Converter to input for MSstats.

This util consumes an ID-mapped consensusXML file and OpenMS experimental design in TSV format to create a CSV file which can subsequently be used as input for the R package MSstats [1].

[1] M. Choi et al. MSstats: an R package for statistical analysis for quantitative mass spectrometry-based proteomic experiments. Bioinformatics (2014), 30 (17): 2524-2526

The command line parameters of this tool are:

MSstatsConverter -- Converter to input for MSstats
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_MSstatsConverter.html
Version: 3.6.0-pre-nightly-2026-03-06 Mar  7 2026, 01:46:19, Revision: c92c980
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:
  MSstatsConverter <options>

Options (mandatory options marked with '*'):
  -in <in>*                                     Input consensusXML with peptide intensities (valid formats: 
                                                'consensusXML')
  -in_design <in_design>*                       Experimental Design file (valid formats: 'tsv')
  -method <method>                              Method used in the experiment(label free [LFQ], isobaric labe
                                                ling [ISO])) (default: 'LFQ') (valid: 'LFQ', 'ISO')
  -msstats_bioreplicate <msstats_bioreplicate>  Which column in the condition table should be used for MSstat
                                                s 'BioReplicate' (default: 'MSstats_BioReplicate')
  -msstats_condition <msstats_condition>        Which column in the condition table should be used for MSstat
                                                s 'Condition' (default: 'MSstats_Condition')
  -msstats_mixture msstats_mixture              Which column in the condition table should be used for MSstat
                                                s 'Mixture' (default: 'MSstats_Mixture')
  -labeled_reference_peptides                   If set, IsotopeLabelType is 'H', else 'L'
  -out <out>*                                   Input CSV file for MSstats. (valid formats: 'csv')
                                                
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.

+MSstatsConverterConverter to input for MSstats

version3.6.0-pre-nightly-2026-03-06 Version of the tool that generated this parameters file.

++1Instance '1' section for 'MSstatsConverter'

in Input consensusXML with peptide intensitiesinput file*.consensusXML

in_design Experimental Design fileinput file*.tsv

methodLFQ Method used in the experiment(label free [LFQ], isobaric labeling [ISO]))LFQ, ISO

msstats_bioreplicateMSstats_BioReplicate Which column in the condition table should be used for MSstats 'BioReplicate'

msstats_conditionMSstats_Condition Which column in the condition table should be used for MSstats 'Condition'

msstats_mixtureMSstats_Mixture Which column in the condition table should be used for MSstats 'Mixture'

reannotate_filenames[] Overwrite MS file names in consensusXMLinput file*.mzML

labeled_reference_peptidesfalse If set, IsotopeLabelType is 'H', else 'L'true, false

retention_time_summarization_methodmax How indistinguishable peptidoforms at different retention times should be treated. This is usually necessary for LFQ experiments and therefore defaults to 'max'. In case of TMT/iTRAQ, MSstatsTMT does the aggregation itself later and the parameter always resets to manual (i.e. is unused).manual, max, min, mean, sum

out Input CSV file for MSstats.output file*.csv

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