6 research outputs found
RAId_aPS: MS/MS analysis with multiple scoring functions and spectrum-specific statistics
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 E-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.Comment: 34 pages, 10 figures, 1 supplementary information file
(RAId_aPS_support.pdf). To view the supplementary file, please download and
extract the gzipped tar source file listed under "Other formats