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.

Web Documentation for QualityControl

Options

version
Version of the tool that generated this parameters file.
log
Name of log file (created only when specified)
debug
Sets the debug level
threads
Sets the number of threads allowed to be used by the TOPP tool
no_progress
Disables progress logging to command line
force
Overrides tool-specific checks
test
Enables the test mode (needed for internal use only)
unit
Unit for mass tolerance. 'auto' uses information from FeatureXML
tolerance
m/z search window for matching peaks in two spectra
assume_all_target
Forces the metric to run even if target/decoy annotation is missing (accepts all pep_ids as target hits).
omit_mq_evidence
Do NOT write the evidence.txt into 'out_txt:directory'?
omit_mq_msms
Do NOT write the msms.txt into 'out_txt:directory'?

Input Ports

Icon
ConsensusXML input, generated by FeatureLinker. [consensusXML]
Icon
MzML input (after InternalCalibration, if available) [mzML,opt.]
Icon
FeatureXMLs after FDR filtering [featureXML,opt.]
Icon
Proteins considered contaminants [fasta,opt.]
Icon
FASTA file used during MS/MS identification (including decoys). If the protein description contains 'GN=...' then gene names will be extracted [fasta,opt.]
Icon
trafoXMLs from MapAligners [trafoXML,opt.]

Output Ports

Icon
Output mzTab with QC information [mzTab]
Icon
ConsensusXML with QC information (as metavalues) [consensusXML]
Icon
FeatureXMLs with QC information (as metavalues) [featureXML]

Popular Predecessors

Popular Successors

Views

QualityControl Std Output
The text sent to standard out during the execution of QualityControl.
QualityControl Error Output
The text sent to standard error during the execution of QualityControl. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Workflows

  • No workflows found

Links

Developers

You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.

Installation

To use this node in KNIME, install the extension OpenMS from the below update site following our NodePit Product and Node Installation Guide:

v5.9
Plugin provider: Freie Universitaet Berlin, Universitaet Tuebingen, ZIB (GKN-Team) and the OpenMS Team
Plugin version: 3.5.0.202512111229
On NodePit since: 2025-12-12
Last update: 2026-01-07
KNIME versions: v5.9, v5.8, v5.7, v5.6, v5.5, v5.4, v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0

Deploy, schedule, execute, and monitor your KNIME workflows locally, in the cloud or on-premises – with our brand new NodePit Runner.

Try NodePit Runner!