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

pot. predecessor tools	→ PeakPickerIM →	pot. successor tools
FileConverter	→ PeakPickerIM →	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 file can be an mzML file containing ion mobility data in concatenated format (where each spectrum contains an ion mobility float data array) or a Bruker TimsTOF .d directory (requires OpenMS built with WITH_OPENTIMS).

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 or Bruker .d file
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_PeakPickerIM.html
Version: 3.6.0-pre-nightly-2026-06-11 Jun 11 2026, 09:57:53, Revision: fc66052
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 file (mzML or Bruker .d) (valid formats: 'mzML', 'd')
  -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 (0 = all available cores)
                      (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/nightly/html/TOPP_PeakPickerIM.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.

+PeakPickerIMApplies PeakPickerIM to an mzML or Bruker .d file

version3.6.0-pre-nightly-2026-06-11 Version of the tool that generated this parameters file.

++1Instance '1' section for 'PeakPickerIM'

in Input file (mzML or Bruker .d)input file*.mzML, *.d

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 (0 = all available cores)

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

+++brukerOptions for reading Bruker TimsTOF .d files (requires WITH_OPENTIMS)

export_modeframe Export mode: 'auto' detects DDA/DIA acquisition type, 'frame' returns raw 4D frames without signal processing.auto, frame

calibration_tolerance0.0 m/z recalibration tolerance (0 = library default)0.0:∞

calibratefalse Enable m/z recalibration (may fail on some datasets)true, false

ms1_centroid_mz_ppm10.0 MS1 m/z linking tolerance in ppm. HillBased default 10 ppm tuned for detector-centroided TIMS-PASEF MS1; Greedy2D additionally requires ms1_centroid_im_pct > 0. Set to 0 to disable MS1 centroiding.0.0:∞

ms1_centroid_im_pct0.0 MS1 frame IM-centroiding ion mobility tolerance in percent. Both this and ms1_centroid_mz_ppm must be > 0 to enable. Suggested value: 3.0.0.0:∞

dia_ms2_n_neighbors0 DIA MS2 frame aggregation: 0 = raw per-frame export, 1 = 3-frame sum, 2 = 5-frame sum. Switches the entire DIA-MS2 export pipeline regardless of ms2_centroid_algo.0:∞

dia_ms2_min_support1 DIA MS2 denoising: minimum occupied neighbor cells in a 3x3 (m/z x IM) grid to keep a point (center cell excluded from count). Applied after frame aggregation. Only effective when dia_ms2_n_neighbors > 0. Set to 0 to disable denoising (useful for pure centroiding without noise filtering).0:∞

dia_ms2_centroidfalse Apply 2D Gaussian smoothing + local maxima peak picking to the denoised DIA MS2 grid. Produces IM_CENTROIDED spectra with sub-bin (m/z, IM) precision. Only effective when dia_ms2_n_neighbors > 0.true, false

ms1_centroid_algooff MS1 centroiding algorithm. 'off' = no IM-axis centroiding. 'greedy2d' = legacy 2D box clustering using ms1_centroid_mz_ppm/pct. 'hillbased' = IM-axis hill detection.off, greedy2d, hillbased

ms2_centroid_algooff MS2 centroiding algorithm. Takes precedence over dia_ms2_centroid.off, greedy2d, hillbased

ms2_centroid_mz_ppm20.0 HillBased MS2 m/z linking tolerance in ppm. Default 20.0 is DIA-PASEF-tuned. Set to 0 to refuse to run HillBased MS2 (the algo helper falls back to Off).0.0:∞

centroid_valley_factor1.3 HillBased: hill valley factor (hvf). Smaller = more aggressive splitting.1.0:∞

ms1_centroid_min_hill_length1 HillBased MS1: minimum number of IM scans a hill must span. Default 1 keeps single-IM-scan ions.1:∞

ms2_centroid_min_hill_length2 HillBased MS2: minimum number of IM scans a hill must span. Default 2 is DIA-PASEF-tuned. DDA-PASEF users should override to 1 (most DDA fragments are seen in only one IM scan; min=2 drops ~93% of DDA peaks).1:∞

centroid_max_scan_gap0 HillBased: max consecutive empty IM scans a hill may bridge (0 = strict).0:∞

isotopic_prefilterfalse MS1 + DIA-MS2 isotopic-partner prefilter applied after aggregation (or after raw extraction), before the centroider. Drops peaks lacking an isotopic partner at m/z ± C13C12_MASSDIFF / q (q in {1..5}) within ± isotopic_prefilter_tol_ppm AND |Δscan_id| <= 1. Not applied to DDA-MS2.true, false

isotopic_prefilter_tol_ppm50.0 ppm tolerance for isotopic-partner matching by the prefilter.0.0:∞

expose_hill_boundsfalse HillBased: attach hill bounding-box arrays per centroided spectrum for visual QC.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_im6.0e-04 Tolerance for summing adjacent ion mobility peaks (in 1/K0 units). For CCS data, use larger values (e.g., 1.0).

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 for clustering (in 1/K0 units). For CCS data, use larger values (e.g., 10-20).

++++pickIMElutionProfiles

ppm_tolerance_elution50.0 Mass trace m/z tolerance in ppm

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