Runs peptidoform, peptide, protein, or gene inference on OpenSWATH OSW files.

The tool operates directly on OSW files. Peptidoform inference writes SCORE_IPF. Peptide, protein, and gene inference write SCORE_PEPTIDE, SCORE_PROTEIN, and SCORE_GENE for the selected context. Multiple inference passes can be selected in one invocation via per-level true|false selectors. By default, peptide:global and protein:global are enabled.

For more information, see the original publications describing the underlying algorithms:

Rosenberger, G., Bludau, I., Schmitt, U. et al. Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses. Nat Methods 14, 921–927 (2017). https://doi.org/10.1038/nmeth.4398
Rosenberger, G., Liu, Y., Röst, H. et al. Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS. Nat Biotechnol 35, 781–788 (2017). https://doi.org/10.1038/nbt.3908

The command line parameters of this tool are:

OpenSwathInfer -- Runs inference on OpenSWATH results.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_OpenSwathInfer.html
Version: 3.6.0-pre-nightly-2026-06-23 Jun 24 2026, 01:51:33, Revision: 50ce1ba
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:
  OpenSwathInfer <options>

Options (mandatory options marked with '*'):
  -in <file>*                                             Input OpenSWATH OSW file. (valid formats: 'osw')
  -out <file>                                             Optional output OSW file. If empty, the input file 
                                                          is updated in place. (valid formats: 'osw')

Peptidoform/IPF inference options.:
  -peptidoform:run <true|false>                           Enable peptidoform inference in this invocation. 
                                                          (default: 'false') (valid: 'true', 'false')
  -peptidoform:ipf_ms1_scoring <true|false>               Use MS1 precursor evidence. (default: 'false') (val
                                                          id: 'true', 'false')
  -peptidoform:ipf_ms2_scoring <true|false>               Use MS2 precursor evidence from transition-level 
                                                          precursor rows. (default: 'false') (valid: 'true', 
                                                          'false')
  -peptidoform:propagate_signal_across_runs <true|false>  Propagate confident transition evidence across alig
                                                          ned runs using FEATURE_MS2_ALIGNMENT_CANDIDATE. 
                                                          (default: 'false') (valid: 'true', 'false')

Peptide-level inference selection options.:
  -peptide:global <true|false>                            Enable peptide inference in the global context. 
                                                          (default: 'true') (valid: 'true', 'false')
  -peptide:experiment_wide <true|false>                   Enable peptide inference in the experiment-wide 
                                                          context. (default: 'false') (valid: 'true', 'false'
                                                          )
  -peptide:run_specific <true|false>                      Enable peptide inference in the run-specific contex
                                                          t. (default: 'false') (valid: 'true', 'false')

Protein-level inference selection options.:
  -protein:global <true|false>                            Enable protein inference in the global context. 
                                                          (default: 'true') (valid: 'true', 'false')
  -protein:experiment_wide <true|false>                   Enable protein inference in the experiment-wide 
                                                          context. (default: 'false') (valid: 'true', 'false'
                                                          )
  -protein:run_specific <true|false>                      Enable protein inference in the run-specific contex
                                                          t. (default: 'false') (valid: 'true', 'false')

Gene-level inference selection options.:
  -gene:global <true|false>                               Enable gene inference in the global context. (defau
                                                          lt: 'false') (valid: 'true', 'false')
  -gene:experiment_wide <true|false>                      Enable gene inference in the experiment-wide contex
                                                          t. (default: 'false') (valid: 'true', 'false')
  -gene:run_specific <true|false>                         Enable gene inference in the run-specific context. 
                                                          (default: 'false') (valid: 'true', 'false')

                                                          
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)

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.

+OpenSwathInferRuns inference on OpenSWATH results.

version3.6.0-pre-nightly-2026-06-23 Version of the tool that generated this parameters file.

++1Instance '1' section for 'OpenSwathInfer'

in Input OpenSWATH OSW file.input file*.osw

out Optional output OSW file. If empty, the input file is updated in place.output file*.osw

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

+++peptidoformPeptidoform/IPF inference options.

runfalse Enable peptidoform inference in this invocation.true, false

ipf_ms1_scoringfalse Use MS1 precursor evidence.true, false

ipf_ms2_scoringfalse Use MS2 precursor evidence from transition-level precursor rows.true, false

ipf_h0true Include the null hypothesis in IPF transition inference.true, false

ipf_grouped_fdrfalse Compute model FDR separately per num_peptidoforms group.true, false

ipf_max_peakgroup_pep0.7 Maximum peakgroup PEP for entering precursor inference.

ipf_max_precursor_pep0.7 Maximum precursor-level evidence PEP for precursor inference.

ipf_max_precursor_peakgroup_pep0.4 Maximum precursor-peakgroup PEP retained for transition inference.

ipf_max_transition_pep0.6 Maximum transition evidence PEP retained for IPF.

propagate_signal_across_runsfalse Propagate confident transition evidence across aligned runs using FEATURE_MS2_ALIGNMENT_CANDIDATE.true, false

ipf_min_alignment_mapping_confidence0.5 Minimum mapping confidence retained for across-run propagation from FEATURE_MS2_ALIGNMENT_CANDIDATE.

across_run_confidence_threshold0.5 Maximum transition PEP eligible for across-run propagation.

+++peptidePeptide-level inference selection options.

globaltrue Enable peptide inference in the global context.true, false

experiment_widefalse Enable peptide inference in the experiment-wide context.true, false

run_specificfalse Enable peptide inference in the run-specific context.true, false

+++proteinProtein-level inference selection options.

globaltrue Enable protein inference in the global context.true, false

experiment_widefalse Enable protein inference in the experiment-wide context.true, false

run_specificfalse Enable protein inference in the run-specific context.true, false

+++geneGene-level inference selection options.

globalfalse Enable gene inference in the global context.true, false

experiment_widefalse Enable gene inference in the experiment-wide context.true, false

run_specificfalse Enable gene inference in the run-specific context.true, false

+++error_estimationContext-level error estimation options.

parametricfalse Use parametric p-value estimation instead of empirical estimation.true, false

pfdrfalse Use positive FDR in q-value and s-value calculations.true, false

pi0_lambda[0.1, 0.15, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45] Lambda grid for pi0 estimation.

pi0_methodbootstrap Method for pi0 estimation.bootstrap, smoother

pi0_smooth_df3 Degrees of freedom for smoother-based pi0 estimation.1:∞

pi0_smooth_log_pi0false Smooth log(pi0) instead of pi0 directly.true, false

lfdr_truncatetrue Truncate local FDR/PEP values to [0,1].true, false

lfdr_monotonetrue Enforce monotone local FDR/PEP estimates.true, false

lfdr_transformationprobit Transformation used by local FDR estimation.probit, logit

lfdr_adj1.5 Adjustment factor for local FDR estimation bandwidth.

lfdr_eps1.0e-08 Epsilon used to clip p-values before local FDR estimation.