IonMobilityBinning

Splits an mzML file with IonMobility frames into multiple mzML files by binning(merging) spectra by their IM values.

This tool supports two modes:

• Regular ion mobility: Splits data into a user-defined number of bins
• FAIMS: Automatically splits data by the FAIMS compensation voltages (CVs) present in the file

For regular ion mobility data:

• Useful to convert IM data to a format that can be processed by tools that do not support IM data (e.g. FeatureFinderCentroided or SearchEngines)
• The results of individual bins can be processed separately and then recombined afterwards
• To decide on the number of bins, try running FileInfo on the input file to get an idea of the range of IM values present

For FAIMS data:

• Automatically detects FAIMS compensation voltages in the input file
• Creates one output file per unique CV value
• MS2 spectra without explicit FAIMS CV are assigned to the preceding MS1 FAIMS CV
• No binning parameters required as the splitting is based on the discrete CV values

The command line parameters of this tool are:

IonMobilityBinning -- Splits an mzML file with IonMobility frames into multiple mzML files by binning(merging
) spectra by their IM values
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_IonMobilityBinning.html
Version: 3.6.0-pre-nightly-2026-03-12 Mar 13 2026, 01:45:58, Revision: 88f2819
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:
  IonMobilityBinning <options>

Options (mandatory options marked with '*'):
  -in <file>*                                   Input file (containing RT, IM, m/z, i.e. IM-frames). (valid 
                                                formats: 'mzML')
  -out <directory>*                             Path to the output directory to write the binned mzML files 
                                                to.
  -bins <number>                                Number of ion mobility bins to split the input file into (def
                                                ault: '5')
  -bin_extension_abs <number>                   Absolute extension of the bin in IM dimension (causes bins 
                                                to overlap by 2x this value) (default: '0.0')

Options for merging spectra within the same IM bin (from the same IM-frame):
  -SpectraMerging:mz_binning_width <number>     Width of the m/z bins (default: '0.01')
  -SpectraMerging:mz_binning_width_unit <unit>  Unit of the m/z bin width (default: 'Da') (valid: 'Da', 'ppm'
                                                )

                                                
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.

+IonMobilityBinningSplits an mzML file with IonMobility frames into multiple mzML files by binning(merging) spectra by their IM values

version3.6.0-pre-nightly-2026-03-12 Version of the tool that generated this parameters file.

++1Instance '1' section for 'IonMobilityBinning'

in Input file (containing RT, IM, m/z, i.e. IM-frames).input file*.mzML

out Path to the output directory to write the binned mzML files to.output prefix

bins5 Number of ion mobility bins to split the input file into

bin_extension_abs0.0 Absolute extension of the bin in IM dimension (causes bins to overlap by 2x this value)

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

+++SpectraMergingOptions for merging spectra within the same IM bin (from the same IM-frame)

mz_binning_width0.01 Width of the m/z bins

mz_binning_width_unitDa Unit of the m/z bin widthDa, ppm