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

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 16.6
DOI:  10.1002/0471140864.ps1606s14
Online Posting Date:  May, 2001
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Abstract

Although peptide mass mapping is fast and simple, its success can be compromised by the purity of the protein in one gel spot, errors in the sequence database, and the detection of too few peptides in the MS map of a given protein to permit reliable database matching. In those cases, partial amino acid sequence that is determined using post‐source decay (PSD) analysis or tandem mass spectrometry is required to establish the correct protein identification among possibilities suggested by MS‐Fit. Post‐source decay (PSD) involves the detection of the fragmentation product ions (metastable ions) of a selected mass value window containing the precursor ion chosen, that occur in the field‐free region between the ion source and the reflectron. This unit covers some of the practical issues in obtaining and analyzing a typical PSD spectrum using MS‐Tag, a database interrogation program that enables the identification of proteins with a limited number of peptide fragment ions by matching existing database sequences. It is a user‐friendly program that simultaneously considers a variety of ion types, but still allows single‐mismatch‐tolerant searching. Although MALDI‐PSD database searching is a widely used tool, an alternative method also described in this unit is analysis by MALDI collision‐induced dissociation (MALDI‐CID).

     
 
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Table of Contents

  • Basic Protocol 1: Database Searching with MS‐Tag
  • Alternate Protocol 1: Sequence Analysis Using MALDI‐CID
  • Commentary
  • Figures
     
 
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Materials

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Figures

Videos

Literature Cited

Literature Cited
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   Biemann, K. 1990. Sequencing of peptides by tandem mass spectrometry and high‐energy collision‐induced dissociation. Methods Enzymol. 193: 455‐479.
   Cordero, M.M., Cornish, T.J., Cotter, R.J., and Lys, I.A. 1995. Sequencing peptides without scanning the reflectron—post source decay with a curved field reflectron time‐of‐flight mass spectrometer. Rapid Commun. Mass Spectrom. 9: 1356‐1361.
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   Medzihradszky, K.F. and Burlingame, A.L. 1994. The advantages and versatility of a high‐energy collision‐induced dissociation‐based strategy for the sequence and structural determination of proteins. Methods Comp. Methods Enzymol. 6: 284‐303.
   Medzihradszky, K.F., Adams, G.W., Burlingame, A.L., Green, M., and Bateman, R. 1996. Peptide sequence determination by matrix‐assisted laser desorption ionization employing a tandem double focusing magnetic orthogonal acceleration time‐of‐flight mass spectrometer. J. Am. Soc. Mass Spectrom. 7: 1‐10.
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   Qiu, Y., Burlingame, A.L., and Benet, L.Z. 1998. Mechanisms for covalent binding of benoxaprofen glucuronide to human serum albumin—studies by tandem mass spectrometry. Drug Metab. Dispos. 26: 246‐256.
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Internet Resources
   http://prospector.ucsf.edu
  University of California's ProteinProspector site.
   http://donatello.ucsf.edu/onramp.html
  University of California site for programs employing fragment ion information to search databases (also see sites listed therein).
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