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 SiriusAdpater
1. Input mzML (and optional featureXML)
2. Preprocessing (see below)
3. Parsed by SiriusMSConverter into (sirius internal) .ms format
4. Submission of .ms and additional parameters to wrapped SIRIUS.jar
5. Sirius output saved in interal temporary folder structure
6. Sirius output is parsed (SiriusMzTabWriter/CsiFingerIDMzTabWriter)
7. 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/documentation/UTILS_SiriusAdapter.html
Version: 2.6.0 Sep 30 2020, 12:54:34, Revision: c26f752
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 SiriusAdapter 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_workspace_directory <directory>                 Output directory for SIRIUS workspace
                                                       

Preprocessing:
  -preprocessing:filter_by_num_masstraces <number>     Features have to have at least x MassTraces. To use 
                                                       this parameter feature_only is neccessary (default:
                                                       '1' min: '1')
  -preprocessing:precursor_mz_tolerance <value>        Tolerance window for precursor selection (Feature sele
                                                       ction in regard to the precursor) (default: '5.0e-03')
  -preprocessing:precursor_mz_tolerance_unit <choice>  Unit of the precursor_mz_tolerance (default: 'Da' vali
                                                       d: 'Da', 'ppm')
  -preprocessing:precursor_rt_tolerance <number>       Tolerance window (left and right) for precursor select
                                                       ion [seconds] (default: '5')
  -preprocessing:feature_only                          Uses the feature information from in_featureinfo to 
                                                       reduce the search space to MS2 associated with a featu
                                                       re.

Parameters for SIRIUS and CSI:FingerID:
  -sirius:profile <choice>                             Specify the used analysis profile (default: 'qtof' 
                                                       valid: 'qtof', 'orbitrap', 'fticr')
  -sirius:candidates <number>                          The number of candidates in the SIRIUS output. (defaul
                                                       t: '5' min: '1')
  -sirius:database <choice>                            Search formulas in given database (default: 'all' vali
                                                       d: 'all', 'chebi', 'custom', 'kegg', 'bio', 'natural
                                                       products', 'pubmed', 'hmdb', 'biocyc', 'hsdb', 'knapsa
                                                       ck', 'biological', 'zinc bio', 'gnps', 'pubchem', 'mes
                                                       h', 'maconda')
  -sirius:noise <number>                               Median intensity of noise peaks (default: '0' min: 
                                                       '0')
  -sirius:ppm_max <number>                             Allowed ppm for decomposing masses (default: '10')
  -sirius:isotope <choice>                             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. (default: 'both'
                                                       valid: 'score', 'filter', 'both', 'omit')
  -sirius:elements <text>                              The allowed elements. Write CHNOPSCl to allow the elem
                                                       ents 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[8]Cl
                                                       [1]')
  -sirius:compound_timeout <number>                    Time out in seconds per compound. To disable the timeo
                                                       ut set the value to 0 (default: '10' min: '0')
  -sirius:tree_timeout <number>                        Time out in seconds per fragmentation tree computation
                                                       . (default: '0' min: '0')
  -sirius:top_n_hits <number>                          The number of top hits for each compound written to 
                                                       the CSI:FingerID output (default: '10' min: '1')
  -sirius:cores <number>                               The number of cores SIRIUS is allowed to use on the 
                                                       system (default: '1' min: '1')
  -sirius:auto_charge                                  Use this option if the charge of your compounds is 
                                                       unknown and you do not want to assume [M+H]+ as defaul
                                                       t. With the auto charge option SIRIUS will not care
                                                       about charges and allow arbitrary adducts for the prec
                                                       ursor peak.

                                                       
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

version2.6.0 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 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

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

out_workspace_directory Output directory for SIRIUS workspace

converter_modefalse Use this flag in combination with the out_ms file to only convert the input mzML and featureXML to an .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

+++preprocessingPreprocessing

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

precursor_mz_tolerance5.0e-03 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.

feature_onlyfalse Uses the feature information from in_featureinfo to reduce the search space to MS2 associated with a feature.true,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 instead.true,false

+++siriusParameters for SIRIUS and CSI:FingerID

profileqtof Specify the used analysis profileqtof,orbitrap,fticr

candidates5 The number of candidates in the SIRIUS output.1:∞

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 peaks0:∞

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 00:∞

tree_timeout0 Time out in seconds per fragmentation tree computation.0:∞

top_n_hits10 The number of top hits for each compound written to the CSI:FingerID output1:∞

cores1 The number of cores SIRIUS is allowed to use on the system1:∞

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