RAId_deNovo: using de novo based spectrum-specific statistics to combine search results from multiple scoring functions and more

Comparing or combining results of peptide identification from different search methods with firm foundation is impeded by the lack of a universal statistical standard. Providing an E-value calibration protocol, we demonstrated earlier the possiblity to translate 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. RAId deNovo circumvents these issues. We show, for a class of scoring functions, how RAId deNovo uses the respective score histograms from scoring all possible de novo peptides to assign accurate, spectrum-specific E-values, thereby creating a calibration-free protocol for accurate significance assignment and for combining search results. RAId deNovo 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 user-selected scoring functions. In modes (iii) and (iv), RAId deNovo is capable of combining results from different scoring functions using spectrum-specific statistics. The web link is http://www.ncbi.nlm.nih.gov/CBBresearch/qmbp/raid denovo/index.html. Relevant binaries for Linux, Windows, and Mac OS X are available from the same page.