In Mascot Server 2.2 and later, any search can be run against a decoy (randomised) database generated on the fly. Each sequence in the database is randomised and then searched along with the original sequence. Results for matches against the original sequence are stored as normal, while results against the randomised sequence are saved in the
It is easy for existing code to switch between the decoy results and the standard results. To view the decoy results, specify MSRES_DECOY when creating the
ms_proteinsummary object. This flag cannot be used with MSRES_INTEGRATED_ERR_TOL and MSRES_ERR_TOL.
To determine false discovery rates, the following functions can be used:
For a peptide summary, the number of hits is the number of peptide matches, while for a protein summary, the number of hits is the number of protein matches.
You can use ms_searchparams::getDECOY() to decide whether to display false discovery rates.
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