 |
OpenMS
|
Generates an assay library from SIRIUS fragmentation trees (Metabolomics)
| potential predecessor tools | → AssayGeneratorMetaboSirius → | potential successor tools |
|---|---|---|
| FeatureFinderMetabo | OpenSWATH pipeline | |
| AccurateMassSearch | ||
| SiriusExport |
Build an assay library from a SIRIUS project directory using fragmentation trees.
The command line parameters of this tool are:
AssayGeneratorMetaboSirius -- Assay library generation from a SIRIUS project directory (Metabolomics)
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_AssayGeneratorMetaboSirius.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:
AssayGeneratorMetaboSirius <options>
Options (mandatory options marked with '*'):
-in <directory>* SIRIUS project directory
-in_compoundinfo <file>* Compound info table (.tsv file) (valid formats: 'tsv')
-out <file>* Assay library output file (valid formats: 'tsv', 'traML', 'pqp'
)
-ambiguity_resolution_mz_tolerance <num> Mz tolerance for the resolution of identification ambiguity
over multiple files (default: '10.0')
-ambiguity_resolution_rt_tolerance <num> RT tolerance in seconds for the resolution of identification
ambiguity over multiple files (default: '10.0')
-total_occurrence_filter <num> Filter compound based on total occurrence in analysed samples
(default: '0.1') (min: '0.0' max: '1.0')
-fragment_annotation_score_threshold <num> Filters annotations based on the explained intensity of the
peaks in a spectrum (default: '0.8') (min: '0.0' max: '1.0')
-method <choice> Spectrum with the highest precursor intensity or a consensus
spectrum is used for assay library construction (if no fragment
annotation is used). (default: 'highest_intensity') (valid:
'highest_intensity', 'consensus_spectrum')
-use_exact_mass Use exact mass for precursor and fragment annotations
-exclude_ms2_precursor Excludes precursor in ms2 from transition list
-use_known_unknowns Use features without identification information
-min_transitions <int> Minimal number of transitions (default: '3')
-max_transitions <int> Maximal number of transitions (default: '6')
-transition_threshold <num> Further transitions need at least x% of the maximum intensity
(default 5%) (default: '5.0')
-decoy_generation Decoys will be generated using the fragmentation tree re-rootin
g approach. This option does only work in combination with the
fragment annotation via Sirius.
-decoy_generation_method <choice> Uses different methods for decoy generation. Basis for the meth
od is the fragmentation-tree re-rooting approach ('original').
This approach can be extended by using 'resolve_overlap', which
will resolve overlapping target/decoy fragments by adding -CH2
mass to the overlapping decoy fragments. 'generate_missing_dec
oys' will add a -CH2 mass shift to the target fragments and
use them as decoys if fragmentation-tree re-rooting failed.
'Both' combines the extended methods (resolve_overlap, generate
_missing_decoys). (default: 'original') (valid: 'original',
'resolve_overlap', 'generate_missing_decoys', 'both')
-decoy_resolution_mz_tolerance <num> Mz tolerance for the resolution of overlapping m/z values for
targets and decoys of one compound. (default: '10.0')
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