The Fixed Value PSM Validator node validates PSMs on the basis of the fixed score thresholds that you defined for each search node on the Administration page that opens when you choose Administration > Configuration.
The application has two ways of validating PSMs:
- Uses score thresholds without a decoy search.
- Performs a decoy search and then calculates the score-based FDRs with the Target Decoy PSM Validator node or uses a more sophisticated machine-learning approach with the Percolator node.
You can connect a search node like MSPepSearch, which cannot perform a decoy search, only to the Fixed Value PSM Validator node.
The following table describes the parameters for the Fixed Value PSM Validator node.
Parameter | Definition |
|---|---|
Maximum Delta Cn | Specifies a Δ Cn threshold and filters out all PSMs with a Δ Cn larger than this value. Δ Cn is the normalized score difference between the currently selected PSM and the highest-scoring PSM for that spectrum. The default value of 0.05 for the Maximum Delta Cn parameter means that from every spectrum, the PSM with the best score is selected, plus the PSMs that have scores with a normalized difference of no more than 5 percent. The Maximum Delta Cn parameter is a kind of flexible rank filter. PSMs that are excluded from processing by Percolator are classified as low-confidence. Range: 0–1; default: 0.05 |
Maximum Rank | Specifies a maximum search engine rank threshold and filters out all PSMs with a search engine rank higher than this value. Range: 0–no maximum; default: 0 If you set this value to 0, the application uses all available PSMs. |