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RAId_DbS is a software design to identify peptides in a specified protein database using the information contained in the MS/MS spectrum. One of the key features of RAId_DbS is that for each identified peptide it reports an E-value based on a theoretical distribution (Alves G., Ogurtsov Y.A., Yu Yi-Kuo. Biology Direct 2007, 2:25). Another feature of RAId_DbS is that for each MS/MS spectrum RAId_DbS reports a measure of goodness of its model.

RAId_DbS has a unique database structure which incorporates information from post-translational modifications (PTM), single amino acid polymorphism (SAP) and diseases associated with mutations (Alves G, Ogurtsov AY, Yu YK. BMC Genomics 2008, 9:505). The information used to generated the annotated database is obtained mainly from GeneBank. Annotated databases from various species can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/pub/RAId/Software/RAId_DbS/.

RAId_DbS's unique database structure permits the user to customize searches by including specific information related to PTMs, SAPs and diseases by creating one's own database which can be searched separately or together with a specified database (Alves G., Ogurtsov Y.A., Yu Yi-Kuo. arXiv:0803.2395).


RAId_DeNovo is a new options available as part of RAId. RAId_deNovo can generate, for a given tandem mass spectrum, the score distribution resulting from scoring all possible peptides under a certain class of scoring functions. This valuable information may aid development of a better measure for assigning statistical significance to the peptide candidates. Using a novel algorithm, RAId_deNovo keeps track of the score distribution together with the associated peptide lengths for each score, providing proper score normalization (Alves G., Ogurtsov Y.A., Yu Yi-Kuo. arXiv:0806.2685). The current version of RAId_deNovo allows the user to select from four scoring functions to compute the DeNovo score histogram: RAId_DbS scoring function (Alves G., Ogurtsov Y.A., Yu Yi-Kuo. Biology Direct, 2:25), the second scoring function is Kscore plugin (Mol Syst Biol. 2005;1:2005.0017.) to X!Tandem, the third scoring function is X!Tandem hyperscore (Anal. Chem., 75, 768-774), and the forth scoring function is the SEQUEST XCorr implementation by Crux (J Proteome Res. 2008 Jul;7(7):3022-7.).