Proline handles decoy searches performed from two different strategies:
Concatenated searches:
A protein databank is created by concatenating target protein sequence to decoy protein sequence. Decoy could be created using reverse or random strategy. From Mascot or OMSSA point of view, a unique search is done using that databank.
Separated searches:
Two searches are done using the same peaklist, one on a target protein databank and one on a decoy protein databank. These searches are then combined to retrieve useful information such as FDR … Mascot allows user to check a decoy option and will automatically create a decoy databank.
Decoy and Target Search Result
Concatenated searches:
When importing search result from a decoy concatenated databank, decoy data are extracted from the Result File and stored in Proline databases as an independent/unique Search Result as well as target Search result data. These both searches are linked to each other.
Separated searches
The two performed searches are stored in Proline databases and are linked together.
See Search Result to view which information is saved