Generates an assay library from SIRIUS fragmentation trees (Metabolomics)

potential predecessor tools	→ AssayGeneratorMetaboSirius →	potential successor tools
FeatureFinderMetabo	→ AssayGeneratorMetaboSirius →	OpenSWATH pipeline
AccurateMassSearch
SiriusExport

Build an assay library from a SIRIUS project directory using fragmentation trees.

Use the SiriusExport TOPP tool with each samples mzML and featureXML files to generate a SIRIUS input ms file.
SiriusExport -in sample.mzML -in_featureinfo sample.featureXML -out_ms sample.ms
Run SIRIUS externally with "--no-compression" flag and the formula, passatutto (optional, for decoy generation) and write-summaries tools.
This tool was tested with the SIRIUS project directory generated with SIRIUS versions >= 5.5.1 and <= 5.8.6.
sirius --input sample.ms --project sirius-project --maxmz 300 --no-compression formula passatutto write-summaries
Provide the path to SIRIUS project as input parameter for this tool.

The command line parameters of this tool are:

stty: 'standard input': Inappropriate ioctl for device

AssayGeneratorMetaboSirius -- Assay library generation from a SIRIUS project directory (Metabolomics)
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_AssayGeneratorMetaboSirius.html
Version: 3.4.0-pre-nightly-2024-12-16 Dec 17 2024, 02:41:12, Revision: 96ad74c
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry 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-rooting 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 method 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_decoys' 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:

Legend:

required parameter

advanced parameter

+AssayGeneratorMetaboSiriusAssay library generation from a SIRIUS project directory (Metabolomics)

version3.4.0-pre-nightly-2024-12-16 Version of the tool that generated this parameters file.

++1Instance '1' section for 'AssayGeneratorMetaboSirius'

in SIRIUS project directoryinput file

in_compoundinfo Compound info table (.tsv file)input file*.tsv

out Assay library output fileoutput file*.tsv, *.traML, *.pqp

ambiguity_resolution_mz_tolerance10.0 Mz tolerance for the resolution of identification ambiguity over multiple files

ambiguity_resolution_mz_tolerance_unitppm Unit of the ambiguity_resolution_mz_toleranceppm, Da

ambiguity_resolution_rt_tolerance10.0 RT tolerance in seconds for the resolution of identification ambiguity over multiple files

total_occurrence_filter0.1 Filter compound based on total occurrence in analysed samples0.0:1.0

fragment_annotation_score_threshold0.8 Filters annotations based on the explained intensity of the peaks in a spectrum0.0:1.0

methodhighest_intensity Spectrum with the highest precursor intensity or a consensus spectrum is used for assay library construction (if no fragment annotation is used).highest_intensity, consensus_spectrum

use_exact_massfalse Use exact mass for precursor and fragment annotationstrue, false

exclude_ms2_precursorfalse Excludes precursor in ms2 from transition listtrue, false

use_known_unknownsfalse Use features without identification informationtrue, false

min_transitions3 Minimal number of transitions

max_transitions6 Maximal number of transitions

transition_threshold5.0 Further transitions need at least x% of the maximum intensity (default 5%)

min_fragment_mz0.0 Minimal m/z of a fragment ion choosen as a transition

max_fragment_mz2000.0 Maximal m/z of a fragment ion choosen as a transition

decoy_generationfalse Decoys will be generated using the fragmentation tree re-rooting approach. This option does only work in combination with the fragment annotation via Sirius.true, false

decoy_generation_methodoriginal Uses different methods for decoy generation. Basis for the method 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_decoys' 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).original, resolve_overlap, generate_missing_decoys, both

decoy_resolution_mz_tolerance10.0 Mz tolerance for the resolution of overlapping m/z values for targets and decoys of one compound.

decoy_resolution_mz_tolerance_unitppm Unit of the decoy_resolution_mz_toleranceppm, Da

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