Protein identification with N and C-terminal sequence tags in proteome projects

Journal of Molecular Biology

Volumn 278, Issue 3, 1998, Pages 599-608

  Wilkins, Marc R ^a,b,c   Gasteiger, Elisabeth ^b   Tonella, Luisa ^a   Ou, Keli ^c   Tyler, Margaret ^c   Sanchez, Jean Charles ^a   Gooley, Andrew A ^c   Walsh, Bradley J ^c   Bairoch, Amos ^b   Appel, Ron D ^a   Williams, Keith L ^c   Hochstrasser, Denis F ^a,b  

^a GENEVA UNIVERSITY HOSPITALS   (Switzerland)

^b UNIVERSITY OF GENEVA   (Switzerland)

^c MACQUARIE UNIVERSITY   (Australia)

Author keywords

Protein identification; Proteome; Sequence tag; Two dimensional gel electrophoresis

Indexed keywords

AMINO ACID; PROTEIN;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; BACILLUS SUBTILIS; CARBOXY TERMINAL SEQUENCE; COMPUTER PROGRAM; ESCHERICHIA COLI; GENE SEQUENCE; INTERNET; MYCOPLASMA GENITALIUM; NONHUMAN; PRIORITY JOURNAL; PROKARYOTE; PROTEIN ANALYSIS; SACCHAROMYCES CEREVISIAE; SEQUENCE TAGGED SITE; TWO DIMENSIONAL GEL ELECTROPHORESIS;

BACILLUS SUBTILIS; ESCHERICHIA COLI; EUKARYOTA; MYCOPLASMA GENITALIUM; PROKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 18344410995     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1726     Document Type: Article

References (27)

1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J. Mol. Biol. 215:1990;403-410.
2. Appel R. D., Bairoch A., Hochstrasser D. F. A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server. Trend Biochem. Sci. 19:1994;258-260.
3. Bairoch A., Apweiler R. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998. Nucl. Acids Res. 26:1998;38-42.
4. Bartlet-Jones M., Jeffery W. A., Hansen H. F., Pappin D. J. Peptide ladder sequencing by mass spectrometry using a novel, volatile degradation reagent. Rapid Commun. Mass Spectrom. 8:1994;737-742.
5. Burkhurt W. A., Moyer M. A., Bailey J. M., Miller C. G. Electroblotting of proteins to Teflon tape and membranes for N- and C-terminal sequence analysis. Anal. Biochem. 236:1996;364-367.
6. Gooley A. A., Ou K., Russell J., Wilkins M. R., Sanchez J. C., Hochstrasser D. F., Williams K. L. A role for Edman degradation in proteome studies. Electrophoresis. 18:1997;in the press.
7. Griffin P. R., MacCoss M. J., Eng J. K., Blevins R. A., Aaronson J. S., Yates J. R. III. Direct database searching with MALDI-PSD spectra of peptides. Rapid Commun. Mass. Spectrom. 9:1995;1546-1551.
8. Hochstrasser D. F., Harrington M., Hochstrasser A.-C., Miller M. J., Merril C. R. Methods for increasing the resolution of two-dimensional protein electrophoresis. Anal. Biochem. 173:1988a;424-435.
9. Hochstrasser D. F., Patchornik A., Merril C. R. Development of polyacrylamide gels that improve the separation of proteins and their detection by silver staining. Anal. Biochem. 173:1988b;412-423.
10. James P. Of genomes and proteomes. Biochem. Biophys. Res. Commun. 231:1997;1-6.
11. Knierman M. D., Coligan J. E., Parker K. C. Peptide fingerprints after partial acid hydrolysis: analysis by matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom. 8:1994;1007-1010.
12. Mann M. Sequence database searching by mass spectrometric data. Kellner R., Lottspeich F., Meyer H. E. Microcharacterisation of Proteins. 1994;223-245 VCH, Weinheim.
13. Mann M., Wilm M. Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal. Chem. 66:1994;4390-4399.
14. Ou K., Wilkins M. R., Jan J. X., Gooley A. A., Fung Y., Scheumack D., Williams K. L. Improved high-performance liquid chromatography of amino acids derivatised with 9-fluorenylmethyl chloroformate. J. Chromatog. sect. A. 723:1996;219-225.
15. Packer N. H., Wilkins M. R., Golaz O., Lawson M., Gooley A. A., Hochstrasser D. F., Redmond J. W., Williams K. L. Characterisation of human plasma glycoproteins separated by 2-D gel electrophoresis. Bio/Technology. 14:1996;66-70.
16. Pasquali C., Frutiger S., Wilkins M. R., Hughes G. J., Appel R. D., Bairoch A., Schaller D., Sanchez J.-C., Hochstrasser D. F. Two-dimensional gel electrophoresis of Escherichia coli homogenates: the E. coli SWISS-2DPAGE database. Electrophoresis. 17:1996;547-555.
17. Patterson D. H., Tarr G. E., Regnier F. E., Martin S. A. C-terminal ladder sequencing via matrix assisted laser desorption mass spectrometry coupled with carboxypeptidase Y time-dependent and concentration-dependent digestions. Anal. Chem. 67:1995;3971-3978.
18. Pearson W. R., Lipman D. J. Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA. 85:1988;2444-2448.
19. Rabilloud T., Valette C., Lawrence J. J. Sample application by in-gel rehydration improves the resolution of two-dimensional electrophoresis with immobilized pH gradients in the first dimension. Electrophoresis. 15:1994;1552-1558.
20. Sanchez J.-C., Rouge V., Pisteur M., Ravier F., Tonella L., Wilkins M. R., Hochstrasser D. F. Improved and simplified sample application using reswelling of dry immobilized pH gradients. Electrophoresis. 18:1997;324-327.
21. Thiede B., Wittmann-Liebold B., Bienert M., Krause E. MALDI-MS for C-terminal sequence determination of peptides and proteins degraded by carboxypeptidase Y and P. FEBS Letters. 357:1995;65-69.
22. Wilkins M. R., Gooley A. A. Protein identification in proteome projects. Wilkins M. R., Williams K. L., Appel R. D., Hochstrasser D. F. Proteome Research: New Frontiers in Functional Genomics. 1997;35-64 Springer-Verlag, Berlin, Heidelberg.
23. Wilkins M. R., Sanchez J-C., Gooley A. A., Appel R. D., Humphery-Smith I., Hochstrasser D. F., Williams K. L. Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol. Genet. Eng. Rev. 13:1995;19-50.
24. Wilkins M. R., Ou K., Appel R. D., Sanchez J.-C., Yan J. X., Golaz O., Farnsworth V., Cartier P., Hochstrasser D. F., Williams K. L., Gooley A. A. Rapid protein identification using N-terminal "sequence tag" and amino acid analysis. Biochem. Biophys. Res. Commun. 221:1996a;609-613.
25. Wilkins M. R., Pasquali C., Appel R. D., Ou K., Golaz O., Sanchez J-C., Yan J. X., Gooley A. A., Hughes G., Humphery-Smith I., Williams K. L., Hochstrasser D. F. From proteins to proteomes: large scale protein identification by two-dimensional electrophoresis and amino acid analysis. Bio/Technology. 14:1996b;61-65.
26. Wilkins M. R., Sanchez J.-C., Bairoch A., Hochstrasser D. F., Appel R. D. Integrating 2D gel databases using the Melanie II software. Trends Biochem. 21:1996c;496-497.
27. Yan J. X., Wilkins M. R., Ou K., Gooley A. A., Williams K. L., Sanchez J-C., Golaz O., Pasquali C., Hochstrasser D. F. Large scale amino acid analysis for proteome studies. J. Chromatogr. sect. A. 736:1996;291-302.