Pruned Databases

Within the "Advanced options" of a search task you will find analysis properties for "Post-Search Analysis". Within this drop down menu, you will find "Pruned Database Writing". Here you cans elect for two XML databases be constructed based on the results of your search task, Mod and Mod + Protein pruned. The Mod database contains all of the confidently identified modifications (that you selected) at 1% FDR. The Protein pruned database limits the proteins present in the database to those that were observed in bottom up, as well as containing all of the confidently identified modifications on these 1% FDR proteins. These databases are common constructed when G-PTM-D is performed in order to incorporate novel modifications into a searchable database. These pruned databases can be used to subsequent proteoform analysis, allowing for top-down and intact-mass results to be informed by bottom-up identifications.

Caution! We do not recommend using the pruned databases with the same dataset. These may bias the FDR assessment of subsequent searches of the same dataset. See http://pubs.acs.org/doi/abs/10.1021/pr101143m for more details.