A tool for peak detection in profile data. Executes the peak picking with high_res algorithm.

pot. predecessor tools	→ PeakPickerIterative →	pot. successor tools
BaselineFilter		any tool operating on MS peak data (in mzML format)
NoiseFilterGaussian
NoiseFilterSGolay

The conversion of the ''raw'' ion count data acquired by the machine into peak lists for further processing is usually called peak picking. The choice of the algorithm should mainly depend on the resolution of the data. As the name implies, the high_res algorithm is fit for high resolution data.

The command line parameters of this tool are:

PeakPickerIterative -- Finds mass spectrometric peaks in profile mass spectra.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_PeakPickerIterative.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:
  PeakPickerIterative <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 file  (valid formats: 'mzML')
  -out <file>*       Output file (valid formats: 'mzML')
                     
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_PeakPickerIterative.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.

+PeakPickerIterativeFinds mass spectrometric peaks in profile mass spectra.

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

++1Instance '1' section for 'PeakPickerIterative'

in input file input file*.mzML

out output fileoutput file*.mzML

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

signal_to_noise_1.0 Signal to noise value, each peak is required to be above this value (turn off by setting it to 0.0)

peak_width0.0 Expected peak width half width in Dalton - peaks will be extended until this half width is reached (even if the intensitity is increasing). In conjunction with check_width_internally it will also be used to remove peaks whose spacing is larger than this value.

spacing_difference1.5 Difference between peaks in multiples of the minimal difference to continue. The higher this value is set, the further apart peaks are allowed to be to still extend a peak. E.g. if the value is set to 1.5 and in a current peak the minimal spacing between peaks is 10 mDa, then only peaks at most 15 mDa apart will be added to the peak.

sn_bin_count_30 Bin count for the Signal to Noise estimation.

nr_iterations_5 Nr of iterations to perform (how many times the peaks are re-centered).1:∞

sn_win_len_20.0 Window length for the Signal to Noise estimation.

check_width_internallyfalse Delete peaks where the spacing is larger than the peak width (should be set to true to avoid artefacts)true, false

ms1_onlyfalse Only do MS1true, false

clear_meta_datafalse Delete meta data about peak widthtrue, false