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OpenMS
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MetaboliteSpectralMatcher identifies small molecules from tandem MS spectra using a spectral library.
| pot. predecessor tools | → MetaboliteSpectralMatcher → | pot. successor tools |
|---|---|---|
| PeakPickerHiRes | ||
| processing in R |
By default, MS2 spectra with similar precursor mass are merged before comparison with database spectra, for example when a mass at the beginning of the peak and on the peak apex is selected twice as precursor. Merging can also have disadvantages, for example, for isobaric or isomeric compounds that have similar/same masses but can have different retention times and MS2 spectra.
The command line parameters of this tool are:
MetaboliteSpectralMatcher -- Perform a spectral library search.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_MetaboliteSpectralMatcher.html
Version: 3.6.0-pre-nightly-2026-03-06 Mar 7 2026, 01:46:19, Revision: c92c980
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:
MetaboliteSpectralMatcher <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 spectra. (valid formats: 'mzML')
-database <file>* Default spectral database. (valid formats: 'mzML', 'msp', 'mgf')
-out <file>* MzTab file (valid formats: 'mzTab')
-out_spectra <file> Output spectra as mzML file. Can be useful to inspect the peak map after spectra mergi
ng. (valid formats: 'mzML')
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 Algorithm parameters section
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.
For more information, please consult the online documentation for this tool:
- http://www.openms.de/doxygen/nightly/html/TOPP_MetaboliteSpectralMatcher.html
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