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 $ \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.

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