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/

If you want to use the software with the Gurobi solver (free academic license) instead of GLPK, please follow the instructions in the sirius manual.

Please see the following publications:

Kai Dührkop and Sebastian Böcker. Fragmentation trees reloaded. J Cheminform, 8:5, 2016. (Cite this for fragmentation pattern analysis and fragmentation tree computation)

Kai Dührkop, Huibin Shen, Marvin Meusel, Juho Rousu, and Sebastian Böcker. Searching molecular structure databases with tandem mass spectra using CSI:FingerID. Proc Natl Acad Sci U S A, 112(41):12580-12585, 2015. (Cite this when using CSI:FingerID)

The command line parameters of this tool are:

SiriusAdapter -- Tool for metabolite identification using single and tandem mass spectrometry
Version: 2.3.0 Jan  9 2018, 17:46:23, Revision: 38ae115

Usage:
  SiriusAdapter <options>

Options (mandatory options marked with '*'):
  -executable <executable>  Sirius executable e.g. sirius
  -in <file>*               MzML Input file (valid formats: 'mzml')
  -out_sirius <file>*       MzTab Output file for SiriusAdapter results (valid formats: 'tsv')
  -out_fingerid <file>      MzTab ouput 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: 'tsv')
  -profile <choice>         Specify the used analysis profile (default: 'qtof' valid: 'qtof', 'orbitrap', 
                            'fticr')
  -candidates <num>         The number of candidates in the output. Default 5 best candidates (default: '5')
  -database <choice>        Search formulas in given database (default: 'all' valid: 'all', 'chebi', 'custom'
                            , 'kegg', 'bio', 'natural products', 'pubmed', 'hmdb', 'biocyc', 'hsdb', 'knapsac
                            k', 'biological', 'zinc bio', 'gnps', 'pubchem', '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 ranking or 'filte
                            r' if you just want to remove candidates with bad isotope pattern. With 'both'
                            you can use isotopes for filtering and scoring (default). 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 allowed occurence of these
                            elements: CHNOP[5]S[8]Cl[1]. By default CHNOP[5]S is used. (default: 'CHNOP[5]S')
  -number <num>             The number of compounds used in the 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.
  -iontree                  Print molecular formulas and node labels with the ion formula instead of the neut
                            ral formula
  -no_recalibration         If this option is set, SIRIUS will not recalibrate the spectrum during the analys
                            is.
                            
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

version2.3.0 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

out_sirius MzTab Output file for SiriusAdapter resultsoutput file*.tsv

out_fingerid MzTab ouput 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*.tsv

profileqtof Specify the used analysis profileqtof,orbitrap,fticr

candidates5 The number of candidates in the output. Default 5 best candidates

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 (default). Use 'omit' to ignore isotope pattern.score,filter,both,omit

elementsCHNOP[5]S 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 occurence of these elements: CHNOP[5]S[8]Cl[1]. By default CHNOP[5]S is used.

number10 The number of compounds used in the 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

iontreefalse 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

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