SiriusExport

De novo metabolite identification.

Exports an input file for SIRIUS, a tool for metabolomics data analysis with several subtools, each serving specific purposes:

• SIRIUS: Identify molecular formula for each compound individually using fragmentation trees and isotope patterns. Output from this tool can be used to generate an OpenSwathAssay library with the AssayGeneratorMetabo TOPP tool.
• CSI:FingerID: This subtool is dedicated to predicting molecular structures based on tandem mass spectrometry (MS/MS) data. It utilizes a fragmentation tree approach for the annotation of fragment spectra.
• CANOPUS: Predict compound categories for each compound individually based on its predicted molecular fingerprint (CSI:FingerID) using CANOPUS.
• Passatutto: Compute decoy spectra based on the fragmentation trees of the given input spectra. If no molecular formula is provided in the input, the top scoring computed formula is used. Required to include decoys in an OpenSwathWorkflow assay library generated by the AssayGeneratorMetabo TOPP tool.

Sirius can be found at https://bio.informatik.uni-jena.de/software/sirius/

Internal procedure in SiriusExport

1. Input mzML (and optional featureXML)
   Make sure to input the matching mzML and featureXML files in the correct order.
   
2. Preprocessing
   By providing a featureXML, the feature information can be used for feature mapping.
   Sirius will then process the internally merged MS2 spectra allocated to one feature (instead of all available MS2).
   To reduce the feature space even further a masstrace filter can be set.
   Additional adduct information can be provided using a featureXML from the MetaboliteAdductDecharger or AccurateMassSearch.
   
3. Parsed by SiriusMSConverter into (sirius internal) .ms format

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: 3.3.0-pre-nightly-2024-11-20 Nov 21 2024, 02:34:56, Revision: decb5c8
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:

Legend:

required parameter

advanced parameter

+SiriusExportMetabolite identification using single and tandem mass spectrometry

version3.3.0-pre-nightly-2024-11-20 Version of the tool that generated this parameters file.

++1Instance '1' section for 'SiriusExport'

in[] MzML Input file(s)input file*.mzML

in_featureinfo[] FeatureXML input with feature and adduct informationinput file*.featureXML

out Internal SIRIUS .ms format after OpenMS preprocessingoutput file*.ms

out_compoundinfo File (.tsv) with information on processed compounds which are associated with a feature. Required for AssayGeneratorMetaboSirius tool.output file*.tsv

filter_by_num_masstraces1 Number of mass traces each feature has to have to be included. To use this parameter, setting the feature_only flag is necessary1:∞

precursor_mz_tolerance10.0 Tolerance window for precursor selection (Feature selection in regard to the precursor)

precursor_mz_tolerance_unitppm Unit of the preprocessing_precursor_mz_toleranceppm, Da

precursor_rt_tolerance5.0 Tolerance window (left and right) for precursor selection [seconds]

isotope_pattern_iterations3 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

feature_onlyfalse Uses the feature information from in_featureinfo to reduce the search space to MS2 associated with a featurefalse, true

no_masstrace_info_isotope_patternfalse Set to true if the masstrace information from a feature should be discarded and the isotope_pattern_iterations should be used insteadfalse, true

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