De novo metabolite identification.

CSI:FingerID (Compound Structure Identification: FingerID) is a method for searching a tandem mass spectrum of a small molecule (metabolite) in a database of molecular structures.

To use this feature, the Sirius command line tool as well as a java installation is needed.

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

Please use Sirius Version 4.0.1

If you want to use the software with the Gurobi solver or CPLEX instead of GLPK, please follow the instructions in the sirius manual.

Internal procedure in SiriusAdapter

Input mzML (and optional featureXML)
Preprocessing (see below)
Parsed by SiriusMSConverter into (sirius internal) .ms format
Submission of .ms and additional parameters to wrapped SIRIUS.jar
Sirius output saved in interal temporary folder structure
Sirius output is parsed (SiriusMzTabWriter/CsiFingerIDMzTabWriter)
Merge corresponding output in one mzTab (out_sirius/out_fingerid)
Preprocessing (featureXML): 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.

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/2.7.0/html/UTILS_SiriusAdapter.html
Version: 2.7.0 Sep 13 2021, 20:58:47, Revision: 9110e58
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 Dührkop and Sebastian Böcker. Fragmentation trees reloaded. J Cheminform; 2016. doi:10.1186/s13321-016-0116-8.
  Kai Dührkop, Huibin Shen, Marvin Meusel, Juho Rousu, and Sebastian Böcker. 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 '*'):
  -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_project_space <directory>                       Output directory for SIRIUS project space
                                                       

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                                       Just consider compounds with a precursor mz lower or 
                                                       equal
                                                       this maximum mz. All other compounds in the input fil
                                                       e
                                                       are ignored.
  -project:processors <number>                         Number of cpu cores to use. If not specified SIRIUS 
                                                       uses all available cores. (default: '1')
  -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: '0' 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: 'qtof' 
                                                       valid: 'default', 'qtof', 'orbitrap', 'fticr')
  -sirius:formula <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: '5' min: '1')
  -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. -1 omits parameter in Sirius. (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.
  -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 is 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.
  -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

fingerid:
  -fingerid:candidates <number>                        Number of molecular structure candidates in the output
                                                       . (default: '10' min: '1')
  -fingerid: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: 'BIO')

                                                       
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

version2.7.0 Version of the tool that generated this parameters file.

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

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_project_space Output directory for SIRIUS project space

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

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

processors1 Number of cpu cores to use. If not specified SIRIUS uses all available cores.

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_timeout0 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

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

formula 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.

candidates5 The number of formula candidates in the SIRIUS output1:∞

candidates_per_ion-1 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. -1 omits parameter in Sirius.

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

elements_enforced 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. Default is CHNOP

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 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.

db 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

+++fingerid

candidates10 Number of molecular structure candidates in the output.1:∞

dbBIO 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