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OpenMS
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De novo metabolite identification.
Exports an input file for SIRIUS, a tool for metabolomics data analysis with several subtools, each serving specific purposes:
Sirius can be found at https://bio.informatik.uni-jena.de/software/sirius/
Internal procedure in SiriusExport
The command line parameters of this tool are:
SiriusExport -- Metabolite identification using single and tandem mass spectrometry
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_SiriusExport.html
Version: 3.6.0-pre-nightly-2026-03-21 Mar 22 2026, 01:46:55, Revision: eb804dd
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.
To cite SiriusExport:
+ Kai Duehrkop and Sebastian Boecker. Fragmentation trees reloaded. J Cheminform; 2016. doi:10.1186/s13321-0
16-0116-8.
+ Kai Duehrkop, Huibin Shen, Marvin Meusel, Juho Rousu, and Sebastian Boecker. Searching molecular structure
databases with tandem mass spectra using CSI:FingerID. Proceedings of the National Academy of Sciences;
2015. doi:10.1073/pnas.1509788112.
Usage:
SiriusExport <options>
Options (mandatory options marked with '*'):
-in <file(s)>* MzML Input file(s) (valid formats: 'mzML')
-in_featureinfo <file(s)> FeatureXML input with feature and adduct information (valid
formats: 'featureXML')
-out <file>* Internal SIRIUS .ms format after OpenMS preprocessing (valid
formats: 'ms')
-out_compoundinfo <file> File (.tsv) with information on processed compounds which are
associated with a feature. Required for AssayGeneratorMetaboSi
rius tool. (valid formats: 'tsv')
-filter_by_num_masstraces <number> Number of mass traces each feature has to have to be included.
To use this parameter, setting the feature_only flag is neces
sary (default: '1') (min: '1')
-precursor_mz_tolerance <value> Tolerance window for precursor selection (Feature selection
in regard to the precursor) (default: '10.0')
-precursor_mz_tolerance_unit <choice> Unit of the preprocessing_precursor_mz_tolerance (default:
'ppm') (valid: 'ppm', 'Da')
-precursor_rt_tolerance <value> Tolerance window (left and right) for precursor selection [sec
onds] (default: '5.0')
-isotope_pattern_iterations <number> Number of iterations that should be performed to extract the
C13 isotope pattern. If no peak is found (C13 distance) the
function will abort. Be careful with noisy data - since this
can lead to wrong isotope patterns (default: '3')
-feature_only <choice> Uses the feature information from in_featureinfo to reduce
the search space to MS2 associated with a feature (default:
'false') (valid: 'false', 'true')
-no_masstrace_info_isotope_pattern <choice> Set to true if the masstrace information from a feature should
be discarded and the isotope_pattern_iterations should be
used instead (default: 'false') (valid: 'false', 'true')
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)
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