Target Decoy FDR
Estimate target-decoy PSM false discovery rate using caller database-size ratio.
Description
Target-decoy FDR estimation uses decoy matches as a proxy for false target assignments.
Target-decoy FDR estimation uses decoy matches as a proxy for false target assignments. A database-size ratio scales the decoy count before normalization by target matches.1
Estimate target-decoy PSM false discovery rate using caller database-size ratio.
When to use Target Decoy FDR
Use this tool to estimate target-decoy PSM false discovery rate using caller database-size ratio.
Prepare the canonical sequence, peptide assignments, fitted assay parameters or upstream measurements requested. Keep corresponding entries aligned, use the stated mass and signal units, and remove FASTA headers before entering sequence text.
How to use Target Decoy FDR and understand its results
- Prepare the canonical sequence, peptide assignments, fitted assay parameters or upstream measurements requested. Keep corresponding entries aligned, use the stated mass and signal units, and remove FASTA headers before entering sequence text.
- Enter targetMatches, decoyMatches, decoyToTargetDatabaseRatio using the field table and calculation rules, then run the tool.
- Read estimatedFalseTargets, estimatedFdrPercent. The explanation below defines the units, signs, ordering and any flags or placeholder values.
- If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.
| Input field | Meaning | Value type; see rules below | Requirement |
|---|---|---|---|
| targetMatches | Target matches | number | Required |
| decoyMatches | Decoy matches | number | Required |
| decoyToTargetDatabaseRatio | Decoy to target database ratio | number | Required |
Enter positive safe-integer target matches, nonnegative safe-integer decoys and positive decoy-to-target database ratio. Read estimated false targets and FDR percentage.
estimatedFalseTargets=decoys/databaseRatio; FDR%=100 estimatedFalseTargets/targets Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| estimatedFalseTargets | Estimated false targets | number |
| estimatedFdrPercent | Estimated fdr percent | number |
{
"input": {
"targetMatches": 100,
"decoyMatches": 2,
"decoyToTargetDatabaseRatio": 1
},
"output": {
"estimatedFalseTargets": 2,
"estimatedFdrPercent": 2
}
}Limitations and assumptions
The estimate is not capped at 100%. Search design, decoy validity, score thresholds and peptide/protein-level error rates are not inferred.
Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.
Alternative or Complementary methods
Use PSM Qvalue Gate: Gate peptide-spectrum matches by supplied q-value threshold. For a complementary task, use Protein Volcano Coordinates: Build protein volcano-plot log2 effect and negative-log10 FDR coordinates.
References
-
Target Decoy FDR — tool.io
Similar or alternative tools
- PSM Qvalue Gate
Gate peptide-spectrum matches by supplied q-value threshold.
- Protein Volcano Coordinates
Build protein volcano-plot log2 effect and negative-log10 FDR coordinates.