In the advanced section of the MPQ and HCP workflows' settings, "auto decoys" can be configured under the "Proteins" category. This article explores its functionality, particularly in relation to how the false discovery rate (FDR) is applied at the protein level in Byonic (FDR in Byonic).
The value set with this parameter determines the number of decoy proteins included in the final list for quantification in Byologic.
For instance, a small value such as 2 reduces the number of identified hits, allowing Byologic to generate fewer XICs and operate more reliably, especially when dealing with extensive protein lists.
The example below illustrates which proteins are excluded with "auto decoys" set to 2. The dashed line indicates the number of proteins that would have been considered for quantification if 20 decoys had been included.
This setting predates MPQ's integration into the Byos Suite. While still available in MPQ, its necessity is reduced due to MPQ's ability to select top-quality peptides and reduce their number based on criteria.
The "auto-decoys" parameter ranges from 1 to 100. Setting it to 100 effectively disables this function. As a general guideline, set this value to 100 when samples are purified and the expected number of host cell proteins is low. Conversely, for numerous samples with a high protein count, users may opt for a lower "auto-decoys" value.