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/release/3.3.0/html/TOPP_QualityControl.html
Version: 3.3.0 Dec 21 2024, 15:25:20, Revision: 35c5e65
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 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