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.

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 SiriusAdpater 1. Input mzML (and optional featureXML) 2. Parsed by SiriusMSConverter into (sirius internal) .ms format 3. Submission of .ms and additional parameters to wrapped SIRIUS.jar 4. Sirius output saved in interal temporary folder structure 5. Sirius output is parsed (SiriusMzTabWriter/CsiFingerIDMzTabWriter) 6. Merge corresponding output in one mzTab (out_sirius/out_fingerid)

By providing a featureXML, the feature information can be used for feature mapping. Sirius will then process the mappend MS2 spectra (instead of all available MS2). If the featureXML provides additional adduct information (e.g. from the MetaboliteAdductDecharger) this can be used to speed the Sirius calculation.

The command line parameters of this tool are:

SiriusAdapter -- Tool for metabolite identification using single and tandem mass spectrometry
Version: 2.4.0 Oct 29 2018, 15:52:19, Revision: 9690d06
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>               Sirius executable e.g. sirius
  -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 SiriusAdapter results (valid formats: 'mzTab')
  -out_fingerid <file>                   MzTab output file for CSI:FingerID, if this parameter is given, SIRI
                                         US will search for a molecular structure using CSI:FingerID after
                                         determining the sum formula (valid formats: 'mzTab')
  -filter_by_num_masstraces <num>        Features have to have at least x MassTraces. To use this parameter 
                                         feature_only is neccessary (default: '1' min: '1')
  -feature_only                          Uses the feature information from in_featureinfo to reduce the searc
                                         h space to only MS2 associated with a feature
  -precursor_mz_tolerance <num>          Tolerance window for precursor selection (Feature selection in regar
                                         d to the precursor) (default: '0.005')
  -precursor_mz_tolerance_unit <choice>  Unit of the precursor_mz_tolerance (default: 'Da' valid: 'Da', 'ppm'
                                         )
  -precursor_rt_tolerance <num>          Tolerance window (left and right) for precursor selection [seconds] 
                                         (default: '5')
  -profile <choice>                      Specify the used analysis profile (default: 'qtof' valid: 'qtof', 
                                         'orbitrap', 'fticr')
  -candidates <num>                      The number of candidates in the SIRIUS output. (default: '5')
  -database <choice>                     Search formulas in given database (default: 'all' valid: 'all', 'che
                                         bi', 'custom', 'kegg', 'bio', 'natural products', 'pubmed', 'hmdb',
                                         'biocyc', 'hsdb', 'knapsack', 'biological', 'zinc bio', 'gnps', 'pub
                                         chem', 'mesh', 'maconda')
  -noise <num>                           Median intensity of noise peaks (default: '0')
  -ppm_max <num>                         Allowed ppm for decomposing masses (default: '10')
  -isotope <choice>                      How to handle isotope pattern data. Use 'score' to use them for rank
                                         ing or 'filter' if you just want to remove candidates with bad isoto
                                         pe pattern. With 'both' you can use isotopes for filtering and scori
                                         ng. Use 'omit' to ignore isotope pattern. (default: 'both' valid:
                                         'score', 'filter', 'both', 'omit')
  -elements <choice>                     The allowed elements. Write CHNOPSCl to allow the elements C, H, N, 
                                         O, P, S and Cl. Add numbers in brackets to restrict the maximal allo
                                         wed occurrence of these elements: CHNOP[5]S[8]Cl[1]. (default: 'CHNO
                                         P[5]S[8]Cl[1]')
  -compound_timeout <num>                Time out in seconds per compound. To disable the timeout set the 
                                         value to 0 (default: '10')
  -tree_timeout <num>                    Time out in seconds per fragmentation tree computation. (default: 
                                         '0')
  -top_n_hits <num>                      The number of top hits for each compound written to the CSI:FingerID
                                         output (default: '10')
  -auto_charge                           Use this option if the charge of your compounds is unknown and you 
                                         do not want to assume [M+H]+ as default. With the auto charge option
                                         SIRIUS will not care about charges and allow arbitrary adducts for
                                         the precursor peak.
  -ion_tree                              Print molecular formulas and node labels with the ion formula instea
                                         d of the neutral formula
  -no_recalibration                      If this option is set, SIRIUS will not recalibrate the spectrum duri
                                         ng the analysis.
  -most_intense_ms2                      SIRIUS uses the fragmentation spectrum with the most intense precurs
                                         or peak (for each spectrum)
                                         
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 (defa
                                         ult: '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

version2.4.0 Version of the tool that generated this parameters file.

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

executable sirius executable e.g. siriusinput file

in MzML Input fileinput file*.mzml

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

out_sirius MzTab Output file for SiriusAdapter 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

filter_by_num_masstraces1 Features have to have at least x MassTraces. To use this parameter feature_only is neccessary1:∞

feature_onlyfalse Uses the feature information from in_featureinfo to reduce the search space to only MS2 associated with a featuretrue,false

precursor_mz_tolerance0.005 Tolerance window for precursor selection (Feature selection in regard to the precursor)

precursor_mz_tolerance_unitDa Unit of the precursor_mz_toleranceDa,ppm

precursor_rt_tolerance5 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.

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 instead.true,false

profileqtof Specify the used analysis profileqtof,orbitrap,fticr

candidates5 The number of candidates in the SIRIUS output.

databaseall search formulas in given databaseall,chebi,custom,kegg,bio,natural products,pubmed,hmdb,biocyc,hsdb,knapsack,biological,zinc bio,gnps,pubchem,mesh,maconda

noise0 median intensity of noise peaks

ppm_max10 allowed ppm for decomposing masses

isotopeboth how to handle isotope pattern data. Use 'score' to use them for ranking or 'filter' if you just want to remove candidates with bad isotope pattern. With 'both' you can use isotopes for filtering and scoring. Use 'omit' to ignore isotope pattern.score,filter,both,omit

elementsCHNOP[5]S[8]Cl[1] The allowed elements. Write CHNOPSCl to allow the elements C, H, N, O, P, S and Cl. Add numbers in brackets to restrict the maximal allowed occurrence of these elements: CHNOP[5]S[8]Cl[1].

compound_timeout10 Time out in seconds per compound. To disable the timeout set the value to 0

tree_timeout0 Time out in seconds per fragmentation tree computation.

top_n_hits10 The number of top hits for each compound written to the CSI:FingerID output

auto_chargefalse Use this option if the charge of your compounds is unknown and you do not want to assume [M+H]+ as default. With the auto charge option SIRIUS will not care about charges and allow arbitrary adducts for the precursor peak.true,false

ion_treefalse Print molecular formulas and node labels with the ion formula instead of the neutral formulatrue,false

no_recalibrationfalse If this option is set, SIRIUS will not recalibrate the spectrum during the analysis.true,false

most_intense_ms2false SIRIUS uses the fragmentation spectrum with the most intense precursor peak (for each spectrum)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 Overwrite tool specific checks.true,false

testfalse Enables the test mode (needed for internal use only)true,false