 |
OpenMS
|
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: 3.6.0-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:
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:
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:
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.
1.9.8