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Bioinformatics Advance Access originally published online on August 16, 2005
Bioinformatics 2005 21(19):3726-3732; doi:10.1093/bioinformatics/bti620
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Published by Oxford University Press 2005
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Robust accurate identification of peptides (RAId): deciphering MS2 data using a structured library search with de novo based statistics

Gelio Alves and Yi-Kuo Yu *

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

*To whom correspondence should be addressed.

Motivation: The key to MS -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. Since 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 designed 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 on request.

Contact: yyu{at}ncbi.nlm.nih.gov

Supplementary information: ftp://ftp.ncbi.nih.gov/pub/yyu/Proteomics/MSMS/RAId/MSMS_bioinfo_supp.pdf

Received on June 15, 2005; revised on July 26, 2005; accepted on August 8, 2005

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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]


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