Generates an mzTab file from various sources of a pipeline (mainly a ConsensusXML) which can be used for QC plots (e.g. via the R package 'PTXQC').

pot. predecessor tools	→ QualityControl →	pot. successor tools
FeatureLinkerUnlabeledKD (or FLs; for consensusXML)		PTX-QC
IDMapper (for featureXMLs)
InternalCalibration

The command line parameters of this tool are:

QualityControl -- Computes various QC metrics.
Many input formats are supported only the consensusXML is required.
The more optional files you provide, the more metrics you get.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_QualityControl.html
Version: 3.3.0-pre-nightly-2024-11-20 Nov 21 2024, 02:34:56, Revision: decb5c8
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:
  QualityControl <options>

Options (mandatory options marked with '*'):
  -in_cm <file>*                         ConsensusXML input, generated by FeatureLinker. (valid formats: 'con
                                         sensusXML')
  -in_raw <files>                        MzML input (after InternalCalibration, if available) (valid formats:
                                          'mzML')
  -in_postFDR <files>                    FeatureXMLs after FDR filtering (valid formats: 'featureXML')
  -out <file>                            Output mzTab with QC information (valid formats: 'mzTab')
  -out_cm <file>                         ConsensusXML with QC information (as metavalues) (valid formats: 
                                         'consensusXML')
  -out_feat <files>                      FeatureXMLs with QC information (as metavalues) (valid formats: 'fea
                                         tureXML')

Fragment Mass Error settings:
  -FragmentMassError:unit <unit>         Unit for mass tolerance. 'auto' uses information from FeatureXML 
                                         (default: 'auto') (valid: 'auto', 'ppm', 'da')
  -FragmentMassError:tolerance <double>  M/z search window for matching peaks in two spectra (default: '20.0'
                                         )

  -in_contaminants <file>                Proteins considered contaminants (valid formats: 'fasta')
  -in_fasta <file>                       FASTA file used during MS/MS identification (including decoys). If 
                                         the protein description contains 'GN=...' then gene names will be 
                                         extracted (valid formats: 'fasta')
  -in_trafo <file>                       TrafoXMLs from MapAligners (valid formats: 'trafoXML')

MS2 ID Rate settings:
  -MS2_id_rate:assume_all_target         Forces the metric to run even if target/decoy annotation is missing 
                                         (accepts all pep_ids as target hits).

Write MaxQuant-compatible .txt files:
  -out_txt:directory <Path>              If a Path is given, '.txt' files compatible with MaxQuant will be 
                                         created in this directory. If the directory does not exist, it will 
                                         be created.
  -out_txt:omit_mq_evidence              Do NOT write the evidence.txt into 'out_txt:directory'?
  -out_txt:omit_mq_msms                  Do NOT write the msms.txt into 'out_txt:directory'?

                                         
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 (defa
                                         ult: '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

+QualityControlComputes various QC metrics.
Many input formats are supported only the consensusXML is required.
The more optional files you provide, the more metrics you get.

version3.3.0-pre-nightly-2024-11-20 Version of the tool that generated this parameters file.

++1Instance '1' section for 'QualityControl'

in_cm ConsensusXML input, generated by FeatureLinker.input file*.consensusXML

in_raw[] MzML input (after InternalCalibration, if available)input file*.mzML

in_postFDR[] FeatureXMLs after FDR filteringinput file*.featureXML

out Output mzTab with QC informationoutput file*.mzTab

out_cm ConsensusXML with QC information (as metavalues)output file*.consensusXML

out_feat[] FeatureXMLs with QC information (as metavalues)output file*.featureXML

in_contaminants Proteins considered contaminantsinput file*.fasta

in_fasta FASTA file used during MS/MS identification (including decoys). If the protein description contains 'GN=...' then gene names will be extractedinput file*.fasta

in_trafo[] trafoXMLs from MapAlignersinput file*.trafoXML

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

+++FragmentMassErrorFragment Mass Error settings

unitauto Unit for mass tolerance. 'auto' uses information from FeatureXMLauto, ppm, da

tolerance20.0 m/z search window for matching peaks in two spectra

+++MS2_id_rateMS2 ID Rate settings

assume_all_targetfalse Forces the metric to run even if target/decoy annotation is missing (accepts all pep_ids as target hits).true, false

+++out_txtWrite MaxQuant-compatible .txt files

directory If a Path is given, '.txt' files compatible with MaxQuant will be created in this directory. If the directory does not exist, it will be created.output dir

omit_mq_evidencefalse Do NOT write the evidence.txt into 'out_txt:directory'?true, false

omit_mq_msmsfalse Do NOT write the msms.txt into 'out_txt:directory'?true, false