Performs an mass recalibration on an MS experiment using an external calibration function.

pot. predecessor tools → ExternalCalibration → pot. successor tools
PeakPickerHiRes any tool operating on MS peak data
(in mzML format)

Recalibrates an MS experiment globally using a constant, linear or quadratic calibration on the observed ppm error, i.e. using offset=-5, slope=0, power=0 assumes the observed data has -5 ppm decalibration, i.e. the observed m/z is too small and should be increased by 5 ppm! Slope and power are coefficients for the observed m/z, i.e. y = offset + x * slope + x * x * power, where x is the observed m/z and y is the resulting mass correction in ppm. Usually slope and offset are very small (< 0.01). If you only want a 'rough' recalibration, using offset is usually sufficient.

The calibration function is applied to all scans (with the desired level, see below), i.e. time dependent recalibration cannot be modeled.

The user can select what MS levels are subjected to calibration. Spectra with other MS levels remain unchanged. Calibration must be done once for each mass analyzer.

Either raw or centroided data can be used as input. The command line parameters of this tool are:

ExternalCalibration -- Applies an external mass recalibration.
Full documentation:
Version: 3.2.0-pre-nightly-2024-07-19 Jul 20 2024, 02:06:43, Revision: f10e72e
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.

  ExternalCalibration <options>

Options (mandatory options marked with '*'):
  -in <file>*        Input peak file (valid formats: 'mzML')
  -out <file>*       Output file  (valid formats: 'mzML')
  -offset            Mass offset in ppm (default: '0.0')
  -slope             Slope (dependent on m/z) (default: '0.0')
  -power             Power (dependent on m/z) (default: '0.0')
  -ms_level i j ...  Target MS levels to apply the transformation onto. Scans with other levels remain unchan
                     ged. (default: '[1 2 3]')
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:

required parameter
advanced parameter
+ExternalCalibrationApplies an external mass recalibration.
version3.2.0-pre-nightly-2024-07-19 Version of the tool that generated this parameters file.
++1Instance '1' section for 'ExternalCalibration'
in Input peak fileinput file*.mzML
out Output file output file*.mzML
offset0.0 Mass offset in ppm
slope0.0 Slope (dependent on m/z)
power0.0 Power (dependent on m/z)
ms_level[1, 2, 3] Target MS levels to apply the transformation onto. Scans with other levels remain unchanged.
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