OpenMS
2.8.0
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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
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/2.8.0/html/UTILS_SiriusAdapter.html Version: 2.8.0 Feb 22 2022, 11:52:07, Revision: d203985 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 '*'): -sirius_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: