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