OpenMS
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/doxygen/nightly/html/TOPP_AccurateMassSearch.html
Version: 3.2.0-pre-nightly-2024-07-21 Jul 22 2024, 02:13:52, Revision: b650df0
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
   trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

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', 'oms')

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 TOPP 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/doxygen/nightly/html/TOPP_AccurateMassSearch.html

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+AccurateMassSearchMatch MS signals to molecules from a database by mass.
version3.2.0-pre-nightly-2024-07-21 Version of the tool that generated this parameters file.
++1Instance '1' section for 'AccurateMassSearch'
in featureXML or consensusXML fileinput file*.featureXML, *.consensusXML
out mzTab fileoutput file*.mzTab
out_annotation A copy of the input file, annotated with matching hits from the database.output file*.featureXML, *.consensusXML, *.oms
positive_adductsCHEMISTRY/PositiveAdducts.tsv 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.input file*.tsv
negative_adductsCHEMISTRY/NegativeAdducts.tsv 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.input file*.tsv
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 Overrides tool-specific checkstrue, false
testfalse Enables the test mode (needed for internal use only)true, false
+++dbDatabase files which contain the identifications
mapping[CHEMISTRY/HMDBMappingFile.tsv] 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.input file*.tsv
struct[CHEMISTRY/HMDB2StructMapping.tsv] 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/HMDB2StructMapping.tsv in OpenMS/share is used! If empty, the default will be used.input file*.tsv
+++algorithmAlgorithm parameters section
mass_error_value5.0 Tolerance allowed for accurate mass search.
mass_error_unitppm Unit of mass error (ppm or Da)ppm, Da
ionization_modepositive Positive or negative ionization mode? If 'auto' is used, the first feature of the input map must contain the meta-value 'scan_polarity'. If its missing, the tool will exit with error.positive, negative, auto
isotopic_similarityfalse Computes a similarity score for each hit (only if the feature exhibits at least two isotopic mass traces).false, true
use_feature_adductsfalse Whether to filter AMS candidates mismatching available feature adduct annotation.false, true
keep_unidentified_massestrue Keep features that did not yield any DB hit.true, false
id_formatlegacy Use legacy (ProteinID/PeptideID based storage of metabolomics data) with mzTab-v1.0.0 as output format or novel Identification Data (ID) with mzTab-v2.0.0-M as output format (ID and its MzTab-M output is currently only support for featureXML files).legacy, ID
++++mzTab
exportIsotopeIntensitiesfalse [featureXML input only] Export column with available isotope trace intensities (opt_global_MTint)false, true