Performs an internal calibration on an MS experiment.
pot. predecessor tools | ![]() ![]() | 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.
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:
OpenMS / TOPP release 2.0.0 | Documentation generated on Tue Aug 25 2015 05:53:56 using doxygen 1.8.9.1 |