protein processing.
-
2.
To develop tools specifically, but not exclusively, applicable to proteins prepared by twodimensional gel electrophoresis and peptide mass fingerprinting experiments.
-
3.
To make all tools available on the World-Wide Web (WWW), and freely usable by the scientific community.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Boeckmann, B., Bairoch, A., Apweiler, R., et al. (2003) The Swiss-Prot protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31, 354–370.
Gasteiger, E., Gattiker, A., Hoogland, C., Ivanyi, I., Appel, R. D. and Bairoch, A. (2003). ExPASy—the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 31, 3784–3788.
Apweiler, R., Bairoch, A., Wu, C. H., et al. (2004) UniProt: the Universal Protein knowledgebase. Nucleic Acids Res. 432, D115–D119.
Jung, E., Gasteiger, E., Veuthey, A.-L., and Bairoch A. (2001) Annotation of glycoproteins in the SWISS-PROT database. Proteomics 1, 262–268.
Farriol-Mathis, N., Garavelli, J. S., Boeckmann, B., et al. (2004), Annotation of post-translational modifications in the Swiss-Prot knowledgebase. Proteomics, in press.
Gill, S. C, von Hippel P. H. (1989) Calculation of protein extinction coefficients from amino acid sequence data. Anal. Biochem. 182, 319–326.
Kyte, J., and Doolittle, R. F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105–132.
Wilkins, M. R., Lindskog, I., Gasteiger, E., et al. (1997) Detailed peptide characterization using PEPTIDEMASS—a World-Wide-Web-accessible tool. Electrophoresis 18, 403–408.
Keil, B. (1992) Specificity of proteolysis. Springer-Verlag Berlin-Heidelberg New York, p. 335.
Wilkins, M. R., Gasteiger, E., Sanchez, J.-C., Appel, R. D., and Hochstrasser, D. F. (1996) Protein identification with sequence tags. Curr. Biol. 6, 1543–1544.
Wilkins, M. R., Gasteiger, E., Tonella, L., et al. (1998) Protein identification with N-and C-terminal sequence tags in proteome projects. J. Mol. Biol. 278, 599–608.
Ashburner, M., Ball, C. A., Blake, J. A., et al. (2000), Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25–29.
Wilkins, M. R., Pasquali, C., Appel, R. D., 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., et al. (1996) Rapid protein identification using Nterminal “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., 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., 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.
Wilkins, M. R., Gasteiger, E., Wheeler, C., et al. (1998) Multiple parameter cross-species protein identification using MultiIdent—a world wide web accessible tool. Electrophoresis 19, 3199–3206.
Wilkins, M. R., Gasteiger E., Gooley, A. A., et al. (1999) High-throughput mass spectrometric discovery of protein post-translational modifications. J. Mol. Biol. 289, 645–657.
Hulo, N., Sigrist, C. J., Le Saux V., et al. (2004) Recent improvements to the PROSITE database. Nucleic Acids Res. 32, D134–D137.
Henikoff, S., and Henikoff, J. G. (1993) Performance evaluation of amino acid substitution matrices. Proteins 17, 49–61.
Cooper, C. A., Gasteiger, E., and Packer, N. (2001) GlycoMod—a software tool for determining glycosylation compositions from mass spectrometric data. Proteomics 1, 340–349.
Cooper, C. A., Gasteiger, E., and Packer, N. (2003) Predicting glycan composition from experimental mass using GlycoMod. In: (Conn, P.M., ed.) Handbook of Proteomic Methods (Humana, Totowa, NJ: pp. 225–231.
Gattiker, A., Bienvenut, W. V., Bairoch, A., and Gasteiger, E. (2002) FindPept, a tool to identify unmatched masses in peptide mass fingerprinting protein identification. Proteomics 2, 1435–1444.
Bjellqvist, B., Hughes, G., Pasquali, 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.
Hoogland, C., Sanchez, J.-C., Tonella, L., et al. (2000) The 1999 SWISS-2DPAGE database update. Nucleic Acids Res. 28, 286–288.
Nielsen, H., Engelbrecht, J., Brunak, S., and von Heijne, G. (1997) Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10, 1–6.
Bachmair, A., Finley, D., and Varshavsky, A. (1986) In vivo half-life of a protein is a function of its amino-terminal residue. Science 234, 179–186.
Gonda, D. K., Bachmair, A., Wunning, I., Tobias, J. W., Lane, W. S., and Varshavsky, A. J. (1989) Universality and structure of the N-end rule. J. Biol. Chem. 264, 16,700–16,712.
Tobias, J. W., Shrader, T. E., Rocap, G., and Varshavsky, A. (1991) The N-end rule in bacteria. Science 254, 1374–1377.
Ciechanover, A. and Schwartz, A. L. (1989) How are substrates recognized by the ubiquitin-mediated proteolytic system? Trends Biochem. Sci. 14, 483–488.
Guruprasad, K., Reddy, B. V. B., and Pandit, M. W. (1990) Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Eng. 4, 155–161.
Ikai, A. J. (1980) Thermostability and aliphatic index of globular proteins. J. Biochem. 88, 1895–1898.
Gattiker, A., Gasteiger, E., and Bairoch, A. (2002) ScanProsite: a reference implementation of a PROSITE scanning tool. Applied Bioinform. 1, 107–108.
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.
Hara, S., Rosenfeld, R., and Lu, H. S. (1996) Preventing the generation of artifacts during peptide map analysis of recombinant human insulin-like growth factor-I. Anal. Biochem. 243, 74–79.
Parker, K. C., Garrels, J. I., Hines, W., et al. (1998) Identification of yeast proteins from twodimensional gels: working out spot cross-contamination. Electrophoresis 19, 1920–1932.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Humana Press Inc., Totowa, NJ
About this protocol
Cite this protocol
Gasteiger, E. et al. (2005). Protein Identification and Analysis Tools on the ExPASy Server. In: Walker, J.M. (eds) The Proteomics Protocols Handbook. Springer Protocols Handbooks. Humana Press. https://doi.org/10.1385/1-59259-890-0:571
Download citation
DOI: https://doi.org/10.1385/1-59259-890-0:571
Publisher Name: Humana Press
Print ISBN: 978-1-58829-343-5
Online ISBN: 978-1-59259-890-8
eBook Packages: Springer Protocols