title: RAId_aPS: MS/MS analysis with multiple scoring functions and spectrum-specific statistics.
abstract: Statistically meaningful comparison/combination of peptide identification results from various search methods is impeded by the lack of a universal statistical standard. Providing an E-value calibration protocol, we demonstrated earlier the feasibility of translating either the score or heuristic E-value reported by any method into the textbook-defined E-value, which may serve as the universal statistical standard. This protocol, although robust, may lose spectrum-specific statistics and might require a new calibration when changes in experimental setup occur. To mitigate these issues, we developed a new MS/MS search tool, RAId_aPS, that is able to provide spectrum-specific-values for additive scoring functions. Given a selection of scoring functions out of RAId score, K-score, Hyperscore and XCorr, RAId_aPS generates the corresponding score histograms of all possible peptides using dynamic programming. Using these score histograms to assign E-values enables a calibration-free protocol for accurate significance assignment for each scoring function. RAId_aPS features four different modes: (i) compute the total number of possible peptides for a given molecular mass range, (ii) generate the score histogram given a MS/MS spectrum and a scoring function, (iii) reassign E-values for a list of candidate peptides given a MS/MS spectrum and the scoring functions chosen, and (iv) perform database searches using selected scoring functions. In modes (iii) and (iv), RAId_aPS is also capable of combining results from different scoring functions using spectrum-specific statistics. The web link is http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/raid_aps/index.html. Relevant binaries for Linux, Windows, and Mac OS X are available from the same page.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America.
authors.forename: Gelio
authors.initials: G
authors.lastname: Alves
authors.forename: Aleksey Y
authors.initials: AY
authors.lastname: Ogurtsov
authors.forename: Yi-Kuo
authors.initials: YK
authors.lastname: Yu
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D013058:Mass Spectrometry / Q000379:methods*; D008970:Molecular Weight; D019151:Peptide Library; D010455:Peptides / Q000032:analysis* / Q000737:chemistry; D040901:Proteomics / Q000379:methods; D015203:Reproducibility of Results; D012984:Software
chemical_list: D019151:Peptide Library; D010455:Peptides