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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 |
|---|---|---|
| CometAdapter (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:
FalseDiscoveryRate -- Estimates the false discovery rate on peptide and protein level using decoy searches.
Full documentation: http://www.openms.de/doxygen/release/3.4.1/html/TOPP_FalseDiscoveryRate.html
Version: 3.4.1 May 19 2025, 14:24:34, Revision: 8aec8ec
To cite OpenMS:
+ Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.
Usage:
FalseDiscoveryRate <options>
This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript
ion or use the --helphelp option
Options (mandatory options marked with '*'):
-in <file>* Identifications from searching a target-decoy database. (vali
d formats: 'idXML')
-out <file>* Identifications with annotated FDR (valid formats: 'idXML')
-PSM <FDR level> Perform FDR calculation on PSM level (default: 'true') (valid
: 'true', 'false')
-peptide <FDR level> Perform FDR calculation on peptide level and annotates it as
meta value
(Note: if set, also calculates FDR/q-value on PSM level.)
(default: 'false') (valid: 'true', 'false')
-PSM_peptide_base_score <score name or type> Set if you want to choose a different score than the last
calculated main score for PSM or peptide level.
-protein <FDR level> Perform FDR calculation on protein level (default: 'true')
(valid: 'true', 'false')
-proteingroup <FDR level> Perform FDR calculation on (indist.) protein group level,
too. Currently, this will enable protein FDR automatically
(since internals need to be in-sync) but will affect the leve
l at which it filters (if enabled). (default: 'false') (valid
: 'true', 'false')
-protein_base_score <score name or type> Set if you want to choose a different score than the last
calculated main score for protein (group) level.
FDR control:
-FDR:PSM <fraction> Filter PSMs based on q-value (e.g., 0.05 = 5% FDR, disabled
for 1) (default: '1.0') (min: '0.0' max: '1.0')
-FDR:protein <fraction> Filter proteins based on q-value (e.g., 0.05 = 5% FDR, disabl
ed for 1) (default: '1.0') (min: '0.0' max: '1.0')
Common TOPP options:
-ini <file> Use the given TOPP INI file
-threads <n> Sets the number of threads allowed to be used by the TOPP
tool (default: '1')
-write_ini <file> Writes the default configuration file
--help Shows options
--helphelp Shows all options (including advanced)
The following configuration subsections are valid:
- algorithm Parameter section for the FDR calculation algorithm
You can write an example INI file using the '-write_ini' option.
Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.
For more information, please consult the online documentation for this tool:
- http://www.openms.de/doxygen/release/3.4.1/html/TOPP_FalseDiscoveryRate.html
INI file documentation of this tool:
1.9.1