Search predicted peptides from proteomes

I created a fasta containing my target around 1000 predicted peptide sequences. It is concatenated with Uniprot reference fasta to create a target-decoy database. Then the search engine will search proteome data to look up for any hits in the reference database.

I have some questions.

1. I would like to set 5% FDR for peptide identification filtering. Someone suggested that I should do this step exclusively for my predicted peptides. But I found few literatures mentioned details about how to perform this step. Some of them performed FDR filtering for the whole reference (Uniprot ref+predicted peptides). May I ask what is the preferred one?

2. If I would like to do the FDR filtering only for my target sequences, how could I do this?