OpenMS
QualityControl

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: 3.2.0-pre-nightly-2024-07-19 Jul 20 2024, 02:06:43, Revision: f10e72e
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).

  -out_evd <Path>                        If a Path is given, a MQEvidence txt-file will be created in this 
                                         directory. If the directory does not exist, it will be created as 
                                         well.
  -out_msms <Path>                       If a Path is given, a MQMsms txt-file will be created in this direct
                                         ory. If the directory does not exist, it will be created as well.
                                         
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.
version3.2.0-pre-nightly-2024-07-19 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
out_evd If a Path is given, a MQEvidence txt-file will be created in this directory. If the directory does not exist, it will be created as well.
out_msms If a Path is given, a MQMsms txt-file will be created in this directory. If the directory does not exist, it will be created as well.
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