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InternalCalibration

Performs an internal calibration on an MS experiment.

pot. predecessor tools $ \longrightarrow $ InternalCalibration $ \longrightarrow $ pot. successor tools
PeakPickerWavelet any tool operating on MS peak data
(in mzML format) or feature data
FeatureFinderCentroided

This a simple calibration method: given a list of reference masses and an MS experiment or a feature map, the relative errors of the peaks in the data are approximated by linear regression and subtracted from the data. The user can choose whether the calibration function shall be calculated for each spectrum separately or once for the whole map. If this is done scanwise, at least two reference masses need to be present in each scan to calculate the calibration function, otherwise the spectrum can't be calibrated. For the global calibration it is also possible to use a list of (significant) peptide identifications.

Note
The tool assumes the input data is already picked or feature maps.
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:

InternalCalibration -- Applies an internal calibration.
Version: 2.0.0 Aug 25 2015, 00:02:58, Revision: GIT-NOTFOUND

Usage:
  InternalCalibration <options>

This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript
ion or use the --helphelp option.

Options (mandatory options marked with '*'):
  -in <file>*               Input peak file  (valid formats: 'mzML', 'featureXML')
  -out <file>*              Output file  (valid formats: 'mzML', 'featureXML')
  -ref_peaks <file>         Input file containing reference m/z values (either as textfile with one m/z per 
                            line and no header or as idXML file) (valid formats: 'csv', 'idXML')
  -type <calibration type>  The kind of internal calibration that should be applied. (default: 'spectrumwise'
                            valid: 'spectrumwise', 'global')
  -trafo <file>             Output transformation file (only for global calibration) (valid formats: 'trafoXM
                            L')
                            
                            
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)

The following configuration subsections are valid:
 - algorithm   Settings for the internal calibration.

You can write an example INI file using the '-write_ini' option.
Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.
Have a look at the OpenMS documentation for more information.

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+InternalCalibrationApplies an internal calibration.
version2.0.0 Version of the tool that generated this parameters file.
++1Instance '1' section for 'InternalCalibration'
in input peak file input file*.mzML,*.featureXML
out output file output file*.mzML,*.featureXML
ref_peaks input file containing reference m/z values (either as textfile with one m/z per line and no header or as idXML file)input file*.csv,*.idXML
typespectrumwise The kind of internal calibration that should be applied.spectrumwise,global
trafo output transformation file (only for global calibration)output file*.trafoXML
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 Overwrite tool specific checks.true,false
testfalse Enables the test mode (needed for internal use only)true,false
+++algorithmSettings for the internal calibration.
mz_tolerance1 Allowed tolerance between peak and reference m/z.0:∞
mz_tolerance_unitDa Unit for mz_tolerance.Da,ppm
rt_tolerance10 Allowed tolerance between peak and reference rt.

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Aug 25 2015 05:53:56 using doxygen 1.8.9.1