AssayGeneratorMetabo

Assay library generation from DDA data (Metabolomics)

Web Documentation for AssayGeneratorMetabo

Options

version
Version of the tool that generated this parameters file.
fragment_annotation
Fragment annotation method
ambiguity_resolution_mz_tolerance
Mz tolerance for the resolution of identification ambiguity over multiple files
ambiguity_resolution_mz_tolerance_unit
Unit of the ambiguity_resolution_mz_tolerance
ambiguity_resolution_rt_tolerance
RT tolerance in seconds for the resolution of identification ambiguity over multiple files
total_occurrence_filter
Filter compound based on total occurrence in analysed samples
fragment_annotation_score_threshold
Filters annotations based on the explained intensity of the peaks in a spectrum
decoy_generation
Decoys will be generated using the fragmentation tree re-rooting approach. This option does only work in combination with the fragment annotation via Sirius.
decoy_generation_method
Uses different methods for decoy generation. Basis for the method is the fragmentation-tree re-rooting approach ('original'). This approach can be extended by using 'resolve_overlap', which will resolve overlapping fragments of the highest intensity fragments chosen, by adding -CH2 mass to the overlapping fragments. 'Add_shift' will add a -CH2 mass shift to the target fragments and use them as additional decoys if fragmentation-tree re-rooting failed. 'Both' combines the extended methods (resolve_overlap, add_shift).
method
Spectrum with the highest precursor intensity or a consensus spectrum is used for assay library construction (if no fragment annotation is used).
use_exact_mass
Use exact mass for precursor and fragment annotations
exclude_ms2_precursor
Excludes precursor in ms2 from transition list
precursor_mz_distance
Max m/z distance of the precursor entries of two spectra to be merged in [Da].
precursor_recalibration_window
Tolerance window for precursor selection (Annotation of precursor mz and intensity)
precursor_recalibration_window_unit
Unit of the precursor_mz_tolerance_annotation
consensus_spectrum_precursor_rt_tolerance
Tolerance window (left and right) for precursor selection [seconds], for consensus spectrum generation (only available without fragment annotation)
use_known_unknowns
Use features without identification information
min_transitions
Minimal number of transitions
max_transitions
Maximal number of transitions
cosine_similarity_threshold
Threshold for cosine similarity of MS2 spectra from the same precursor used in consensus spectrum creation
transition_threshold
Further transitions need at least x% of the maximum intensity (default 5%)
min_fragment_mz
Minimal m/z of a fragment ion choosen as a transition
max_fragment_mz
Maximal m/z of a fragment ion choosen as a transition
out_workspace_directory
Output directory for SIRIUS workspace
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)
use_deisotoper
Use Deisotoper (if no fragment annotation is used)
fragment_tolerance
Tolerance used to match isotopic peaks
fragment_unit
Unit of the fragment tolerance
min_charge
The minimum charge considered
max_charge
The maximum charge considered
min_isopeaks
The minimum number of isotopic peaks (at least 2) required for an isotopic cluster
max_isopeaks
The maximum number of isotopic peaks (at least 2) considered for an isotopic cluster
keep_only_deisotoped
Only monoisotopic peaks of fragments with isotopic pattern are retained
annotate_charge
Annotate the charge to the peaks
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(s) used for assay library generation [mzML]
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FeatureXML input file(s) containing identification information (e.g. AccurateMassSearch) [featureXML]

Output Ports

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Assay library output file [tsv,traML,pqp]

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

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