| OpenMS 2.5.0

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
  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.

    Full documentation: http://www.openms.de/documentation/UTILS_AccurateMassSearch.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:

      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: 'mzTab')

      -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. (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. (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.

    For more information, please consult the online documentation for this tool:

      - http://www.openms.de/documentation/UTILS_AccurateMassSearch.html