Generates an assay library using DDA data (Metabolomics)

potential predecessor tools	→ AssayGeneratorMetabo →	potential successor tools
FeatureFinderMetabo	→ AssayGeneratorMetabo →	OpenSWATH pipeline
AccurateMassSearch

Build an assay library from DDA data (MS and MS/MS) (mzML). Please provide a list of features found in the data (featureXML).

Features can be detected using the FeatureFinderMetabo (FFM) and identifcation information can be added using the AccurateMassSearch feautreXML output.

If the FFM featureXML is provided the "use_known_unknowns" flag is used automatically.

Internal procedure AssayGeneratorMetabo:

Input mzML and featureXML
Reannotate precursor mz and intensity
Filter feature by number of masstraces
Assign precursors to specific feature (FeatureMapping)
Extract feature meta information (if possible)
Find MS2 spectrum with highest intensity precursor for one feature
Dependent on the method fragment annotation via SIRIUS is used for transition extraction.
If not fragment annotation is performed either the MS2 with the highest intensity precursor or a consensus spectrum can be used for the transition extractuib.
Calculate thresholds (maximum and minimum intensity for transition peak)

Extract and write transitions (tsv, traml)
The command line parameters of this tool are:

SiriusAdapter -- Tool for metabolite identification using single and tandem mass spectrometry
Full documentation: http://www.openms.de/doxygen/release/3.0.0/html/UTILS_SiriusAdapter.html
Version: 3.0.0 Jul 14 2023, 11:57:33, Revision: be787e9
To cite OpenMS:
 + Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for 
   mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.
To cite SiriusAdapter:
 + 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:
  SiriusAdapter <options>

Options (mandatory options marked with '*'):
  -sirius_executable <executable>                      The Sirius executable. Provide a full or relative path
                                                       , or make sure it can be found in your PATH environmen
                                                       t.
  -in <file>*                                          MzML Input file (valid formats: 'mzML')
  -in_featureinfo <file>                               FeatureXML input with feature and adduct information 
                                                       (valid formats: 'featureXML')
  -out_sirius <file>                                   MzTab output file for SIRIUS results (valid formats: 
                                                       'mzTab')
  -out_fingerid <file>                                 MzTab output file for CSI:FingerID, if this parameter 
                                                       is given, SIRIUS will search for a molecular structure
                                                        using CSI:FingerID after determining the sum formula 
                                                       (valid formats: 'mzTab')
  -out_ms <file>                                       Internal SIRIUS .ms format after OpenMS preprocessing 
                                                       (valid formats: 'ms')
  -out_annotated_spectra <file>                        Export spectra with fragment annotations from SIRIUS 
                                                       (valid formats: 'mzML')
  -out_project_space <directory>                       Output directory for SIRIUS project space
  -sirius_user_email <string>                          E-mail for your SIRIUS account.
  -sirius_user_password <string>                       Password for your SIRIUS account.
                                                       

preprocessing:
  -preprocessing:filter_by_num_masstraces <number>     Number of mass traces each feature has to have to be 
                                                       included. To use this parameter, setting the feature_o
                                                       nly flag is necessary (default: '1') (min: '1')
  -preprocessing:precursor_mz_tolerance <value>        Tolerance window for precursor selection (Feature sele
                                                       ction in regard to the precursor) (default: '10.0')
  -preprocessing:precursor_mz_tolerance_unit <choice>  Unit of the precursor_mz_tolerance (default: 'ppm') 
                                                       (valid: 'Da', 'ppm')
  -preprocessing:precursor_rt_tolerance <value>        Tolerance window (left and right) for precursor select
                                                       ion [seconds] (default: '5.0')
  -preprocessing:isotope_pattern_iterations <number>   Number of iterations that should be performed to extra
                                                       ct 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 patt
                                                       erns (default: '3')
  -preprocessing:feature_only                          Uses the feature information from in_featureinfo to 
                                                       reduce the search space to MS2 associated with a featu
                                                       re
  -preprocessing:no_masstrace_info_isotope_pattern     Use this flag if the masstrace information from a feat
                                                       ure should be discarded and the isotope_pattern_iterat
                                                       ions should be used instead

project:
  -project:maxmz <number>                              Just consider compounds with a precursor mz lower or 
                                                       equal
                                                       this maximum mz. All other compounds in the input file
                                                       
                                                       are ignored. (default: '-1')
  -project:loglevel <text>                             Set logging level of the Jobs SIRIUS will execute.
                                                       Valid values: SEVERE, WARNING, INFO, FINER, ALL
                                                       Default: WARNING
  -project:ignore_formula                              Ignore given molecular formula in internal .ms format,
                                                        while processing.
  -project:q                                           Suppress shell output

sirius:
  -sirius:ppm_max <value>                              Maximum allowed mass deviation in ppm for decomposing 
                                                       masses [ppm]. (default: '10.0')
  -sirius:ppm_max_ms2 <value>                          Maximum allowed mass deviation in ppm for decomposing 
                                                       masses in MS2 [ppm].If not specified, the same value 
                                                       as for the MS1 is used.  (default: '10.0')
  -sirius:tree_timeout <number>                        Time out in seconds per fragmentation tree computation
                                                       s. 0 for an infinite amount of time (default: '100') 
                                                       (min: '0')
  -sirius:compound_timeout <number>                    Maximal computation time in seconds for a single compo
                                                       und. 0 for an infinite amount of time. (default: '100'
                                                       ) (min: '0')
  -sirius:no_recalibration                             Disable recalibration of input spectra
  -sirius:profile <choice>                             Name of the configuration profile (default: 'default')
                                                        (valid: 'default', 'qtof', 'orbitrap', 'fticr')
  -sirius:formulas <text>                              Specify the neutral molecular formula of the measured 
                                                       compound to compute its tree or a list of candidate 
                                                       formulas the method should discriminate. Omit this 
                                                       option if you want to consider all possible molecular 
                                                       formulas
  -sirius:ions_enforced <text>                         The iontype/adduct of the MS/MS data. Example: [M+H]+,
                                                        
                                                       [M-H]-, [M+Cl]-, [M+Na]+, [M]+. You can also provide 
                                                       a 
                                                       comma separated list of adducts.
  -sirius:candidates <number>                          The number of formula candidates in the SIRIUS output 
                                                       (default: '10') (min: '0')
  -sirius:candidates_per_ion <number>                  Minimum number of candidates in the output for each 
                                                       ionization. Set to force output of results for each 
                                                       possible ionization, even if not part of highest ranke
                                                       d results. (default: '1')
  -sirius:elements_considered <text>                   Set the allowed elements for rare element detection. 
                                                       Write SBrClBSe to allow the elements S,Br,Cl,B and 
                                                       Se. (default: 'SBrClBSe')
  -sirius:elements_enforced <text>                     Enforce elements for molecular formula determination. 
                                                       Write CHNOPSCl to allow the elements C, H, N, O, P, S 
                                                       and Cl. Add numbers in brackets to restrict the minima
                                                       l and maximal allowed occurrence of these elements: 
                                                       CHNOP[5]S[8]Cl[1-2]. When one number is given then it 
                                                       is interpreted as upper bound. (default: 'CHNOP')
  -sirius:no_isotope_score                             Disable isotope pattern score.
  -sirius:no_isotope_filter                            Disable molecular formula filter. When filtering is 
                                                       enabled, molecular formulas are excluded if their theo
                                                       retical isotope pattern does not match the theoretical
                                                        one, even if their MS/MS pattern has high score.
  -sirius:ions_considered <text>                       The iontype/adduct of the MS/MS data. Example: [M+H]+,
                                                        [M-H]-, [M+Cl]-, [M+Na]+, [M]+. You can also provide 
                                                       a comma separated list of adducts. (default: '[M+H]+,[
                                                       M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[
                                                       M+Cl]-,[M-H2O-H]-,[M+Br]-')
  -sirius:db <text>                                    Search formulas in the Union of the given databases 
                                                       db-name1,db-name2,db-name3. If no database is given 
                                                       all possible molecular formulas will be respected (no 
                                                       database is used). Example: possible DBs: ALL,BIO,PUBC
                                                       HEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,
                                                       METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIO
                                                       NAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEM
                                                       ANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMIN
                                                       E,ECOCYCMINE,YMDBMINE (default: 'none')
  -sirius:solver <text>                                For GUROBI and CPLEX environment variables need to be 
                                                       configured. 
                                                       (see SIRIUS manual: https://boecker-lab.github.io/docs
                                                       .sirius.github.io/install/). (default: 'CLP')

fingerid:
  -fingerid:db <text>                                  Search structures in the Union of the given databases 
                                                       db-name1,db-name2,db-name3. If no database is given 
                                                       all possible molecular formulas will be respected (no 
                                                       database is used). Example: possible DBs: ALL,BIO,PUBC
                                                       HEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,
                                                       METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIO
                                                       NAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEM
                                                       ANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMIN
                                                       E,ECOCYCMINE,YMDBMINE

                                                       
Common UTIL 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

+SiriusAdapterTool for metabolite identification using single and tandem mass spectrometry

version3.0.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'SiriusAdapter'

sirius_executablesirius The Sirius executable. Provide a full or relative path, or make sure it can be found in your PATH environment.input file

in MzML Input fileinput file*.mzML

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

out_sirius MzTab output file for SIRIUS resultsoutput file*.mzTab

out_fingerid MzTab output file for CSI:FingerID, if this parameter is given, SIRIUS will search for a molecular structure using CSI:FingerID after determining the sum formulaoutput file*.mzTab

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

out_annotated_spectra Export spectra with fragment annotations from SIRIUSoutput file*.mzML

out_project_space Output directory for SIRIUS project space

sirius_user_email E-mail for your SIRIUS account.

sirius_user_password Password for your SIRIUS account.

converter_modefalse Use this flag in combination with the out_ms file to convert the input mzML and featureXML to a .ms file. Without further SIRIUS processing.true, false

read_sirius_stdoutfalse Read and print the standard output and error of the Sirius executable, even if it succeeds.true, false

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

+++preprocessing

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 precursor_mz_toleranceDa, ppm

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 featuretrue, false

no_masstrace_info_isotope_patternfalse Use this flag if the masstrace information from a feature should be discarded and the isotope_pattern_iterations should be used insteadtrue, false

+++project

maxmz-1 Just consider compounds with a precursor mz lower or equal
this maximum mz. All other compounds in the input file
are ignored.

loglevel Set logging level of the Jobs SIRIUS will execute.
Valid values: SEVERE, WARNING, INFO, FINER, ALL
Default: WARNING

ignore_formulafalse Ignore given molecular formula in internal .ms format, while processing.true, false

qfalse Suppress shell outputtrue, false

+++sirius

ppm_max10.0 Maximum allowed mass deviation in ppm for decomposing masses [ppm].

ppm_max_ms210.0 Maximum allowed mass deviation in ppm for decomposing masses in MS2 [ppm].If not specified, the same value as for the MS1 is used.

tree_timeout100 Time out in seconds per fragmentation tree computations. 0 for an infinite amount of time0:∞

compound_timeout100 Maximal computation time in seconds for a single compound. 0 for an infinite amount of time.0:∞

no_recalibrationfalse Disable recalibration of input spectratrue, false

profiledefault Name of the configuration profiledefault, qtof, orbitrap, fticr

formulas Specify the neutral molecular formula of the measured compound to compute its tree or a list of candidate formulas the method should discriminate. Omit this option if you want to consider all possible molecular formulas

ions_enforced The iontype/adduct of the MS/MS data. Example: [M+H]+,
[M-H]-, [M+Cl]-, [M+Na]+, [M]+. You can also provide a
comma separated list of adducts.

candidates10 The number of formula candidates in the SIRIUS output0:∞

candidates_per_ion1 Minimum number of candidates in the output for each ionization. Set to force output of results for each possible ionization, even if not part of highest ranked results.

elements_consideredSBrClBSe Set the allowed elements for rare element detection. Write SBrClBSe to allow the elements S,Br,Cl,B and Se.

elements_enforcedCHNOP Enforce elements for molecular formula determination. Write CHNOPSCl to allow the elements C, H, N, O, P, S and Cl. Add numbers in brackets to restrict the minimal and maximal allowed occurrence of these elements: CHNOP[5]S[8]Cl[1-2]. When one number is given then it is interpreted as upper bound.

no_isotope_scorefalse Disable isotope pattern score.true, false

no_isotope_filterfalse Disable molecular formula filter. When filtering is enabled, molecular formulas are excluded if their theoretical isotope pattern does not match the theoretical one, even if their MS/MS pattern has high score.true, false

ions_considered[M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]- the iontype/adduct of the MS/MS data. Example: [M+H]+, [M-H]-, [M+Cl]-, [M+Na]+, [M]+. You can also provide a comma separated list of adducts.

dbnone Search formulas in the Union of the given databases db-name1,db-name2,db-name3. If no database is given all possible molecular formulas will be respected (no database is used). Example: possible DBs: ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE

solverCLP For GUROBI and CPLEX environment variables need to be configured.
(see SIRIUS manual: https://boecker-lab.github.io/docs.sirius.github.io/install/).

+++fingerid

db Search structures in the Union of the given databases db-name1,db-name2,db-name3. If no database is given all possible molecular formulas will be respected (no database is used). Example: possible DBs: ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE