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:

stty: 'standard input': Inappropriate ioctl for device

MetaboliteSpectralMatcher -- Perform a spectral library search.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_MetaboliteSpectralMatcher.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:
  MetaboliteSpectralMatcher <options>

This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed description 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 merging. (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:

Legend:

required parameter

advanced parameter

+MetaboliteSpectralMatcherPerform a spectral library search.

version3.4.0-pre-nightly-2024-12-16 Version of the tool that generated this parameters file.

++1Instance '1' section for 'MetaboliteSpectralMatcher'

in Input spectra.input file*.mzML

database Default spectral database.input file*.mzML, *.msp, *.mgf

out mzTab fileoutput file*.mzTab

out_spectra Output spectra as mzML file. Can be useful to inspect the peak map after spectra merging.output file*.mzML

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

+++algorithmAlgorithm parameters section

prec_mass_error_value100.0 Error allowed for precursor ion mass.

frag_mass_error_value500.0 Error allowed for product ions.

mass_error_unitppm Unit of mass error (ppm or Da)ppm, Da

report_modetop3 Which results shall be reported: the top-three scoring ones or the best scoring one?top3, best

ionization_modepositive Positive or negative ionization mode?positive, negative

merge_spectratrue Merge MS2 spectra with the same precursor mass.true, false