QPXConverter

Converts IdXML files to parquet format following QPX PSM specification.

potential predecessor tools	→ QPXConverter →	potential successor tools
Any identification tool producing idXML		QPX analysis tools

QPXConverter reads peptide and protein identifications from idXML files and converts them to parquet format following the QPX PSM (Peptide Spectrum Match) specification.

The output parquet file contains PSM data with structured columns following the QPX PSM specification including ProForma peptidoform notation, structured modifications with UniMod accessions, structured additional scores, protein accessions as list, and metavalue columns.

The command line parameters of this tool are:

QPXConverter -- Converts IdXML files to parquet format following QPX PSM specification.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_QPXConverter.html
Version: 3.6.0-pre-nightly-2026-04-01 Apr  2 2026, 01:47:25, Revision: bbb059e
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:
  QPXConverter <options>

Options (mandatory options marked with '*'):
  -in <file>*        Input idXML file (valid formats: 'idXML')
  -out <file>*       Output parquet file (valid formats: 'parquet')
  -export_all_psms   Export all PSMs per spectrum (not just the best hit)
                     
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 (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.

+QPXConverterConverts IdXML files to parquet format following QPX PSM specification.

version3.6.0-pre-nightly-2026-04-01 Version of the tool that generated this parameters file.

++1Instance '1' section for 'QPXConverter'

in Input idXML fileinput file*.idXML

out Output parquet fileoutput file*.parquet

export_all_psmsfalse Export all PSMs per spectrum (not just the best hit)true, false

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

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