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

read_sirius_stdout

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

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

maxmz

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

processors

Number of cpu cores to use. If not specified SIRIUS uses all available cores.

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

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.)

Workflows

• DIAMetAlyzer_2.0OpenMS
• DIAMetAlyzer_2.0KNIME Hub
• DIAMetAlyzer_ABKNIME Forum

Links

• No links available

Developers