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 Feb 20 2020, 20:13:06, Revision: f649042
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 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