Skip Navigation



Bioinformatics Advance Access published online on August 16, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti620
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrowOA All Versions of this Article:
21/19/3726    most recent
bti620v1
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 Alves, G.
Right arrow Articles by Yu, Y.-K.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Alves, G.
Right arrow Articles by Yu, Y.-K.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received June 15, 2005
Revised July 26, 2005
Accepted August 8, 2005

Article

Robust Accurate Identification of Peptides (RAId): deciphering MS2 data using a structured library search with de novo based statistics

Gelio Alves 1 and Yi-Kuo Yu 1*

1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894

* To whom correspondence should be addressed.
Yi-Kuo Yu, E-mail: yyu{at}ncbi.nlm.nih.gov


  Abstract

Motivation: The key to mass-spectrometry-based proteomics is peptide sequencing. The major challenge in peptide sequencing, whether library search or de novo, is to better infer statistical significance and better attain noise reduction. Because the noise in a spectrum depends on experimental conditions, the instrument used, and many other factors, it cannot be predicted even if the peptide sequence is known. The characteristics of the noise can only be uncovered once a spectrum is given. We wish to overcome such issues.

Results: We design RAId to identify peptides from their associated tandem mass spectrometry data. RAId performs a novel de novo sequencing followed by a search in a peptide library that we created. Through de novo sequencing, we establish the spectrum-specific background score statistics for the library search. When the database search fails to return significant hits, the top-ranking de novo sequences become potential candidates for new peptides that are not yet in the database. The use of spectrum-specific background statistics seems to enable RAId to perform well even when the spectral quality is marginal. Other important features of RAId include its potential in de novo sequencing alone and the ease of incorporating post-translational modifications.

Availability: Programs implementing the methods described are available from the authors upon request.


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
S. Kim, N. Bandeira, and P. A. Pevzner
Spectral Profiles, a Novel Representation of Tandem Mass Spectra and Their Applications for de Novo Peptide Sequencing and Identification
Mol. Cell. Proteomics, June 1, 2009; 8(6): 1391 - 1400.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
S. Kim, N. Gupta, N. Bandeira, and P. A. Pevzner
Spectral Dictionaries: Integrating de novo Peptide Sequencing with Database Search of Tandem Mass Spectra
Mol. Cell. Proteomics, January 1, 2009; 8(1): 53 - 69.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
N. Bandeira, J. V. Olsen, M. Mann, and P. A. Pevzner
Multi-spectra peptide sequencing and its applications to multistage mass spectrometry
Bioinformatics, July 1, 2008; 24(13): i416 - i423.
[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.