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OpenMS
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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.
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: 3.6.0-pre-nightly-2026-03-06 Mar 7 2026, 01:46:19, Revision: c92c980
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:
This section lists all parameters supported by the tool. Parameters are organized into hierarchical subsections that group related settings together. Subsections may contain further subsections or individual parameters.
Each parameter entry contains the following information:
Parameter tags provide additional information about how a parameter is used. Some tags indicate whether a parameter is required or intended for advanced configuration, while others may be used internally by OpenMS or workflow tools.
Parameters highlighted as required must be specified for the tool to run successfully. Parameters marked as advanced allow fine-tuning of algorithm behavior and are typically not needed for standard workflows.
1.9.8