| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH |
|
|
|
|||||||
|
|||||||||
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Submitted on December 22, 2004
CCRC, University of Georgia, Athens, GA 30602
Corresponding Author: orlando{at}ccrc.uga.edu
Tandem mass spectrometry 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. While 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 were separated by multidimensional liquid chromatography and analyzed by tandem mass spectrometry. 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.
Revised on February 5, 2005
Accepted on February 9, 2005
A heuristic method for assigning a false discovery rate for protein identifications from mascot database search results
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]
|
|
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH |
| All ASBMB Journals | Journal of Biological Chemistry |
| Journal of Lipid Research | ASBMB Today |
