Pruned Databases

Once you search your dataset with a G-PTM-D database, you have the option of writing a pruned database (option located under "Post-Search Analysis" options). This database contains all of the confidently identified modifications at 1% FDR ("pruned") or only the confidently identified proteins and modifications at 1% FDR ("proteinPruned").

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. (For this reason, we do not add the pruned database to the database list in the application.)