TransitionListEvidenceFilter

Filters a transition list by quick precursor evidence in raw data.

This tool scans one or more mzML/sqMass input runs with the OpenMS::TransitionListEvidenceFilter module and writes a filtered transition list for follow-up inspection or downstream DIA processing.

For multiple input files, the default behavior is a union across runs: a target precursor is kept if it has evidence in any mzML file. Use aggregation_method all to keep only targets observed in every input run. If split_file_input is set, all input files are interpreted as split SWATH windows from one run, matching OpenSwathWorkflow's split-input mode.

The evidence filter itself is target-only. If the output is meant for full target-decoy scoring, use decoy_handling keep_all or decoy_handling keep_matching; otherwise decoy transitions are removed from the filtered output.

Experimental classes:

This tool is experimental and intended for evaluating prefiltering strategies before integrating filtered libraries into production workflows.

The command line parameters of this tool are:

TransitionListEvidenceFilter -- Filter transition-list precursors by quick raw-data evidence.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_TransitionListEvidenceFilter.html
Version: 3.7.0-pre-nightly-2026-11-08 Nov  9 2026, 01:20:48, Revision: a335fa6
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:
  TransitionListEvidenceFilter <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 mzML/sqMass files. By default each file is treated as one run. (valid 
                              formats: 'mzML', 'mzXML', 'sqMass', 'd')
  -tr <file>*                 Input transition file ('TraML', 'tsv', 'pqp', or 'oswpq'). (valid formats: 'tra
                              ML', 'tsv', 'pqp', 'oswpq')
  -tr_type <type>             Input transition file type. Default: determined from file extension or content.
                               (valid: 'traML', 'tsv', 'pqp', 'oswpq')
  -out <file>*                Filtered output transition file. (valid formats: 'tsv', 'pqp', 'oswpq')
  -out_type <type>            Output transition file type. Default: determined from file extension. (valid: 
                              'tsv', 'pqp', 'oswpq')
  -pasef                      Data is PASEF data. If omitted, the tool auto-detects ion mobility SWATH window
                              s.
  -swath_windows_file <file>  Optional tab-separated file containing SWATH windows for extraction: lower_offs
                              et upper_offset. The first line is a header and will be skipped.
  -keep_cached_files          If set, do not remove cached files created in tempDirectory.
                              
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 availab
                              le 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   Raw-data precursor evidence filtering parameters.
 - Library     Transition TSV/PQP parsing parameters.

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_TransitionListEvidenceFilter.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.

+TransitionListEvidenceFilterFilter transition-list precursors by quick raw-data evidence.

version3.7.0-pre-nightly-2026-11-08 Version of the tool that generated this parameters file.

++1Instance '1' section for 'TransitionListEvidenceFilter'

in[] Input mzML/sqMass files. By default each file is treated as one run.input file*.mzML, *.mzXML, *.sqMass, *.d

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

tr_type Input transition file type. Default: determined from file extension or content.traML, tsv, pqp, oswpq

out Filtered output transition file.output file*.tsv, *.pqp, *.oswpq

out_type Output transition file type. Default: determined from file extension.tsv, pqp, oswpq

aggregation_methodany How to combine evidence across multiple input runs. 'any' keeps a target if it is supported in at least one run; 'all' requires support in every run.any, all

decoy_handlingremove How to handle decoys in the output. 'remove' writes target-only output. 'keep_all' keeps all original decoys. 'keep_matching' keeps decoys whose peptide_ref maps to a kept target after removing decoy_prefix.remove, keep_all, keep_matching

decoy_prefixDECOY_ Prefix used by decoy_handling=keep_matching to map decoy peptide_ref values back to target peptide_ref values.

min_upper_edge_dist0.0 Minimal distance to the upper edge of a SWATH window to still consider a precursor, in Thomson.0.0:∞

paseffalse Data is PASEF data. If omitted, the tool auto-detects ion mobility SWATH windows.true, false

prmfalse Data is targeted DIA / PRM-like data with potentially overlapping DIA windows.true, false

forcefalse Overrides tool-specific checkstrue, false

swath_windows_file Optional tab-separated file containing SWATH windows for extraction: lower_offset upper_offset. The first line is a header and will be skipped.input file

sort_swath_mapsfalse Sort input SWATH files when matching to SWATH windows from swath_windows_file.true, false

split_file_inputfalse Treat all input files as one split SWATH run, with each file containing one SWATH window.true, false

readOptionsnormal Whether to run directly on input data or cache data to disk first. If 'cache', set tempDirectory as needed.normal, cache

tempDirectory/tmp Temporary directory for cached data.

keep_cached_filesfalse If set, do not remove cached files created in tempDirectory.true, false

outer_loop_threads-1 How many threads the evidence filter should use (-1 uses the OpenMP maximum).

mz_extraction_window_ms150.0 MS1 precursor m/z extraction window full width, in Thomson or ppm.0.0:∞

mz_extraction_window_ms1_unitppm Unit of mz_extraction_window_ms1.Th, ppm

im_extraction_window_ms1-1.0 MS1 ion mobility extraction window full width. -1 disables MS1 IM filtering.

mz_extraction_window_ms250.0 MS2 fragment m/z extraction window full width, in Thomson or ppm.0.0:∞

mz_extraction_window_ms2_unitppm Unit of mz_extraction_window_ms2.Th, ppm

im_extraction_window_ms2-1.0 MS2 ion mobility extraction window full width. -1 disables MS2 IM filtering.

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

testfalse Enables the test mode (needed for internal use only)true, false

+++AlgorithmRaw-data precursor evidence filtering parameters.

evidence_sourceshybrid Evidence source used to keep precursor candidates: 'ms1', 'ms2', or 'hybrid' (MS1 OR MS2).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_hits4 Minimum number of distinct indexed fragments that must match in one MS2 spectrum to support a precursor.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

+++LibraryTransition TSV/PQP parsing parameters.

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