OpenMS  2.5.0
MetaboliteSpectralMatcher

MetaboliteSpectralMatcher identifies small molecules from tandem MS spectra using a spectral library.

pot. predecessor tools $ \longrightarrow $ MetaboliteSpectralMatcher $ \longrightarrow $ pot. successor tools
PeakPickerHiRes
processing in R

The command line parameters of this tool are:


MetaboliteSpectralMatcher -- Perform a spectral library search.

Full documentation: http://www.openms.de/documentation/UTILS_MetaboliteSpectralMatcher.html

Version: 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Sep 10 2020, 12:20:39, Revision: GIT-NOTFOUND

To cite OpenMS:

  Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.



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')

  -out <file>*       MzTab file (valid formats: 'mzTab')

                     

Common UTIL 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/documentation/UTILS_MetaboliteSpectralMatcher.html



INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+MetaboliteSpectralMatcherPerform a spectral library search.
version2.5.0-GIT-NOTFOUND-GIT-NOTFOUND 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
out mzTab fileoutput file*.mzTab
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 Overwrite tool specific checks.true,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