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OpenMS
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Tool to estimate the false discovery rate on peptide and protein level.
pot. predecessor tools | → FalseDiscoveryRate → | pot. successor tools |
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MascotAdapter (or other ID engines) | IDFilter | |
PeptideIndexer |
This TOPP tool calculates the false discovery rate (FDR) for results of target-decoy searches. The FDR calculation can be performed for proteins and/or for peptides (more exactly, peptide spectrum matches).
The false discovery rate is defined as the number of false discoveries (decoy hits) divided by the number of false and correct discoveries (both target and decoy hits) with a score better than a given threshold.
PeptideIndexer must be applied to the search results (idXML file) to index the data and to annotate peptide and protein hits with their target/decoy status.
The command line parameters of this tool are:
INI file documentation of this tool: