Searching Sequence Databases Over the Internet: Protein Identification Using MS‐Fit

C.R. Jiménez1, L. Huang1, Y. Qiu1, A.L. Burlingame1

1 University of California San Francisco, San Francisco
Publication Name:  Current Protocols in Protein Science
Unit Number:  Unit 16.5
DOI:  10.1002/0471140864.ps1605s14
Online Posting Date:  May, 2001
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Abstract

Peptide fingerprint mass mapping is widely used for initial identification of proteins separated by gel electrophoresis. This method involves the enzymatic in‐gel digestion of proteins to generate peptides, followed by mass measurement of the cleaved peptides. The experimental mass values are then compared with theoretical values from protein databases, calculated using the cleavage specificity of the enzyme. This unit describes the use of the search program MS‐Fit to identify the closest match or matches.

     
 
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Table of Contents

  • Commentary
  • Figures
     
 
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Materials

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Figures

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Literature Cited

Literature Cited
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   Cordwell, S.J., Wasinger, V.C., Cerpa‐Poljak, A., Duncan, M.W., and Humphrey‐Smith, I. 1997. Conserved motifs as the basis for recognition of homologous proteins across species boundaries using peptide‐mass fingerprinting. J. Mass Spectrom. 32: 370‐378.
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   Pappin, D.J.C., Hojrup, P., and Bleasby, A.J. 1993. Rapid identification of proteins by peptide‐mass finger‐printing. Curr. Biol. 3: 327‐332.
   Shevchenko, A., Jesen, O.N., Podtelejnikov, A.V., Sagliocco, F., Wilm, M., Vorm, O., Mortensen, P., Boucherie, H., and Mann, M. 1996. Linking genome and proteome by mass spectrometry: Large scale identification of yeast proteins from two dimensional gels. Proc. Natl. Acad. Sci. U.S.A. 93: 14440‐14445.
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Internet Resources
   http://prospector.ucsf.edu
  University of California's ProteinProspector site.
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