OpenMS
QCCalculator

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

pot. predecessor tools → QCCalculator → pot. successor tools
FeatureFinderCentroided QCMerger
XTandemAdapter QCExporter

The calculated quality parameters or data compiled as attachments for easy plotting input include file origin, spectra distribution, aquisition details, ion current stability ( & TIC ), id accuracy statistics and feature statistics. The MS experiments base name is used as name to the qcML element that is comprising all quality parameter values for the given run (including the given downstream analysis data).

  • 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; this file can be either mapped or unmapped, the latter reulting in less metrics available.
  • consensus produces quality parameter values for the consensus file; some quality parameter calculation are only available if both feature and ids are given.
  • remove_duplicate_features only needed when you work with a set of merged features. Then considers duplicate features only once.
  • name only for mzQC: name of the person creating the mzQC file
  • address only for mzQC: contact address (mail/e-mail or phone) of the person creating the mzQC file
  • label only for mzQC: RECOMMENDED unique and informative label for the run, so that it can be used as a figure label
  • description only for mzQC: description and comments about the mzQC file contents
  • out_type specifies the output file type, default: determined by output file extension

Output is in mzQC with JSON formatting or qcML format (see parameter out) which can be viewed directly in a modern browser (chromium, firefox, safari). The output file specified by the user determines which output file format will be used.

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: 

stty: 'standard input': Inappropriate ioctl for device

QCCalculator -- Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_QCCalculator.html
Version: 3.4.0-pre-nightly-2024-12-16 Dec 17 2024, 02:41:12, Revision: 96ad74c
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry 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 precursor peak information) (valid formats: 'mzML')
  -out <file>*                 Your QC file. (valid formats: 'mzQC', 'qcML')
  -out_type <type>             Output file type -- default: determined from file extension or content (valid: 'mzQC', 'qcML')
  -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: 'featureXML')
  -consensus <file>            Consensus input file (this is only used for charge state deconvoluted output. Use the consensusXML output form the DeCharger) (valid formats: 'consensusXML')
  -remove_duplicate_features   This flag should be set, if you work with a set of merged features.
                               
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 (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
+QCCalculatorCalculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.
version3.4.0-pre-nightly-2024-12-16 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, *.qcML
out_type Output file type -- default: determined from file extension or contentmzQC, qcML
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
consensus consensus input file (this is only used for charge state deconvoluted output. Use the consensusXML output form the DeCharger)input file*.consensusXML
remove_duplicate_featuresfalse This flag should be set, if you work with a set of merged features.true, false
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