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Bioinformatics Advance Access published online on August 16, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti620
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© 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.


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