AccurateMassSearch

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

pot. predecessor tools	AccurateMassSearch	pot. successor tools
FeatureFinderMetabo		NA

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

Note

For mzid in-/out- put, due to legacy reason issues you are temporarily asked to use IDFileConverter as a wrapper. The command line parameters of this tool are:

AccurateMassSearch -- Find potential HMDB ids within the given mass error window.
Version: 2.0.0 May 16 2015, 09:22:21, Revision: GIT-NOTFOUND

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: 'csv')
  -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>*             Database input file, containing three tab-separated columns of mass, formul
                                  a, 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>*              Database input file, 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/HMDB2StructMapping.tsv in OpenMS/share is used! If empty, the
                                  default will be used. (valid formats: 'tsv')

  -positive_adducts_file <file>*  This file contains the list of potential positive adducts that will be look
                                  ed for in the database. Edit the list if you wish to exclude/include adduct
                                  s. By default CHEMISTRY/PositiveAdducts.tsv in OpenMS/share is used! If
                                  empty, the default will be used. (valid formats: 'tsv')
  -negative_adducts_file <file>*  This file contains the list of potential negative adducts that will be look
                                  ed for in the database. Edit the list if you wish to exclude/include adduct
                                  s. 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.