MSstatsConverter

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/release/3.5.0/html/TOPP_MSstatsConverter.html
Version: 3.5.0 May  9 2025, 17:07:55, Revision: 12ccccf
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

+MSstatsConverterConverter to input for MSstats

version3.5.0 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