OpenMS
PeakPickerIM

A tool for peak detection in the ion mobility dimension for mzML files.

pot. predecessor tools → PeakPickerIM → pot. successor tools
FileConverter any tool operating on MS peak data
(in mzML format)

This tool applies peak picking in the ion mobility dimension to raw LC-IMS-MS data. The input mzML file should contain ion mobility data in concatenated format (where each spectrum contains an ion mobility float data array).

Three peak picking methods are available:

  • mobilogram: Picks peaks along the ion mobility dimension using a peak picker.
  • cluster: Clusters peaks in the ion mobility dimension.
  • traces: Picks peaks using ion mobility elution profiles.

The command line parameters of this tool are: 

PeakPickerIM -- Applies PeakPickerIM to an mzML file
Full documentation: http://www.openms.de/doxygen/release/3.5.0/html/TOPP_PeakPickerIM.html
Version: 3.5.0 Dec 11 2025, 12:37:51, Revision: c1370fb
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:
  PeakPickerIM <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 mzML file (valid formats: 'mzML')
  -out <file>*       Output mzML 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 for PeakPickerIM (organized into pickIMTraces, pickIMCluster, pickIMEluti

               onProfiles).

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/release/3.5.0/html/TOPP_PeakPickerIM.html

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+PeakPickerIMApplies PeakPickerIM to an mzML file
version3.5.0 Version of the tool that generated this parameters file.
++1Instance '1' section for 'PeakPickerIM'
in Input mzML fileinput file*.mzML
out Output mzML fileoutput file*.mzML
processOptioninmemory Whether to load all data and process them in-memory or process on-the-fly (lowmemory) without loading the whole file into memory firstinmemory, lowmemory
methodmobilogram Method to pick peaks in IM dimensionmobilogram, cluster, traces
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 for PeakPickerIM (organized into pickIMTraces, pickIMCluster, pickIMElutionProfiles).
++++pickIMTraces
sum_tolerance_mz1.0 Tolerance for summing adjacent m/z peaks (ppm)
sum_tolerance_im5.999999999999999e-04 Tolerance for summing adjacent ion mobility peaks (1/k0)
gauss_ppm_tolerance5.0 Gaussian smoothing m/z tolerance in ppm
sgolay_frame_length5 Savitzky-Golay smoothing frame length
sgolay_polynomial_order3 Savitzky-Golay smoothing polynomial order
++++pickIMCluster
ppm_tolerance_cluster50.0 m/z tolerance in ppm for clustering
im_tolerance_cluster0.1 Ion mobility tolerance in 1/k for clustering
++++pickIMElutionProfiles
ppm_tolerance_elution50.0 Mass trace m/z tolerance in ppm

For the parameters of the algorithm section see the algorithm documentation: PeakPickerIM