HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Full Text Full Text (PDF) All Versions of this Article: M400215-MCP200v1 4/6/762    most recent Submit a response Alert me when this article is cited Alert me when eLetters are posted Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Request Permissions Glossary Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Weatherly, D. B. Articles by Orlando, R. Search for Related Content PubMed PubMed Citation Articles by Weatherly, D. B. Articles by Orlando, R. Social Bookmarking                      What's this?

Molecular & Cellular Proteomics 4:762-772, 2005.
© 2005 by The American Society for Biochemistry and Molecular Biology, Inc.

---

Research

A Heuristic Method for Assigning a False-discovery Rate for Protein Identifications from Mascot Database Search Results ^*

D. Brent Weatherly^,, James A. Atwood, III^¶,, Todd A. Minning, Cameron Cavola^¶, Rick L. Tarleton and Ron Orlando^¶,||

From the Center for Tropical and Emerging Global Diseases and ^¶ Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602

MS/MS and database searching has emerged as a valuable technology for rapidly analyzing protein expression, localization, and post-translational modifications. The probability-based search engine Mascot has found widespread use as a tool to correlate tandem mass spectra with peptides in a sequence database. Although the Mascot scoring algorithm provides a probability-based model for peptide identification, the independent peptide scores do not correlate with the significance of the proteins to which they match. Herein, we describe a heuristic method for organizing proteins identified at a specified false-discovery rate using Mascot-matched peptides. We call this method PROVALT, and it uses peptide matches from a random database to calculate false-discovery rates for protein identifications and reduces a complex list of peptide matches to a nonredundant list of homologous protein groups. This method was evaluated using Mascot-identified peptides from a Trypanosoma cruzi epimastigote whole-cell lysate, which was separated by multidimensional LC and analyzed by MS/MS. PROVALT was then compared with the two traditional methods of protein identification when using Mascot, the single peptide score and cumulative protein score methods, and was shown to be superior to both in regards to the number of proteins identified and the inclusion of lower scoring nonrandom peptide matches.

CiteULike    Complore    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				R. Raaijmakers, W. Pluk, C. H. Schroder, J. Gloerich, E. A.M. Cornelissen, H. J.C.T. Wessels, J. L. Willems, L. A.H. Monnens, and L. P.W.J. van den Heuvel Proteomic profiling and identification in peritoneal fluid of children treated by peritoneal dialysis Nephrol. Dial. Transplant., July 1, 2008; 23(7): 2402 - 2405. [Abstract] [Full Text] [PDF]

				P. D. Curtis, J. Atwood III, R. Orlando, and L. J. Shimkets Proteins Associated with the Myxococcus xanthus Extracellular Matrix J. Bacteriol., November 1, 2007; 189(21): 7634 - 7642. [Abstract] [Full Text] [PDF]

				W. Yang, R. L. Woltjer, I. Sokal, C. Pan, Y. Wang, M. Brodey, E. R. Peskind, J. B. Leverenz, J. Zhang, D. P. Perl, et al. Quantitative Proteomics Identifies Surfactant-Resistant {alpha}-Synuclein in Cerebral Cortex of Parkinsonism-Dementia Complex of Guam but Not Alzheimer's Disease or Progressive Supranuclear Palsy Am. J. Pathol., September 1, 2007; 171(3): 993 - 1002. [Abstract] [Full Text] [PDF]

				S. Sun, K. Meyer-Arendt, B. Eichelberger, R. Brown, C.-Y. Yen, W. M. Old, K. Pierce, K. J. Cios, N. G. Ahn, and K. A. Resing Improved Validation of Peptide MS/MS Assignments Using Spectral Intensity Prediction Mol. Cell. Proteomics, January 1, 2007; 6(1): 1 - 17. [Abstract] [Full Text] [PDF]

				J. A. Atwood III, D. B. Weatherly, T. A. Minning, B. Bundy, C. Cavola, F. R. Opperdoes, R. Orlando, and R. L. Tarleton The Trypanosoma cruzi Proteome Science, July 15, 2005; 309(5733): 473 - 476. [Abstract] [Full Text] [PDF]