Validation of Tandem Mass Spectrometry Database Search Results Using DTASelect

Daniel Cociorva1, David L. Tabb1, John R. Yates1

1 The Scripps Research Institute, La Jolla, California
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 13.4
DOI:  10.1002/0471250953.bi1304s16
Online Posting Date:  January, 2007
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DTASelect provides a means by which complex SEQUEST results can be filtered, organized, and viewed. A single sample may produce tens of thousands of tandem mass spectra. Manually perusing and selecting SEQUEST matches among such a mass of data carries a risk of inconsistency. DTASelect allows the user to set complex criteria for acceptance or rejection of individual spectrum results. It also features rules for dealing with multiple, identical peptide matches and for removing proteins that are insufficiently evidenced. It provides its sorted and filtered summary as HTML and text documents for easy review and also offers several auxiliary reports. DTASelect is a powerful tool for automatic analysis of complex mixture tandem mass spectrometry.

Keywords: tandem mass spectrometry; database searching; statistical validation; data filtering.

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Table of Contents

  • Basic Protocol 1: Using DTASelect to Analyze and Display Sequest Results
  • Support Protocol 1: Downloading and Installing DTASelect
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
  • Tables
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Literature Cited

   Eng, J., McCormack, A.L., and Yates, J.R. 1994. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5:976‐989.
   Keller, A., Nesvizhskii, A.I., Kolker, E., and Aebersold, R. 2002. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74:5383‐5392.
   McDonald, W.H., Tabb, D.L., Sadygov, R.G., MacCoss, M.J., Venable, J., Graumann, J., Johnson, J.R., Cociorva, D., and Yates, J.R. 2004. MS1, MS2, and SQT: Three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications. Rapid Commun. Mass Spectrom. 18:2162‐2168.
   Nesvizhskii, A.I., Keller, A., Kolker, E., and Aebersold, R. 2003. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75:4646‐4658.
   Peng, J., Elias, J.E., Thoreen, C.C., Licklider, L.F., and Gygi, S.P. 2003. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC‐MS/MS) for large‐scale protein analysis: The yeast proteome. J. Proteome Res. 2:43‐50.
   Tabb, D.L., McDonald, W.H., and Yates, J.R. 2002. DTASelect and Contrast: Tools for assembling and comparing protein identifications from shotgun proteomics. J. Proteome Res. 1:21‐26.
   Washburn, M.P., Wolters, D., and Yates, J.R. 2001. Large‐scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19:242‐247.
Key References
   Tabb et al., 2002. See above.
  The original description of the DTASelect algorithm.
Internet Resources
  This is the official DTASelect site. It contains user manuals, as well as various examples and screenshots. Software updates are also posted on this site, along with instructions on how to download the latest version of the software.
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