Calculates basic quality parameters from MS experiments and compiles data for subsequent QC into an mzQC file.

pot. predecessor tools	→ QCCalculator →	pot. successor tools
FeatureFinderCentroided		any tool reading mzQC files
CometAdapter		any tool reading mzQC files

The calculated quality parameters include spectra counts, acquisition ranges, ion current stability (TIC), identification statistics and feature statistics.

id produces quality parameter values for the identification file; this file should contain either only the final psm to each spectrum (1 PeptideHit per identified spectrum) or have the PeptideHits sorted to 'best' first, where 'best' depends on the use case.
feature produces quality parameter values for the feature file.
name name of the person creating the mzQC file
address contact address (mail/e-mail or phone) of the person creating the mzQC file
label RECOMMENDED unique and informative label for the run, so that it can be used as a figure label
description description and comments about the mzQC file contents

Output is in mzQC with JSON formatting.

Note: Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

QCCalculator -- Calculates basic quality parameters from MS experiments and subsequent analysis data as ident
ification or feature detection.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_QCCalculator.html
Version: 3.7.0-pre-nightly-2026-11-08 Nov  9 2026, 01:20:15, Revision: a335fa6
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.
To cite QCCalculator:
 + Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P,  Martens, L. qcML: An Exchange 
   Format for Quality Control Metrics from Mass Spectrometry Experiments. Molecular & Cellular Proteomics 
   2014; 13(8). doi:10.1074/mcp.M113.035907.

Usage:
  QCCalculator <options>

Options (mandatory options marked with '*'):
  -in <file>*                 Raw data input file (this is relevant if you want to look at MS1, MS2 and precu
                              rsor peak information) (valid formats: 'mzML')
  -out <file>*                Your QC file. (valid formats: 'mzQC')
  -label <label>              Unique name for the run that can be used in a figure label (default: 'label')
  -name <contact_name>        Name of the person creating this mzQC file
  -address <contact_address>  Contact address (mail/e-mail or phone)
  -description <description>  Description and comments about the mzQC file contents
  -id <file>                  Input idXML file containing the identifications. Your identifications will be 
                              exported in an easy-to-read format (valid formats: 'idXML')
  -feature <file>             Feature input file (this is relevant for most QC issues) (valid formats: 'featu
                              reXML')
                              
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 (0 = all availab
                              le cores) (default: '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

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:

Name The identifier used in configuration files and on the command line.
Default value The value used if the parameter is not explicitly specified.
Description A short explanation describing the purpose and behavior of the parameter.
Tags Additional metadata associated with the parameter.
Restrictions Allowed value ranges for numeric parameters or valid options for string parameters.

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.

+QCCalculatorCalculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.

version3.7.0-pre-nightly-2026-11-08 Version of the tool that generated this parameters file.

++1Instance '1' section for 'QCCalculator'

in raw data input file (this is relevant if you want to look at MS1, MS2 and precursor peak information)input file*.mzML

out Your QC file.output file*.mzQC

labellabel unique name for the run that can be used in a figure label

name name of the person creating this mzQC file

address contact address (mail/e-mail or phone)

description description and comments about the mzQC file contents

id Input idXML file containing the identifications. Your identifications will be exported in an easy-to-read formatinput file*.idXML

feature feature input file (this is relevant for most QC issues)input file*.featureXML

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 (0 = all available cores)

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