Export scored OpenSWATH OSW files to user-facing TSV / Parquet results tables and quantification matrices.

OpenSwathExport operates on scored OpenSWATH OSW files and can generate multiple exports in one invocation:

scored feature Parquet exports (*.precursor.feature.scores.parquet, optional *.transition.feature.scores.parquet)
filtered user-facing results exports (*.results.tsv or *.results.parquet)
quantification matrices at precursor, peptide, protein, or gene level

The tool currently supports OSW input. OpenSWATH Parquet input (.oswpq) is reserved for future work and is rejected with a clear error for now.

The command line parameters of this tool are:

OpenSwathExport -- Export scored OpenSWATH results to TSV or Parquet tables.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_OpenSwathExport.html
Version: 3.6.0-pre-nightly-2026-06-22 Jun 23 2026, 01:53:23, Revision: 9a7cdde
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:
  OpenSwathExport <options>

Options (mandatory options marked with '*'):
  -in <file>*                                      Input scored OpenSWATH result file in OSW format. (valid 
                                                   formats: 'osw', 'oswpq')
  -out_dir <dir>                                   Optional output directory. If omitted, files are written 
                                                   next to the input OSW.

Options for scored feature parquet export:
  -parquet:run <true|false>                        Whether to export scored feature parquet tables. (default:
                                                    'false') (valid: 'true', 'false')
  -parquet:include_transition_data <true|false>    Whether to also export transition-level parquet tables. 
                                                   (default: 'true') (valid: 'true', 'false')
  -parquet:exclude_decoys <true|false>             Whether to exclude decoys from parquet feature exports. 
                                                   (default: 'false') (valid: 'true', 'false')

Options for user-facing results export:
  -results:run <true|false>                        Whether to export the filtered results table. (default: 
                                                   'true') (valid: 'true', 'false')
  -results:format <choice>                         Output format for the filtered results table. (default: 
                                                   'parquet') (valid: 'tsv', 'parquet')
  -results:ipf <choice>                            How IPF results should be represented when SCORE_IPF is 
                                                   present. (default: 'peptidoform') (valid: 'peptidoform', 
                                                   'augmented', 'disable')
  -results:transition_quantification <true|false>  Whether to aggregate transition-level quantification colum
                                                   ns. (default: 'true') (valid: 'true', 'false')
  -results:max_transition_pep <num>                Maximum transition PEP used for aggregated transition quan
                                                   tification. (default: '0.7')
  -results:ipf_max_peptidoform_pep <num>           Maximum IPF PEP used for peptidoform export filtering. 
                                                   (default: '0.4')
  -results:max_rs_peakgroup_qvalue <num>           Maximum run-specific peakgroup q-value retained. (default:
                                                    '0.05')
  -results:use_peptide_scores <true|false>         Whether to append peptide-level scores if SCORE_PEPTIDE 
                                                   is present and to require passing the peptide-level thresh
                                                   old. (default: 'true') (valid: 'true', 'false')
  -results:max_global_peptide_qvalue <num>         Maximum global peptide-level q-value retained when peptide
                                                    filtering is enabled. (default: '0.01')
  -results:use_protein_scores <true|false>         Whether to append protein-level scores if SCORE_PROTEIN 
                                                   is present and to require passing the protein-level thresh
                                                   old. (default: 'true') (valid: 'true', 'false')
  -results:max_global_protein_qvalue <num>         Maximum global protein-level q-value retained when protein
                                                    filtering is enabled. (default: '0.01')
  -results:use_gene_scores <true|false>            Whether to append gene-level scores if SCORE_GENE is prese
                                                   nt and to require passing the gene-level threshold. (defau
                                                   lt: 'false') (valid: 'true', 'false')
  -results:max_global_gene_qvalue <num>            Maximum global gene-level q-value retained when gene filte
                                                   ring is enabled. (default: '0.01')
  -results:use_alignment <true|false>              Whether to recover aligned features when legacy alignment 
                                                   tables are present. (default: 'false') (valid: 'true', 
                                                   'false')
  -results:max_alignment_pep <num>                 Maximum alignment PEP retained when alignment recovery is 
                                                   enabled. (default: '0.7')
  -results:exclude_decoys <true|false>             Whether to exclude decoys from the filtered results export
                                                   . (default: 'true') (valid: 'true', 'false')

Options for quantification matrix exports:
  -matrix:precursor <true|false>                   Whether to export the precursor-level quantification matri
                                                   x. (default: 'false') (valid: 'true', 'false')
  -matrix:peptide <true|false>                     Whether to export the peptide-level quantification matrix.
                                                    (default: 'true') (valid: 'true', 'false')
  -matrix:protein <true|false>                     Whether to export the protein-level quantification matrix.
                                                    (default: 'true') (valid: 'true', 'false')
  -matrix:gene <true|false>                        Whether to export the gene-level quantification matrix. 
                                                   (default: 'false') (valid: 'true', 'false')
  -matrix:format <choice>                          Output format for quantification matrices. (default: 'tsv'
                                                   ) (valid: 'tsv', 'parquet')
  -matrix:ipf <choice>                             How IPF results should be represented when SCORE_IPF is 
                                                   present. (default: 'peptidoform') (valid: 'peptidoform', 
                                                   'augmented', 'disable')
  -matrix:transition_quantification <true|false>   Whether to aggregate transition-level quantification colum
                                                   ns onto the filtered feature rows. (default: 'true') (vali
                                                   d: 'true', 'false')
  -matrix:max_transition_pep <num>                 Maximum transition PEP used for aggregated transition quan
                                                   tification. (default: '0.7')
  -matrix:ipf_max_peptidoform_pep <num>            Maximum IPF PEP used for peptidoform export filtering. 
                                                   (default: '0.4')
  -matrix:max_rs_peakgroup_qvalue <num>            Maximum run-specific peakgroup q-value retained. (default:
                                                    '0.05')
  -matrix:use_peptide_scores <true|false>          Whether peptide-level scores should be required when pepti
                                                   de filtering is enabled. (default: 'true') (valid: 'true',
                                                    'false')
  -matrix:max_global_peptide_qvalue <num>          Maximum global peptide-level q-value retained when peptide
                                                    filtering is enabled. (default: '0.01')
  -matrix:use_protein_scores <true|false>          Whether protein-level scores should be required when prote
                                                   in filtering is enabled. (default: 'true') (valid: 'true',
                                                    'false')
  -matrix:max_global_protein_qvalue <num>          Maximum global protein-level q-value retained when protein
                                                    filtering is enabled. (default: '0.01')
  -matrix:use_gene_scores <true|false>             Whether gene-level scores should be required when gene 
                                                   filtering is enabled. (default: 'false') (valid: 'true', 
                                                   'false')
  -matrix:max_global_gene_qvalue <num>             Maximum global gene-level q-value retained when gene filte
                                                   ring is enabled. (default: '0.01')
  -matrix:use_alignment <true|false>               Whether to recover aligned features when legacy alignment 
                                                   tables are present. (default: 'false') (valid: 'true', 
                                                   'false')
  -matrix:max_alignment_pep <num>                  Maximum alignment PEP retained when alignment recovery is 
                                                   enabled. (default: '0.7')
  -matrix:exclude_decoys <true|false>              Whether to exclude decoys from the filtered matrix input 
                                                   rows. (default: 'true') (valid: 'true', 'false')
  -matrix:top_n <num>                              Number of top precursors / peptides retained during matrix
                                                    summarization. (default: '3')
  -matrix:consistent_top <true|false>              Whether to use the same top precursors / peptides across 
                                                   all runs. (default: 'true') (valid: 'true', 'false')
  -matrix:normalization <choice>                   Normalization applied to matrix sample columns after summa
                                                   rization. (default: 'none') (valid: 'none', 'median', 'med
                                                   ianmedian')

                                                   
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.

+OpenSwathExportExport scored OpenSWATH results to TSV or Parquet tables.

version3.6.0-pre-nightly-2026-06-22 Version of the tool that generated this parameters file.

++1Instance '1' section for 'OpenSwathExport'

in Input scored OpenSWATH result file in OSW format.input file*.osw, *.oswpq

out_dir Optional output directory. If omitted, files are written next to the input OSW.output dir

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

+++parquetOptions for scored feature parquet export

runfalse Whether to export scored feature parquet tables.true, false

include_transition_datatrue Whether to also export transition-level parquet tables.true, false

exclude_decoysfalse Whether to exclude decoys from parquet feature exports.true, false

+++resultsOptions for user-facing results export

runtrue Whether to export the filtered results table.true, false

formatparquet Output format for the filtered results table.tsv, parquet

ipfpeptidoform How IPF results should be represented when SCORE_IPF is present.peptidoform, augmented, disable

transition_quantificationtrue Whether to aggregate transition-level quantification columns.true, false

max_transition_pep0.7 Maximum transition PEP used for aggregated transition quantification.

ipf_max_peptidoform_pep0.4 Maximum IPF PEP used for peptidoform export filtering.

max_rs_peakgroup_qvalue0.05 Maximum run-specific peakgroup q-value retained.

use_peptide_scorestrue Whether to append peptide-level scores if SCORE_PEPTIDE is present and to require passing the peptide-level threshold.true, false

max_global_peptide_qvalue0.01 Maximum global peptide-level q-value retained when peptide filtering is enabled.

use_protein_scorestrue Whether to append protein-level scores if SCORE_PROTEIN is present and to require passing the protein-level threshold.true, false

max_global_protein_qvalue0.01 Maximum global protein-level q-value retained when protein filtering is enabled.

use_gene_scoresfalse Whether to append gene-level scores if SCORE_GENE is present and to require passing the gene-level threshold.true, false

max_global_gene_qvalue0.01 Maximum global gene-level q-value retained when gene filtering is enabled.

use_alignmentfalse Whether to recover aligned features when legacy alignment tables are present.true, false

max_alignment_pep0.7 Maximum alignment PEP retained when alignment recovery is enabled.

exclude_decoystrue Whether to exclude decoys from the filtered results export.true, false

+++matrixOptions for quantification matrix exports

precursorfalse Whether to export the precursor-level quantification matrix.true, false

peptidetrue Whether to export the peptide-level quantification matrix.true, false

proteintrue Whether to export the protein-level quantification matrix.true, false

genefalse Whether to export the gene-level quantification matrix.true, false

formattsv Output format for quantification matrices.tsv, parquet

ipfpeptidoform How IPF results should be represented when SCORE_IPF is present.peptidoform, augmented, disable

transition_quantificationtrue Whether to aggregate transition-level quantification columns onto the filtered feature rows.true, false

max_transition_pep0.7 Maximum transition PEP used for aggregated transition quantification.

ipf_max_peptidoform_pep0.4 Maximum IPF PEP used for peptidoform export filtering.

max_rs_peakgroup_qvalue0.05 Maximum run-specific peakgroup q-value retained.

use_peptide_scorestrue Whether peptide-level scores should be required when peptide filtering is enabled.true, false

max_global_peptide_qvalue0.01 Maximum global peptide-level q-value retained when peptide filtering is enabled.

use_protein_scorestrue Whether protein-level scores should be required when protein filtering is enabled.true, false

max_global_protein_qvalue0.01 Maximum global protein-level q-value retained when protein filtering is enabled.

use_gene_scoresfalse Whether gene-level scores should be required when gene filtering is enabled.true, false

max_global_gene_qvalue0.01 Maximum global gene-level q-value retained when gene filtering is enabled.

use_alignmentfalse Whether to recover aligned features when legacy alignment tables are present.true, false

max_alignment_pep0.7 Maximum alignment PEP retained when alignment recovery is enabled.

exclude_decoystrue Whether to exclude decoys from the filtered matrix input rows.true, false

top_n3 Number of top precursors / peptides retained during matrix summarization.

consistent_toptrue Whether to use the same top precursors / peptides across all runs.true, false

normalizationnone Normalization applied to matrix sample columns after summarization.none, median, medianmedian