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OpenMS
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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 |
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: http://www.openms.de/doxygen/nightly/html/TOPP_ExternalCalibration.html
Version: 3.6.0-pre-nightly-2026-03-12 Mar 13 2026, 01:45:58, Revision: 88f2819
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.
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 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:
This section lists all parameters supported by the tool. Parameters are organized into hierarchical subsections that group related settings together. Subsections may contain further subsections or individual parameters.
Each parameter entry contains the following information:
Parameter tags provide additional information about how a parameter is used. Some tags indicate whether a parameter is required or intended for advanced configuration, while others may be used internally by OpenMS or workflow tools.
Parameters highlighted as required must be specified for the tool to run successfully. Parameters marked as advanced allow fine-tuning of algorithm behavior and are typically not needed for standard workflows.
1.9.8