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OpenMS
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Completes peptide multiplets and resolves conflicts within them.
| pot. predecessor tools | → MultiplexResolver → | pot. successor tools |
|---|---|---|
| IDMapper | ProteinQuantifier | |
| IDConflictResolver |
Tools such as FeatureFinderMultiplex can detect peptide feature multiplets in labeled experimental data. The multiplets can then be annotated with peptide sequences using the IDMapper tool (*). The MultiplexResolver tool is consolidating these results in two steps.
(*) Note that the MultiplexResolver tool takes only a single (the first) peptide sequence annotation into account. By running IDConflictResolver first, it is assured that each multiplet has only one peptide sequence annotation, the best one. Multiplets without sequence annotation are passed to the optional out_conflicts output.
The command line parameters of this tool are:
MultiplexResolver -- Completes peptide multiplets and resolves conflicts within them.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_MultiplexResolver.html
Version: 3.6.0-pre-nightly-2026-03-06 Mar 7 2026, 01:46:19, Revision: c92c980
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:
MultiplexResolver <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>* Peptide multiplets with assigned sequence information (valid formats: 'consensusXML'
)
-in_blacklist <file> Optional input containing spectral peaks blacklisted during feature detection. Neede
d for generation of dummy features. (valid formats: 'mzML')
-out <file>* Complete peptide multiplets. (valid formats: 'consensusXML')
-out_conflicts <file> Optional output containing peptide multiplets without ID annotation or with conflict
ing quant/ID information. (valid formats: 'consensusXML')
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 Parameters for the algorithm.
- labels Isotopic labels that can be specified in section 'algorithm:labels'.
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_MultiplexResolver.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