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)
FeatureFinderCentroided		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:

stty: 'standard input': Inappropriate ioctl for device

ExternalCalibration -- Applies an external mass recalibration.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_ExternalCalibration.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.

Usage:
  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 unchanged. (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:

Legend:

required parameter

advanced parameter

+ExternalCalibrationApplies an external mass recalibration.

version3.4.0-pre-nightly-2024-12-16 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