Asoka,

There isn't any built-in Ui for decoy database generation or computation of FDR. The TPP site talks about a new tool Mayu at http://tools.proteomecenter.org/wiki/index.php?title=Software:Mayu . According to the docs, Mayu both generates the reverse sequence decoys and estimates FDRs. It works with pep.xml format so it would probably be the simplest approach. We don't ship it (and probably can't because it is GNU-licensed) but it could be implemented as pipeline tasks with some small effort.

The best use of decoys I know of is the combination of crux (http://noble.gs.washington.edu/proj/crux/) and percolator (http://noble.gs.washington.edu/proj/percolator/) from the University of Washington. That would be more work to incorporate with LabKey/CPAS because of the different file formats.

Peter