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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.
FDR within classes of PSMs (experimental)
With -PSM_class, PSMs are split into classes (by their modifications, or by the value of a peptide hit meta value) and each target PSM also gets a q-value within its class (meta value "class_q-value"). Its PSM q-value becomes the larger of the two, so FDR:PSM holds within every class, not only overall. Without this, a small class (e.g. PSMs with a rare modification) can pass at a much higher error rate than the overall FDR, because its decoys are diluted among the targets of the large class. See ClassFDR for the estimator. Only available for PSM-level FDR (-peptide false).
Since the class q-value can only raise a PSM's q-value, the class FDR only removes PSMs; it never adds any. It is conservative in small classes and in classes whose targets are mostly false: there the null-fraction estimate is clipped at 1, and PSMs of a class that is already calibrated are lost too (in a semi-specific search, about 40% of the semi-specific PSMs at 1%). It cannot correct a large class whose own error rate is too high; that is up to the overall FDR estimate.
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/nightly/html/TOPP_FalseDiscoveryRate.html
Version: 3.7.0-pre-nightly-2026-11-07 Nov 8 2026, 01:17:31, Revision: 5a63f25
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.
-PSM_class <class> (Experimental:) Also control the PSM FDR within classes of
PSMs: 'modification' (by the variable modifications of a PSM)
, or the name of a peptide hit meta value whose values are
the classes. A PSM's q-value becomes the larger of its overal
l and its class q-value, so this only removes PSMs: conservat
ive in small or mostly false classes, and it cannot correct
a large class that is itself miscalibrated. Empty: off.
-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 (0 = all available cores) (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/nightly/html/TOPP_FalseDiscoveryRate.html
INI file documentation of this tool:
This section lists all parameters supported by the tool. Parameters are organized into hierarchical subsections that group related settings together. Subsections may contain further subsections or individual parameters.
Each parameter entry contains the following information:
Parameter tags provide additional information about how a parameter is used. Some tags indicate whether a parameter is required or intended for advanced configuration, while others may be used internally by OpenMS or workflow tools.
Parameters highlighted as required must be specified for the tool to run successfully. Parameters marked as advanced allow fine-tuning of algorithm behavior and are typically not needed for standard workflows.
1.9.8