Cluster mass traces occurring in the same map together.

Cluster mass traces together found in a mass spectrometric map (MS1 or MS2). Input is a consensus map containing individual mass traces, the output may be spectra containing all clustered features.

Mass traces are clustered independent of precursor traces in another map (this is the more simple approach) and pseudo spectra are created without any precursors assigned. This is useful for

clustering of features in an MS1 map (isotope traces, charge states etc)
clustering of features in an SWATH map (fragment ions from the same precursor, isotope traces, charge states etc)

On the clustered fragments in an MS2 map, one can then (optionally) do

de novo searches
calculate the most likely precursor(s) and DB-search

The command line parameters of this tool are:

ClusterMassTraces -- Creates pseudo spectra.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_ClusterMassTraces.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:
  ClusterMassTraces <options>

Options (mandatory options marked with '*'):
  -in <file>*                        Mass traces (valid formats: 'consensusXML')
  -out <file>*                       Output file (valid formats: 'mzML')
  -min_pearson_correlation <double>  Minimal pearson correlation score (default: '0.7')
  -min_peak_nr <number>              Minimal peak nr to output pseudo spectra (default: '1')
  -max_lag <number>                  Maximal lag (default: '1')
  -max_rt_apex_difference <double>   Maximal difference of the apex in retention time (default: '5.0')
  -max_intensity_cutoff <double>     Maximal intensity to be added to a spectrum (default: '0.0')
  -add_precursor <double>            Add a precursor mass (default: '0.0')
                                     
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)

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.

+ClusterMassTracesCreates pseudo spectra.

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

++1Instance '1' section for 'ClusterMassTraces'

in Mass tracesinput file*.consensusXML

out output fileoutput file*.mzML

min_pearson_correlation0.7 Minimal pearson correlation score

min_peak_nr1 Minimal peak nr to output pseudo spectra

max_lag1 Maximal lag

max_rt_apex_difference5.0 Maximal difference of the apex in retention time

max_intensity_cutoff0.0 Maximal intensity to be added to a spectrum

add_precursor0.0 Add a precursor mass

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