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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 same steps are available as a library class (OpenMS::MultiplexResolverAlgorithm), which the MS1LabeledWorkflow tool uses to run the complete MS1-labeled quantification in one go.
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-2026-09-29 Sep 30 2026, 01:45:35, Revision: 55f7bdb
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>
Options (mandatory options marked with '*'):
-in <file>* Peptide multiplets with assigned sequence information (valid forma
ts: 'consensusXML')
-in_blacklist <file> Optional input containing spectral peaks blacklisted during featur
e detection. Needed for generation of dummy features. (valid forma
ts: 'mzML')
-out <file>* Complete peptide multiplets. (valid formats: 'consensusXML')
-out_conflicts <file> Optional output containing peptide multiplets without ID annotatio
n or with conflicting quant/ID information. (valid formats: 'conse
nsusXML')
Parameters for the algorithm.:
-algorithm:labels <text> Labels used for labelling the samples. [...] specifies the labels
for a single sample. For example
[][Lys8,Arg10] ... SILAC
[][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC
[Dimethyl0][Dimethyl6] ... Dimethyl
[Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl
[ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL (default: '[][Lys8,A
rg10]')
-algorithm:max_nr_labelled_aas <number> Maximum number of labelled amino acids per peptide, minus one.
The algorithm searches for peptides with up to (this value + 1)
labelled amino acids. For SILAC with trypsin digestion, this param
eter corresponds to the maximum number of missed cleavages. (defau
lt: '0') (min: '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)
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