This topic provides a brief overview of how to select the appropriate nodes to calculate false discovery rates (FDRs) and various options of handling FDRs in your workflow.
Search engines often provide multiple possible matching peptides as explanations for the same spectrum. Most of the time you can clearly distinguish the top-scoring match from the other PSMs, but sometimes, especially in the presence of dynamic modifications, the best-scoring matches of the same spectrum have very similar scores. In this case, you can filter the results to select the best-scoring PSMs and the matches that have very similar scores by using the Maximum Delta Cn parameter or the Maximum Rank parameter of the following nodes:
- Processing workflow:
- Consensus workflow:
The Ξ Cn value displays the normalized score difference between the currently selected PSM and the highest-scoring PSM for that spectrum:
The Maximum Delta Cn parameter filters out all PSMs with a Ξ Cn score larger than the specified value.
On the PSMs page of the result file, the Ξ Cn column displays the Ξ Cn values.