SiriusAdapter

Tool for metabolite identification using single and tandem mass spectrometry

Web Documentation for SiriusAdapter

Options

version
Version of the tool that generated this parameters file.
out_project_space
Output directory for SIRIUS project space
converter_mode
Use this flag in combination with the out_ms file to convert the input mzML and featureXML to a .ms file. Without further SIRIUS processing.
log
Name of log file (created only when specified)
debug
Sets the debug level
threads
Sets the number of threads allowed to be used by the TOPP tool
no_progress
Disables progress logging to command line
force
Overrides tool-specific checks
test
Enables the test mode (needed for internal use only)
filter_by_num_masstraces
Number of mass traces each feature has to have to be included. To use this parameter, setting the feature_only flag is necessary
precursor_mz_tolerance
Tolerance window for precursor selection (Feature selection in regard to the precursor)
precursor_mz_tolerance_unit
Unit of the precursor_mz_tolerance
precursor_rt_tolerance
Tolerance window (left and right) for precursor selection [seconds]
isotope_pattern_iterations
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_only
Uses the feature information from in_featureinfo to reduce the search space to MS2 associated with a feature
no_masstrace_info_isotope_pattern
Use this flag if the masstrace information from a feature should be discarded and the isotope_pattern_iterations should be used instead
processors
Number of cpu cores to use. If not specified SIRIUS uses all available cores.
ignore_formula
Ignore given molecular formula in internal .ms format, while processing.
q
Suppress shell output
ppm_max
Maximum allowed mass deviation in ppm for decomposing masses [ppm].
ppm_max_ms2
Maximum allowed mass deviation in ppm for decomposing masses in MS2 [ppm].If not specified, the same value as for the MS1 is used.
tree_timeout
Time out in seconds per fragmentation tree computations. 0 for an infinite amount of time
compound_timeout
Maximal computation time in seconds for a single compound. 0 for an infinite amount of time.
no_recalibration
Disable recalibration of input spectra
profile
Name of the configuration profile
formula
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
ions_enforced
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.
candidates
The number of formula candidates in the SIRIUS output
candidates_per_ion
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 ranked results. -1 omits parameter in Sirius.
elements_considered
Set the allowed elements for rare element detection. Write SBrClBSe to allow the elements S,Br,Cl,B and Se.
elements_enforced
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 minimal 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
no_isotope_score
Disable isotope pattern score.
no_isotope_filter
Disable molecular formula filter. When filtering is enabled, molecular formulas are excluded if their theoretical isotope pattern does not match the theoretical one, even if their MS/MS pattern has high score.
ions_considered
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.
db
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,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE
candidates
Number of molecular structure candidates in the output.
db
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,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE

Input Ports

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The Sirius executable. Provide a full or relative path, or make sure it can be found in your PATH environment. [,opt.]
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MzML Input file [mzML]
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FeatureXML input with feature and adduct information [featureXML,opt.]

Output Ports

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MzTab output file for SIRIUS results [mzTab]
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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 [mzTab]
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Internal SIRIUS .ms format after OpenMS preprocessing [ms]

Views

SiriusAdapter Std Output
The text sent to standard out during the execution of SiriusAdapter.
SiriusAdapter Error Output
The text sent to standard error during the execution of SiriusAdapter. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Workflows

Further Links

Developers

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