MassTraceExtractor extracts mass traces from a MSExperiment map and stores them into a FeatureXMLFile.

pot. predecessor tools	→ MassTraceExtractor →	pot. successor tools
PeakPickerHiRes		FeatureFinderMetabo
PeakPickerHiRes		TextExporter

This TOPP tool detects mass traces in centroided LC-MS maps and stores them as features in a FeatureMap. These features may be either used directly as input for an metabolite ID approach or further be assembled to aggregate features according to a theoretical isotope pattern. For metabolomics experiments, the FeatureFinderMetabo tool offers both mass trace extraction and isotope pattern assembly. For proteomics data, please refer to the FeatureFinderCentroided tool.

The command line parameters of this tool are:

MassTraceExtractor -- Detects mass traces in centroided LC-MS data.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_MassTraceExtractor.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:
  MassTraceExtractor <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>*        Input centroided mzML file (valid formats: 'mzML')
  -out <file>*       Output featureXML file with mass traces (valid formats: 'featureXML', 'consensusXML')
  -out_type <type>   Output file type -- default: determined from file extension or content (valid: 'featureX
                     ML', '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   Algorithm parameters section

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_MassTraceExtractor.html

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.

+MassTraceExtractorDetects mass traces in centroided LC-MS data.

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

++1Instance '1' section for 'MassTraceExtractor'

in input centroided mzML fileinput file*.mzML

out output featureXML file with mass tracesoutput file*.featureXML, *.consensusXML

out_type output file type -- default: determined from file extension or contentfeatureXML, consensusXML

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

+++algorithmAlgorithm parameters section

++++common

noise_threshold_int10.0 Intensity threshold below which peaks are regarded as noise.

chrom_peak_snr3.0 Minimum signal-to-noise a mass trace should have.

chrom_fwhm5.0 Expected chromatographic peak width (in seconds).

++++mtd

mass_error_ppm20.0 Allowed mass deviation (in ppm).

ion_mobility_tolerance0.01 Allowed ion mobility deviation (in 1/K0 units, e.g., 0.01-0.05). For CCS data, use larger values (e.g., 2-10 square angstroms).

reestimate_mt_sdtrue Enables dynamic re-estimation of m/z variance during mass trace collection stage.true, false

quant_methodarea Method of quantification for mass traces. For LC data 'area' is recommended, 'median' for direct injection data. 'max_height' simply uses the most intense peak in the trace.area, median, max_height

trace_termination_criterionoutlier Termination criterion for the extension of mass traces. In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold.outlier, sample_rate

trace_termination_outliers5 Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached.

min_sample_rate0.5 Minimum fraction of scans along the mass trace that must contain a peak.

min_trace_length5.0 Minimum expected length of a mass trace (in seconds).

max_trace_length-1.0 Maximum expected length of a mass trace (in seconds). Set to a negative value to disable maximal length check during mass trace detection.

++++epd

width_filteringfixed Enable filtering of unlikely peak widths. The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution.off, fixed, auto

min_fwhm1.0 Minimum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if parameter width_filtering is off or auto.

max_fwhm60.0 Maximum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if parameter width_filtering is off or auto.

masstrace_snr_filteringfalse Apply post-filtering by signal-to-noise ratio after smoothing.true, false

enabledtrue Enables/disables the chromatographic peak detection of mass tracestrue, false