SiriusAdapter

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 (free academic license) instead of GLPK, please follow the instructions in the sirius manual.

Internal procedure in SiriusAdpater 1. Input mzML 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)

The command line parameters of this tool are:

SiriusAdapter -- Tool for metabolite identification using single and tandem mass spectrometry
Version: 2.3.0 Apr 18 2018, 18:59:40, Revision: 2cda6bd
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_adductinfo <file>     FeatureXML Input with adduct information (valid formats: 'featurexml')
  -out_sirius <file>*       MzTab Output file for SiriusAdapter results (valid formats: 'tsv')
  -out_fingerid <file>      MzTab output file for CSI:FingerID, if this parameter is given, SIRIUS will searc
                            h 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')
  -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. Use 'omit' to ignore isotope patt
                            ern. (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 occurrence of these
                            elements: CHNOP[5]S[8]Cl[1]. (default: 'CHNOP[5]S')
  -tree_timeout <num>       Time out in seconds per fragmenation tree computation. To disable the tree timout
                            set the value to 0 (default: '10')
  -top_n_hits <num>         The top_n_hit for each compound written to 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.
  -ion_tree                 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.
  -most_intense_ms2         Sirius uses the fragmentation sepctrum with the most intense precursor 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 (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

in_adductinfo FeatureXML Input with adduct informationinput file*.featurexml

out_sirius MzTab Output file for SiriusAdapter resultsoutput file*.tsv

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*.tsv

profileqtof Specify the used analysis profileqtof,orbitrap,fticr

candidates5 The number of candidates in the 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 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].

tree_timeout10 Time out in seconds per fragmenation tree computation. To disable the tree timout set the value to 0

top_n_hits10 The top_n_hit for each compound written to 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

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 sepctrum 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