Although heavily concentrated and studied, the statistical accuracy of peptide identification remains challenging. For example, there are many ? peptide identification methods using database searches and assigning the E-value to peptide hits. Unfortunately, the E-values reported among different methods do not agree with each other and none of them agree with the textbook definition of the E-value. ? ? ? This year, we have developed a new database search method for peptide identification, RAId_DbS. From our study, RAId_DbS is able to provide more accurate E-value ( or statistical significance) than other existing methods. In addition, it is also shown that in terms of information retrieval efficiency, RAId_DbS is at least comparable to or better than best existing methods. Our written manuscript is currently submitted to Biology Direct.? ? We have also developed a new protocol to calibrate the statistics for any database search method. This protocol allows the user to transform the score or E-value reported by a certain search method into a standardized E-value that is derived from the fundamental definition of E-value. As a consequence, this protocol enables comparison between results obtained from different search methods, analyzed by different laboratories etc.? The written manuscript is currently submitted to Biology Direct.
