Skip Navigation



Bioinformatics Advance Access published online on July 28, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl379
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow Supplementary Material
Right arrowOA All Versions of this Article:
22/22/2830    most recent
btl379v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by MacLean, B.
Right arrow Articles by McIntosh, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by MacLean, B.
Right arrow Articles by McIntosh, M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2006 The Author(s)
Received May 28, 2006
Revised July 5, 2006
Accepted July 5, 2006

Applications note

General framework for developing and evaluating database scoring algorithms using the TANDEM search engine

Brendan MacLean 1, Jimmy K. Eng 2, Ronald C. Beavis 3, and Martin McIntosh 2 *

1 Fred Hutchinson Cancer Research Center, Seattle, USA; LabKey Software, LLC, Seattle, USA
2 Fred Hutchinson Cancer Research Center, Seattle, USA
3 Beavis Informatics Ltd., Winnipeg, Canada; University of British Columbia, Vancouver Canada


  Abstract

Motivation: Tandem mass spectrometry (MS/MS) identifies protein sequences using database search engines, at the core of which is a score that measures the similarity between peptide MS/MS spectra to a protein sequence database. The TANDEM application was developed as a freely available database search engine for the proteomics research community. To extend TANDEM as a platform for further research on developing improved database scoring methods, we modified the software to allow users to redefine the scoring function and replace the native TANDEM scoring function while leaving the remaining core application intact. Redefinition is performed at run time so multiple scoring functions are available to be selected and applied from a single search engine binary. We introduce the implementation of the pluggable scoring algorithm and also provide implementations of two TANDEM compatible scoring functions, one previously described scoring function compatible with PeptideProphet and one very simple scoring function that quantitative researchers may use to begin their development. This extension builds on the open-source TANDEM project and will facilitate research into and dissemination of novel algorithms for matching MS/MS spectra to peptide sequences. The pluggable scoring schema is also compatible with related search applications P3 and Hunter, which are part of the X! suite of database matching algorithms. The pluggable scores and the X! suite of applications are all written in C++.

Availability: Supplementary materials, including source code for the scoring functions, are available from http://proteomics.fhcrc.org.

Associate Editor: Alfonso Valencia
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Mol. Cell. ProteomicsHome page
Q. Fang, A. Strand, W. Law, V. M. Faca, M. P. Fitzgibbon, N. Hamel, B. Houle, X. Liu, D. H. May, G. Poschmann, et al.
Brain-specific Proteins Decline in the Cerebrospinal Fluid of Humans with Huntington Disease
Mol. Cell. Proteomics, March 1, 2009; 8(3): 451 - 466.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Prevention ResearchHome page
K. E. Hung, V. Faca, K. Song, D. A. Sarracino, L. G. Richard, B. Krastins, S. Forrester, A. Porter, A. Kunin, U. Mahmood, et al.
Comprehensive Proteome Analysis of an Apc Mouse Model Uncovers Proteins Associated with Intestinal Tumorigenesis
Cancer Prevention Research, March 1, 2009; 2(3): 224 - 233.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
M. Goudreault, L. M. D'Ambrosio, M. J. Kean, M. J. Mullin, B. G. Larsen, A. Sanchez, S. Chaudhry, G. I. Chen, F. Sicheri, A. I. Nesvizhskii, et al.
A PP2A Phosphatase High Density Interaction Network Identifies a Novel Striatin-interacting Phosphatase and Kinase Complex Linked to the Cerebral Cavernous Malformation 3 (CCM3) Protein
Mol. Cell. Proteomics, January 1, 2009; 8(1): 157 - 171.
[Abstract] [Full Text] [PDF]

Home page
 Infect. Immun.Home page
C. L. Ventura, R. Higdon, L. Hohmann, D. Martin, E. Kolker, H. D. Liggitt, S. J. Skerrett, and C. E. Rubens
Staphylococcus aureus Elicits Marked Alterations in the Airway Proteome during Early Pneumonia
Infect. Immun., December 1, 2008; 76(12): 5862 - 5872.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Biol. CellHome page
M. Ryan, L. A. Graham, and T. H. Stevens
Voa1p Functions in V-ATPase Assembly in the Yeast Endoplasmic Reticulum
Mol. Biol. Cell, December 1, 2008; 19(12): 5131 - 5142.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
A. Ramos-Fernandez, A. Paradela, R. Navajas, and J. P. Albar
Generalized Method for Probability-based Peptide and Protein Identification from Tandem Mass Spectrometry Data and Sequence Database Searching
Mol. Cell. Proteomics, September 1, 2008; 7(9): 1748 - 1754.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
B.-J. M. Webb-Robertson and W. R. Cannon
Current trends in computational inference from mass spectrometry-based proteomics
Brief Bioinform, September 1, 2007; 8(5): 304 - 317.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
B. M. Balgley, T. Laudeman, L. Yang, T. Song, and C. S. Lee
Comparative Evaluation of Tandem MS Search Algorithms Using a Target-Decoy Search Strategy
Mol. Cell. Proteomics, September 1, 2007; 6(9): 1599 - 1608.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.