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

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