SiriusAdapter

Options

version

Version of the tool that generated this parameters file.

out_project_space

Output directory for SIRIUS project space

sirius_user_email

E-mail for your SIRIUS account.

sirius_user_password

Password for your SIRIUS account.

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.

read_sirius_stdout

Read and print the standard output and error of the Sirius executable, even if it succeeds.

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

maxmz

Just consider compounds with a precursor mz lower or equal this maximum mz. All other compounds in the input file are ignored.

loglevel

Set logging level of the Jobs SIRIUS will execute. Valid values: SEVERE, WARNING, INFO, FINER, ALL Default: WARNING

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

formulas

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.

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.

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

solver

For GUROBI and CPLEX environment variables need to be configured. (see SIRIUS manual: https://boecker-lab.github.io/docs.sirius.github.io/install/).

db

Search structures 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

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

• Metabolite_DeNovoIDOpenMS
• Metabolite_DeNovoIDKNIME Hub

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