MaRaClusterAdapter facilitates the input to, the call of and output integration of MaRaCluster. MaRaCluster (https://github.com/statisticalbiotechnology/maracluster) is a tool to apply unsupervised clustering of ms2 spectra from shotgun proteomics datasets.

Experimental classes:: This tool is work in progress and usage and input requirements might change.

pot. predecessor tools	→ MaRaClusterAdapter →	pot. successor tools
any signal-/preprocessing tool (in mzML format)	→ MaRaClusterAdapter →	MSGFPlusAdapter

MaRaCluster is dependent on the input parameter pcut, which is the logarithm of the pvalue cutoff. The default value is -10, lower values will result in smaller but purer clusters. If specified peptide search results can be provided as idXML files and the MaRaCluster Adapter will annotate cluster ids as attributes to each peptide identification, which will be outputed as a merged idXML. Moreover the merged idXML containing only scan numbers, cluster ids and file origin can be outputed without prior peptide identification searches. The assigned cluster ids in the respective idXML are equal to the scanindex of the produced clustered mzML.

The command line parameters of this tool are:

MaRaClusterAdapter -- Facilitate input to MaRaCluster and reintegrate.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_MaRaClusterAdapter.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.
To cite MaRaClusterAdapter:
 + The M and Käll L. MaRaCluster: A Fragment Rarity Metric for Clustering Fragment Spectra in Shotgun Proteo
   mics. J Proteome Res 2016; 15: 3. doi:10.1021/acs.jproteome.5b00749.

Usage:
  MaRaClusterAdapter <options>

Options (mandatory options marked with '*'):
  -in <files>*                           Input file(s) (valid formats: 'mzML', 'mgf')
  -id_in <files>                         Optional idXML Input file(s) in the same order as mzML files - for 
                                         Maracluster Cluster annotation (valid formats: 'idXML')
  -out <file>                            Output file in idXML format (valid formats: 'idXML')
  -consensus_out <file>                  Consensus spectra in mzML format (valid formats: 'mzML')
  -output_directory <directory>          Output directory for MaRaCluster original consensus output
  -pcut <value>                          Log(p-value) cutoff, has to be < 0.0. Default: -10.0. (default: '-10
                                         .0') (max: '0.0')
  -min_cluster_size <value>              Minimum number of spectra in a cluster for consensus spectra (defaul
                                         t: '1') (min: '1')
  -maracluster_executable <executable>*  The maracluster executable. Provide a full or relative path, or make
                                          sure it can be found in your PATH environment.
                                         
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 (defa
                                         ult: '1')
  -write_ini <file>                      Writes the default configuration file
  --help                                 Shows options
  --helphelp                             Shows all options (including advanced)

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

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:

Name The identifier used in configuration files and on the command line.
Default value The value used if the parameter is not explicitly specified.
Description A short explanation describing the purpose and behavior of the parameter.
Tags Additional metadata associated with the parameter.
Restrictions Allowed value ranges for numeric parameters or valid options for string parameters.

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.

+MaRaClusterAdapterFacilitate input to MaRaCluster and reintegrate.

version3.6.0-pre-nightly-2026-03-06 Version of the tool that generated this parameters file.

++1Instance '1' section for 'MaRaClusterAdapter'

in[] Input file(s)input file*.mzML, *.mgf

id_in[] Optional idXML Input file(s) in the same order as mzML files - for Maracluster Cluster annotationinput file*.idXML

out Output file in idXML formatoutput file*.idXML

consensus_out Consensus spectra in mzML formatoutput file*.mzML

output_directory Output directory for MaRaCluster original consensus output

pcut-10.0 log(p-value) cutoff, has to be < 0.0. Default: -10.0.-∞:0.0

min_cluster_size1 minimum number of spectra in a cluster for consensus spectra1:∞

maracluster_executablemaracluster The maracluster executable. Provide a full or relative path, or make sure it can be found in your PATH environment.input file, is_executable

verbose2 Set verbosity of output: 0=no processing info, 5=all.

precursor_tolerance20.0 Precursor monoisotopic mass tolerance

precursor_tolerance_unitsppm tolerance_mass_units 0=ppm, 1=Dappm, Da

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue, false

forcefalse Overrides tool-specific checkstrue, false

testfalse Enables the test mode (needed for internal use only)true, false

MaRaCluster is written by Matthew The (https://github.com/statisticalbiotechnology/maracluster Copyright Matthew The matth.nosp@m.ew.t.nosp@m.he@sc.nosp@m.ilif.nosp@m.elab..nosp@m.se) Cite Publication: MaRaCluster: A Fragment Rarity Metric for Clustering Fragment Spectra in Shotgun Proteomics Journal of proteome research, 2016, 15(3), pp 713-720 DOI: 10.1021/acs.jproteome.5b00749