AccurateMassSearch

An algorithm to search for exact mass matches from a spectrum against a database (e.g. HMDB).

pot. predecessor tools	$\longrightarrow$ AccurateMassSearch $\longrightarrow$	pot. successor tools
FeatureFinderMetabo		NA

Accurate mass search against a database (usually HMDB). For details see AccurateMassSearchEngine.

Note: Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

AccurateMassSearch -- Match MS signals to molecules from a database by mass.
Version: 2.3.0 Jan  9 2018, 17:46:23, Revision: 38ae115

Usage:
  AccurateMassSearch <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>*                FeatureXML or consensusXML file (valid formats: 'featureXML', 'consensusXML')
  -out <file>*               MzTab file (valid formats: 'tsv')
  -out_annotation <file>     A copy of the input file, annotated with matching hits from the database. (valid
                             formats: 'featureXML', 'consensusXML')

Database files which contain the identifications:
  -db:mapping <file(s)>*     Database input file(s), containing three tab-separated columns of mass, formula,
                             identifier. If 'mass' is 0, it is re-computed from the molecular sum formula.
                             By default CHEMISTRY/HMDBMappingFile.tsv in OpenMS/share is used! If empty, the
                             default will be used. (valid formats: 'tsv')
  -db:struct <file(s)>*      Database input file(s), containing four tab-separated columns of identifier, 
                             name, SMILES, INCHI.The identifier should match with mapping file. SMILES and
                             INCHI are reported in the output, but not used otherwise. By default CHEMISTRY/H
                             MDB2StructMapping.tsv in OpenMS/share is used! If empty, the default will be
                             used. (valid formats: 'tsv')

  -positive_adducts <file>*  This file contains the list of potential positive adducts that will be looked 
                             for in the database. Edit the list if you wish to exclude/include adducts. By
                             default CHEMISTRY/PositiveAdducts.tsv in OpenMS/share is used! If empty, the
                             default will be used. (valid formats: 'tsv')
  -negative_adducts <file>*  This file contains the list of potential negative adducts that will be looked 
                             for in the database. Edit the list if you wish to exclude/include adducts. By
                             default CHEMISTRY/NegativeAdducts.tsv in OpenMS/share is used! If empty, the
                             default will be used. (valid formats: 'tsv')
                             
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.
Have a look at the OpenMS documentation for more information.