OpenSwathPeakMapExtractor

Extract targeted raw mz/RT/IM peak maps from DIA / diaPASEF data.

This tool reuses the OpenSWATH targeting and calibration logic, but instead of integrating chromatograms it retains the full raw point cloud inside each targeted extraction window. The output is written as Parquet .xipm files containing one row per extracted precursor or transition with compressed parallel arrays for m/z, RT, ion mobility, and intensity.

The tool supports:

• single-file and multi-run mzML / sqMass / Bruker TDF style OpenSWATH input
• transition libraries in TraML / TSV / PQP / OSWPQ
• optional RT normalization and auto-iRT calibration
• user-provided or auto-estimated extraction windows
• aggregated multi-run output or one .xipm per run

The command line parameters of this tool are:

OpenSwathPeakMapExtractor -- Extract targeted mz/RT/IM peak maps from DIA or diaPASEF data
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_OpenSwathPeakMapExtractor.html
Version: 3.6.0-pre-nightly-2026-07-03 Jul  4 2026, 01:47:29, Revision: 3ff9e1f
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:
  OpenSwathPeakMapExtractor <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 <files>*                        Input files separated by blank (valid formats: 'mzML', 'mzXML', 'sqMass
                                      ', 'd')
  -tr <file>*                         Transition file ('TraML','tsv','pqp','oswpq') (valid formats: 'traML', 
                                      'tsv', 'pqp', 'oswpq')
  -tr_type <type>                     Input transition file type -- default: determined from file extension 
                                      (valid: 'traML', 'tsv', 'pqp', 'oswpq')
  -swath_windows_file <file>          Optional, tab-separated file containing the SWATH windows for extractio
                                      n: lower_offset upper_offset. The first line is treated as a header.
  -out <file>                         Output .xipm parquet file containing all runs. Required unless -separat
                                      e_runs is set. (valid formats: 'xipm')
  -out_dir <dir>                      Output directory for per-run .xipm files when -separate_runs is set.
  -separate_runs                      Write one .xipm file per input run instead of aggregating all runs into
                                       -out
  -pasef                              Data is PASEF data
  -rt_extraction_window <double>      Only extract RT around this value. This is the full window size. Non-po
                                      sitive values disable RT filtering during peak-map extraction. (default
                                      : '600.0')
  -ion_mobility_window <double>       Extraction window in ion mobility dimension. This is the full window 
                                      size. Non-positive values extract the full IM range. (default: '-1.0')
  -mz_extraction_window <double>      Extraction window in Thomson or ppm (see mz_extraction_window_unit) 
                                      (default: '50.0') (min: '0.0')
  -mz_extraction_window_ms1 <double>  Extraction window used in MS1 in Thomson or ppm (see mz_extraction_wind
                                      ow_ms1_unit) (default: '50.0') (min: '0.0')
  -im_extraction_window_ms1 <double>  Extraction window in ion mobility dimension for MS1. -1 extracts the 
                                      full IM range. (default: '-1.0')
  -keep_cached_files                  Do not remove cached files created in tempDirectory

Debugging:
  -Debugging:irt_mzml <file>          Chromatogram mzML containing the iRT peptides (valid formats: 'mzML')
  -Debugging:irt_trafo <file>         Transformation file for RT transform (valid formats: 'trafoXML')

                                      
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:
 - Calibration                    Parameters for calibrant iRT peptides for RT normalization and mass / ion 
                                  mobility correction.
 - Calibration:MassIMCorrection   Parameters for the m/z and ion mobility calibration.
 - Calibration:RTNormalization    Parameters for the RTNormalization for iRT peptides.
 - Library                        Library parameters section
 - MRMMapping                     Parameters for mapping chromatograms to transitions during iRT calibration.


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_OpenSwathPeakMapExtractor.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.

+OpenSwathPeakMapExtractorExtract targeted mz/RT/IM peak maps from DIA or diaPASEF data

version3.6.0-pre-nightly-2026-07-03 Version of the tool that generated this parameters file.

++1Instance '1' section for 'OpenSwathPeakMapExtractor'

in[] Input files separated by blankinput file*.mzML, *.mzXML, *.sqMass, *.d

tr transition file ('TraML','tsv','pqp','oswpq')input file*.traML, *.tsv, *.pqp, *.oswpq

tr_type Input transition file type -- default: determined from file extensiontraML, tsv, pqp, oswpq

swath_windows_file Optional, tab-separated file containing the SWATH windows for extraction: lower_offset upper_offset. The first line is treated as a header.input file

sort_swath_mapsfalse Sort input SWATH files when matching to SWATH windows from swath_windows_filetrue, false

out Output .xipm parquet file containing all runs. Required unless -separate_runs is set.output file*.xipm

out_dir Output directory for per-run .xipm files when -separate_runs is set.output dir

separate_runsfalse Write one .xipm file per input run instead of aggregating all runs into -outtrue, false

enable_ms1true Extract precursor peak maps from the MS1 map if presenttrue, false

ms1_isotopes0 The number of additional MS1 isotopes used for extraction0:∞

min_upper_edge_dist0.0 Minimal distance to the upper edge of a SWATH window to still consider a precursor, in Thomson

paseffalse Data is PASEF datatrue, false

matching_window_onlyfalse Assume the input data is targeted / PRM-like data with potentially overlapping DIA windows. Only extract each assay from the best matching DIA window.true, false

rt_extraction_window600.0 Only extract RT around this value. This is the full window size. Non-positive values disable RT filtering during peak-map extraction.

extra_rt_extraction_window0.0 Extract additional RT beyond the primary window for inspection.0.0:∞

ion_mobility_window-1.0 Extraction window in ion mobility dimension. This is the full window size. Non-positive values extract the full IM range.

mz_extraction_window50.0 Extraction window in Thomson or ppm (see mz_extraction_window_unit)0.0:∞

mz_extraction_window_unitppm Unit for mz extractionTh, ppm

mz_extraction_window_ms150.0 Extraction window used in MS1 in Thomson or ppm (see mz_extraction_window_ms1_unit)0.0:∞

mz_extraction_window_ms1_unitppm Unit of the MS1 m/z extraction windowppm, Th

im_extraction_window_ms1-1.0 Extraction window in ion mobility dimension for MS1. -1 extracts the full IM range.

use_ms1_ion_mobilitytrue Also apply ion mobility extraction to MS1 peak-map extractiontrue, false

irt_mz_extraction_window50.0 Extraction window used for iRT and m/z correction in Thomson or ppm (see irt_mz_extraction_window_unit)0.0:∞

irt_mz_extraction_window_unitppm Unit for iRT mz extractionTh, ppm

irt_im_extraction_window-1.0 Ion mobility extraction window used for iRT calibration. -1 disables IM calibration.

split_file_inputfalse The input files each contain one single SWATH window (alternatively: all SWATHs are in separate files)true, false

readOptionsnormal Whether to run directly on the input data, cache data to disk first, or load working sets into memorynormal, cache, cacheWorkingInMemory, workingInMemory

tempDirectory/tmp Temporary directory used for cached files

keep_cached_filesfalse Do not remove cached files created in tempDirectorytrue, false

extraction_functiontophat Function used to extract the signaltophat

batchSize1000 Compound batch size per SWATH window. Set 0 to process all compounds for a window in one batch.0:∞

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

+++DebuggingDebugging

irt_mzml Chromatogram mzML containing the iRT peptidesoutput file*.mzML

irt_trafo Transformation file for RT transformoutput file*.trafoXML

+++CalibrationParameters for calibrant iRT peptides for RT normalization and mass / ion mobility correction.

tr_irt_priority_sampling Optional custom transition file (TSV format only) containing additional priority peptides for iRT sampling.

rt_norm RT normalization file (how to map the RTs of this run to the ones stored in the library). If set, no automatic RT calibration is performed.

++++auto_irt

enabledtrue Whether to sample iRTs on‐the‐fly (true) from the input targeted transition file (instead of passing specific iRT files). This may be useful if standard iRTs (Biognosys iRT kit) were not spiked-in. If set to false, and no additional iRT files are provided, and no transformation is provided, then no calibration is performed.true, false

irt_bins100 Number of RT bins for linear iRT sampling1:10000

irt_peptides_per_bin5 Peptides sampled per bin for linear iRT1:∞

irt_seed5489 RNG seed for reproducible sampling (0 = non-deterministic)0:∞

irt_bins_nonlinear2000 Number of RT bins for nonlinear iRT sampling1:10000

irt_peptides_per_bin_nonlinear50 Peptides sampled per bin for nonlinear iRT (0 = skip nonlinear)0:∞

linear_top_fraction0.4 Top fraction of intense peptides to sample for linear iRT0.01:1.0

nonlinear_top_fraction0.7 Top fraction of intense peptides to sample for nonlinear iRT0.01:1.0

irt_nonlinear_rt_extraction_window600.0 Only extract RT around this value for non linear iRT calibration (set to -1 to use whole range)-1.0:∞

+++++prefilter

enabledtrue Enable raw-data evidence prefiltering for sampled iRT peptides.true, false

evidence_sourcesms2 Evidence source for iRT prefiltering: use MS2 fragments only (more stringent than hybrid).ms1, ms2, hybrid

ms1_top_peaks_per_spectrum1000 Number of most intense MS1 peaks to keep per spectrum before precursor m/z matching.1:∞

ms2_top_peaks_per_spectrum1000 Number of most intense MS2 peaks to keep per spectrum before fragment m/z matching.1:∞

ms2_top_transitions_per_precursor6 Number of highest library-intensity fragment transitions to index per precursor for MS2 evidence.1:64

ms2_min_fragment_hits6 Minimum fragment hits for iRT prefiltering (higher threshold ensures robust iRT peptides).1:64

min_supported_precursors3 Minimum number of supported precursors required when the prefilter is enabled.1:∞

++++++peak_picking

enabledfalse Run PeakPickerHiRes on spectra before top-N matching. This is intended for profile data and is disabled by default.true, false

use_gausstrue Use Gaussian smoothing before PeakPickerHiRes. If false, use Savitzky-Golay smoothing.true, false

+++++++PeakPickerHiRes

signal_to_noise0.0 Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)0.0:∞

spacing_difference_gap4.0 The extension of a peak is stopped if the spacing between two subsequent data points exceeds 'spacing_difference_gap * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. '0' to disable the constraint. Not applicable to chromatograms.0.0:∞

spacing_difference1.5 Maximum allowed difference between points during peak extension, in multiples of the minimal difference between the peak apex and its two neighboring points. If this difference is exceeded a missing point is assumed (see parameter 'missing'). A higher value implies a less stringent peak definition, since individual signals within the peak are allowed to be further apart. '0' to disable the constraint. Not applicable to chromatograms.0.0:∞

missing1 Maximum number of missing points allowed when extending a peak to the left or to the right. A missing data point occurs if the spacing between two subsequent data points exceeds 'spacing_difference * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. Not applicable to chromatograms.0:∞

ms_levels[] List of MS levels for which the peak picking is applied. If empty, auto mode is enabled, all peaks which aren't picked yet will get picked. Other scans are copied to the output without changes.1:∞

report_FWHMfalse Add metadata for FWHM (as floatDataArray named 'FWHM' or 'FWHM_ppm', depending on param 'report_FWHM_unit') for each picked peak.true, false

report_FWHM_unitrelative Unit of FWHM. Either absolute in the unit of input, e.g. 'm/z' for spectra, or relative as ppm (only sensible for spectra, not chromatograms).relative, absolute

allow_missing_flankfalse Allow peaks without flanking data points on both sides. This is useful for TimsTOF data where profile peaks may be missing the leading or trailing edge.true, false

++++++++SignalToNoise

max_intensity-1 maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N.-1:∞

auto_max_stdev_factor3.0 parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev0.0:999.0

auto_max_percentile95 parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile0:100

auto_mode0 method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method-1:1

win_len200.0 window length in Thomson1.0:∞

bin_count30 number of bins for intensity values3:∞

min_required_elements10 minimum number of elements required in a window (otherwise it is considered sparse)1:∞

noise_for_empty_window1.0e20 noise value used for sparse windows

write_log_messagestrue Write out log messages in case of sparse windows or median in rightmost histogram bintrue, false

++++files

linear_irt_file Path(s) to linear iRT transition file(s) (TraML, TSV, or PQP). Accepts a string of a single file path or multiple file paths (space-separated, 'run1_irt.pqp run2_irt.pqp ... runN_irt.pqp') for run-specific mapping (positional: nth entry -> nth run).

nonlinear_irt_file Path(s) to nonlinear iRT transition file(s) (TraML, TSV, or PQP). Accepts a string of a single file path or multiple file paths (space-separated, 'run1_irt.pqp run2_irt.pqp ... runN_irt.pqp') for run-specific mapping (positional: nth entry -> nth run). Entries may be empty to indicate no nonlinear iRT for that run.

++++linear

outlier_detectioniter_residual Which outlier detection method to use for linear calibration (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none'). Iterative methods remove one outlier at a time. Jackknife approach optimizes for maximum r-squared improvement while 'iter_residual' removes the datapoint with the largest residual error (removal by residual is computationally cheaper, use this with lots of peptides).iter_residual, iter_jackknife, ransac, none

++++nonlinear

outlier_detectioniter_residual Which outlier detection method to use for nonlinear calibration (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none'). Iterative methods remove one outlier at a time. Jackknife approach optimizes for maximum r-squared improvement while 'iter_residual' removes the datapoint with the largest residual error (removal by residual is computationally cheaper, use this with lots of peptides).iter_residual, iter_jackknife, ransac, none

++++windows

estimate_rttrue Estimate RT extraction windows from calibrationtrue, false

estimate_mztrue Estimate m/z extraction windows from calibrationtrue, false

estimate_imtrue Estimate ion mobility extraction windows from calibrationtrue, false

rt_percentile95.0 Percentile for RT window estimation (25.0-99.9)25.0:99.900000000000006

rt_estimation_padding_factor1.3 A padding factor to multiply the estimated RT window by. For example, a factor of 1.3 will add a 30% padding to the estimated RT window, so if the estimated RT window is 144, then 43 will be added for a total estimated RT window of 187 seconds. A factor of 1.0 will not add any padding to the estimated window.1.0:∞

++++qc

min_rsq0.95 Minimum R-squared required for RT peptides regression0.0:1.0

min_coverage0.6 Minimum relative amount of RT peptides to keep0.0:1.0

++++MassIMCorrectionParameters for the m/z and ion mobility calibration.

mz_extraction_window-1.0 M/z extraction window width

mz_extraction_window_ppmfalse Whether m/z extraction is in ppmtrue, false

ms1_im_calibrationfalse Whether to use MS1 precursor data for the ion mobility calibration (default = false, uses MS2 / fragment ions for calibration)true, false

im_extraction_window-1.0 Ion mobility extraction window width

mz_estimation_padding_factor1.3 A padding factor to multiply the estimated m/z window by. For example, a factor of 1.3 will add a 30% padding to the estimated m/z window, so if the estimated m/z window is 18, then 5.4 will be added for a total estimated m/z window of 23.4. A factor of 1.0 will not add any padding to the estimated window.1.0:∞

im_estimation_padding_factor1.3 A padding factor to multiply the estimated ion_mobility window by. For example, a factor of 1.3 will add a 30% padding to the estimated ion_mobility window, so if the estimated ion_mobility window is 0.03, then 0.009 will be added for a total estimated ion_mobility window of 0.039. A factor of 1.0 will not add any padding to the estimated window.1.0:∞

mz_estimation_percentile99.0 Percentile for m/z window estimation (25.0-99.9)25.0:99.900000000000006

im_estimation_percentile99.0 Percentile for ion mobility window estimation (25.0-99.9)25.0:99.900000000000006

mz_correction_functionnone Type of normalization function for m/z calibration.none, regression_delta_ppm, unweighted_regression, weighted_regression, quadratic_regression, weighted_quadratic_regression, weighted_quadratic_regression_delta_ppm, quadratic_regression_delta_ppm

im_correction_functionlinear Type of normalization function for IM calibration.none, linear

debug_im_file Debug file for Ion Mobility calibration.

debug_mz_file Debug file for m/z calibration.

++++RTNormalizationParameters for the RTNormalization for iRT peptides.

alignmentMethodlinear How to perform the alignment to the normalized RT space using anchor points.linear, interpolated, lowess, b_spline

useIterativeChauvenetfalse Whether to use Chauvenet's criterion when using iterative methods.true, false

RANSACMaxIterations1000 Maximum iterations for the RANSAC outlier detection algorithm.

RANSACMaxPercentRTThreshold3 Maximum threshold in RT dimension for the RANSAC outlier detection algorithm.

RANSACSamplingSize10 Sampling size of data points per iteration for the RANSAC outlier detection algorithm.

estimateBestPeptidesfalse Whether the algorithms should try to choose the best peptides based on their peak shape for normalization.true, false

InitialQualityCutoff0.5 The initial overall quality cutoff for a peak to be scored.

OverallQualityCutoff5.5 The overall quality cutoff for a peak to go into the retention time estimation.

NrRTBins10 Number of RT bins to use to compute coverage.

MinPeptidesPerBin1 Minimal number of peptides that are required for a bin to count as covered.

MinBinsFilled8 Minimal number of bins required to be covered.

+++++lowess

auto_spantrue If true, or if 'span' is 0, automatically select LOWESS span by cross-validation.true, false

span0.05 Span parameter for lowess0.0:1.0

auto_span_min0.15 Lower bound for auto-selected span.1.0e-03:∞

auto_span_max0.8 Upper bound for auto-selected span.-∞:0.99

auto_span_grid0.005,0.01,0.05,0.15,0.25,0.30,0.50,0.70,0.90 Optional explicit grid of span candidates in (0,1].

+++++b_spline

num_nodes5 Number of nodes for b spline0:∞

+++LibraryLibrary parameters section

retentionTimeInterpretationiRT How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)iRT, seconds, minutes

override_group_label_checkfalse Override an internal check that assures that all members of the same PeptideGroupLabel have the same PeptideSequence (this ensures that only different isotopic forms of the same peptide can be grouped together in the same label group). Only turn this off if you know what you are doing.true, false

force_invalid_modsfalse Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification)true, false

+++MRMMappingParameters for mapping chromatograms to transitions during iRT calibration.

precursor_tolerance0.9 Precursor tolerance when mapping (in Th)

product_tolerance1.2 Product tolerance when mapping (in Th)

irt_precursor_tolerance1.5 Precursor tolerance when mapping iRT transitions (in Th)

irt_product_tolerance1.5 Product tolerance when mapping iRT transitions (in Th)

map_multiple_assaysfalse Allow to map multiple assays to chromatograms and duplicate these chromatograms in the output.true, false

error_on_unmappedfalse Treat remaining, unmapped chromatograms as an errortrue, false